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Revision 1704 - Directory Listing
Modified Mon Jan 27 14:32:31 2014 UTC (2 years, 7 months ago) by jmduarteg
Fixed bug in cif file parsing: was not tokenising correctly loop elements that had more multi-line quoting mixed with normal quoted fields and several records. Added one more test case for that.
Revision 1703 - Directory Listing
Modified Mon Jan 27 13:12:26 2014 UTC (2 years, 7 months ago) by nikhilbiyani
Small bug fix with bio units warnings from last commit
Revision 1702 - Directory Listing
Modified Fri Jan 24 15:00:31 2014 UTC (2 years, 8 months ago) by jmduarteg
Removing warnings from biounit parsing: all commented out now. Uncomment them for debugging
Revision 1701 - Directory Listing
Modified Fri Jan 24 11:30:55 2014 UTC (2 years, 8 months ago) by jmduarteg
Finally the cif parser can read (some) non-deposited mmCIF files, tested with one phenix-produced mmCIF file. The PdbParsersTest passed.
Revision 1700 - Directory Listing
Modified Wed Jan 22 08:59:05 2014 UTC (2 years, 8 months ago) by jmduarteg
Removed all remaining warnings
Revision 1699 - Directory Listing
Modified Tue Jan 21 17:01:18 2014 UTC (2 years, 8 months ago) by jmduarteg
Removing some more obsolete stuff after removal of PDBASE support
Revision 1698 - Directory Listing
Modified Tue Jan 21 16:31:59 2014 UTC (2 years, 8 months ago) by jmduarteg
Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. 
Now all instances of PDBASE loading have been converted to mmCIF file loading.
Additionally: massive clean-up of obsolete classes.


Revision 1697 - Directory Listing
Modified Tue Jan 21 08:58:56 2014 UTC (2 years, 8 months ago) by jmduarteg
More improvements in cif parsing: 
- now all non-loop parsed fields can be single or multiline, everything will be parsed correctly
- now always unquoting all parsed strings
- all functionality now encapsulated in a few methods in CifFieldInfo, split into loop and non-loop methods. If either is called in the wrong place an IllegalArgumentException will be thrown
Revision 1696 - Directory Listing
Modified Mon Jan 20 16:43:58 2014 UTC (2 years, 8 months ago) by jmduarteg
More improvements in cif parsing: 
- all tokenising moved to CifFieldInfo. Thanks to that could rationalised all loop parsing, now it is much easier to read
- created a method to parse a field whether it is single or multi line
- some refactoring
Revision 1695 - Directory Listing
Modified Mon Jan 20 14:41:23 2014 UTC (2 years, 8 months ago) by jmduarteg
Complete rewrite of the cif file parser: 
- not using anymore random access file but storing strings in memory: much faster
- using new helper class CifFieldInfo instead of maps: much more readable
- now correctly treats # as comments
- now will parse mmCIF where field definitions don't start at beginning of line but have some spaces in between
Revision 1694 - Directory Listing
Modified Fri Jan 17 11:45:00 2014 UTC (2 years, 8 months ago) by jmduarteg
Tagging for eppic release 2.0.4:
no changes from last owl release.
Revision 1693 - Directory Listing
Modified Wed Nov 27 09:02:57 2013 UTC (2 years, 9 months ago) by jmduarteg
Tagging for eppic release 2.0.3
- more PDB metadata parsing: biounit assembly and release date
- improved rmsd calculation: new OptimalSuperposition class introduced
- improvements in interface calculation: now going to 12th cell
- introduced chain clusters and interface clusters
- some more checks in cif file parsing: now won't crash on phenix files
Revision 1692 - Directory Listing
Modified Fri Nov 15 13:21:02 2013 UTC (2 years, 10 months ago) by jmduarteg
Minimal change in javadoc
Revision 1691 - Directory Listing
Modified Mon Nov 11 15:39:47 2013 UTC (2 years, 10 months ago) by jmduarteg
Now will guess any cif file starting with data_xxxxxx as cif file (before only if xxxxxx was a pdb code). Now also checking that the readFieldsTitles method finds some fields, otherwise throwing exception. Phenix cif files will now be read but will fail with a file format exception. 
Revision 1690 - Directory Listing
Modified Fri Nov 8 12:44:32 2013 UTC (2 years, 10 months ago) by jmduarteg
Introducing chain clusters and interface clusters. We group chains in the same way as before (based on 100% seq identity) but now we have a more flexible scheme where we could introduce chain clustering based on seq-alignment/rmsd when reading from PDB file (not implemented yet). Interface clustering is implemented based on rmsd of superposition of both interface sides.
Revision 1689 - Directory Listing
Modified Thu Oct 17 10:23:10 2013 UTC (2 years, 11 months ago) by kumaran
Cluster calculation method getClusters is added. 
Note: This method requires pdbasymunit object , which one has to pass to the method as parameter. 
At present its not called any where in crkmain. 
Revision 1688 - Directory Listing
Modified Thu Oct 17 09:59:05 2013 UTC (2 years, 11 months ago) by jmduarteg
New default for DEF_NUM_CELLS: 12. After a scan of the whole PDB (Oct 2013) the worst case we found was 4jgc having a contact on the 11th cell.
Revision 1687 - Directory Listing
Modified Wed Oct 16 13:43:14 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Pisa Interface parsing: Few changes in warnings
Revision 1686 - Directory Listing
Modified Wed Oct 16 10:15:54 2013 UTC (2 years, 11 months ago) by jmduarteg
Minor fix: new entry 4gwv has a space group code with an upper case in mirror plane symbol, we now convert all but first letters of space group name to lower case.
Revision 1685 - Directory Listing
Modified Tue Oct 15 14:30:13 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Added few Warnings while parsing Pisa Interface XML file
Revision 1684 - Directory Listing
Modified Tue Oct 15 14:18:23 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Removed few warnings while parsing bio-units in cif files
Revision 1683 - Directory Listing
Modified Tue Oct 15 10:02:42 2013 UTC (2 years, 11 months ago) by jmduarteg
Important change: now interface search goes up to 6th shell of neighbouring cells. This solves bug CRK-101 where no interfaces were found for 1was. It also solves the case of many PDB entries that need 3rd shell (e.g. 24 entries in a test of ~2000 pdbs) and rare but occurring cases that need 5th shell (e.g. 2 entries in test of ~2000 pdbs). It seems that PISA uses 3rd shell and thus they miss interfaces occurring at >3 neighbours. Tested that this doesn't add any overhead at all to the runtime (the overlap check is very fast).
Revision 1682 - Directory Listing
Modified Thu Oct 10 13:08:51 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Added few more features to Pisa Connections.
Revision 1681 - Directory Listing
Modified Fri Oct 4 14:47:37 2013 UTC (2 years, 11 months ago) by jmduarteg
Now interface list can be cut to a minimal area cutoff, with all interfaces below discarded
Revision 1680 - Directory Listing
Modified Fri Oct 4 08:48:59 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Bugfixes for Cif BioUnit parsing, now checking if the assembly size is not present.
Revision 1679 - Directory Listing
Modified Fri Oct 4 08:43:49 2013 UTC (2 years, 11 months ago) by jmduarteg
Moved to core.structure.io the classes that belong there (except for the parsers themselves, we can't move them yet because there are some protected methods needed in core.structure). Removed some warnings from other files.
Revision 1678 - Directory Listing
Modified Fri Oct 4 08:28:21 2013 UTC (2 years, 11 months ago) by jmduarteg
Moved geometry related calculations to the GeometryTools class: rmsd, screw component, axis type, axis-angle etc. Like that the calculations can be used from anywhere. Introduced the OptSuperposition class as output of the rmsd calculation.
Improved the rmsd calculation in PdbChain (and corrected some bugs). Also improved a lot the rmsd unit testing. 
All tests in PdbChainTest are now done with cif files and not anymore with pdbase.
Implemented an optimal superposition method in ChainInterface and some output for that in enumerateInterfaces with the intention of finding the pseudo-symmetric relationship between NCS related chains in an interface.
All tests passed.

Revision 1677 - Directory Listing
Modified Tue Oct 1 10:59:47 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Added features: now parsing release date from pdb file.
Revision 1676 - Directory Listing
Modified Tue Oct 1 09:04:42 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Minor bug fix while parsing pdb-biounits, now removes DNA chains from NMR entries.
Revision 1675 - Directory Listing
Modified Mon Sep 30 15:25:34 2013 UTC (2 years, 11 months ago) by nikhilbiyani
Changes in BioUnit parsing: added few more methods, some changes in design.
Revision 1674 - Directory Listing
Modified Mon Sep 23 16:11:16 2013 UTC (3 years ago) by jmduarteg
Some fixes to the new test
Revision 1673 - Directory Listing
Modified Fri Sep 20 16:02:25 2013 UTC (3 years ago) by jmduarteg
New test for CrystalCell transform methods
Revision 1672 - Directory Listing
Modified Fri Sep 20 15:31:32 2013 UTC (3 years ago) by nikhilbiyani
Bugfix while parsing pdb-biounit: Now transforming properly from orthogonal to crystal coordinates.
Revision 1671 - Directory Listing
Modified Fri Sep 20 15:06:16 2013 UTC (3 years ago) by jmduarteg
Fixed important bug: transfToCrystal(Matrix4d) was not transforming the translation vectors properly. Found yet again another duplicate method for the transformation of vectors, now removed. Hopefully there are no other bugs lurking around...
Revision 1670 - Directory Listing
Modified Fri Sep 20 13:29:37 2013 UTC (3 years ago) by nikhilbiyani
Small bug-fix in the implementation of biounit, was returning null while copying
Revision 1669 - Directory Listing
Modified Fri Sep 20 10:42:28 2013 UTC (3 years ago) by nikhilbiyani
Implemented bio-unit assembly parsing in the pdb and cif file parsers. 
Revision 1668 - Directory Listing
Modified Mon Sep 16 15:13:14 2013 UTC (3 years ago) by jmduarteg
Some clean up and rationalisation: removing methods related to "parallel" interfaces. Now we call them more consistently "infinite" interfaces
Revision 1667 - Directory Listing
Modified Fri Sep 13 15:36:44 2013 UTC (3 years ago) by jmduarteg
Removed duplicated methods for transforming vectors in CrystalCell, also did some clean up of dead code.
Revision 1666 - Directory Listing
Modified Fri Sep 13 13:07:38 2013 UTC (3 years ago) by jmduarteg
Some more clean up in the ChainInterface class
Revision 1665 - Directory Listing
Modified Fri Sep 13 12:44:07 2013 UTC (3 years ago) by nikhilbiyani
Bug fixed for transformations of vectors.
Revision 1664 - Directory Listing
Modified Thu Aug 22 14:20:01 2013 UTC (3 years, 1 month ago) by jmduarteg
Tagging for eppic release 2.0.2
- bug fix: null pointer in pdb file parsing when no TER records present or misplaced
- many improvements in SpaceGroup and its testing
- operators can now be classified into their types, including calculation of screw directions
- bug fix: the axis vectors were wrongly calculated for some operators of some space groups, e.g. in H 3 2 or P 32 2 1
- bug fix in jaligner: sequences longer than 32768 characters were not aligning correctly when the match was occurring after character 32768. We fixed it ourselves in the jaligner source and repackaged the jar into owl. The jaligner developer has fixed it in git.
Revision 1663 - Directory Listing
Modified Thu Aug 22 14:12:33 2013 UTC (3 years, 1 month ago) by jmduarteg
Fixed bug with SIFTS file parsing: after a minor re-formatting of the SIFTS file in August 2013, the parser was crashing. Made it a bit more robust: it should work with both pre and post August 2013 formats.
Revision 1662 - Directory Listing
Modified Thu Aug 22 14:10:10 2013 UTC (3 years, 1 month ago) by jmduarteg
Removing tag because another bug was found and we want to put it into the 2.0.2 release
Revision 1661 - Directory Listing
Modified Thu Aug 22 08:41:56 2013 UTC (3 years, 1 month ago) by jmduarteg
Tagging for eppic release 2.0.2
- bug fix: null pointer in pdb file parsing when no TER records present or misplaced
- many improvements in SpaceGroup and its testing
- operators can now be classified into their types, including calculation of screw directions
- bug fix: the axis vectors were wrongly calculated for some operators of some space groups, e.g. in H 3 2 or P 32 2 1
- bug fix in jaligner: sequences longer than 32768 characters were not aligning correctly when the match was occurring after character 32768. We fixed it ourselves in the jaligner source and repackaged the jar into owl. The jaligner developer has fixed it in git.
Revision 1660 - Directory Listing
Modified Fri Aug 9 10:47:19 2013 UTC (3 years, 1 month ago) by jmduarteg
Changed comment to note that default interface distance cutoff has been changed in eppic 
Revision 1659 - Directory Listing
Modified Fri Aug 2 15:16:28 2013 UTC (3 years, 1 month ago) by jmduarteg
Minimal  change + added reference to wikipedia list of vdw radii. Put the remove hydrogens call in the right place (wasn't in last commit).
Revision 1658 - Directory Listing
Modified Fri Aug 2 08:15:53 2013 UTC (3 years, 1 month ago) by jmduarteg
Now removing hydrogens also in Asa.main
Revision 1657 - Directory Listing
Modified Tue Jul 30 08:13:40 2013 UTC (3 years, 1 month ago) by jmduarteg
Removed many warnings (appearing thanks to better checking in eclipse 4.3)
Revision 1656 - Directory Listing
Modified Mon Jul 29 16:54:53 2013 UTC (3 years, 1 month ago) by jmduarteg
Closing file handles in a few places found thanks to new warnings in eclipse 4.3
Revision 1655 - Directory Listing
Modified Mon Jul 29 13:17:33 2013 UTC (3 years, 1 month ago) by jmduarteg
Fixed bad bug (but with little consequences): the matrix for calculating eigenvectors (for calculation of rotation axes) was transposed, resulting in a few operators in a few space groups to have wrong axes (for instance in H 3 2 or P  32 2 1). Fortunately we weren't using the axes calculation for anything other than output in test programs (that's why it didn't have consequences). Added testing for comparison of axis vectors versus screw translation components (both must be in same direction).
Revision 1654 - Directory Listing
Modified Mon Jul 29 08:24:00 2013 UTC (3 years, 1 month ago) by jmduarteg
Fixed bug in screw character calling: was not properly comparing to 0 with a delta, so in some cases an essentially 0 screw translation component was considered to be non-0.
Revision 1653 - Directory Listing
Modified Sun Jul 28 20:56:01 2013 UTC (3 years, 1 month ago) by jmduarteg
Now possible to write interface pdb files directly gzipped as pdb.gz files
Revision 1652 - Directory Listing
Modified Sat Jul 27 10:52:32 2013 UTC (3 years, 1 month ago) by jmduarteg
Fixed bug in screw/glide calculation: we were only using the original space group transforms (with crystal translations 0,0,0) as the reference for the rotation character (screw/non-screw), all transforms with same id and different crystal translations were considered to be of same character. That's wrong: in order to calculate the screw character one needs to also take into account the crystal translations. This problem affected any space group containing rotation axes on diagonals.
Revision 1651 - Directory Listing
Modified Thu Jul 25 13:29:29 2013 UTC (3 years, 2 months ago) by jmduarteg
Made more clear an error message in PDB file parsing
Revision 1650 - Directory Listing
Modified Wed Jul 17 08:19:10 2013 UTC (3 years, 2 months ago) by jmduarteg
Fixed bug: was not checking for SG==null in getTransformType for non-crystallographic entries
Revision 1649 - Directory Listing
Modified Sun Jul 14 20:48:30 2013 UTC (3 years, 2 months ago) by jmduarteg
Added isInfinite field
Revision 1648 - Directory Listing
Modified Thu Jul 11 14:34:14 2013 UTC (3 years, 2 months ago) by jmduarteg
New feature: now we can classify the operators into their different types, including all screws with correct screw translation components, improper rotations, glides with translational components. New enum class introduced for that.
Many improvements in SpaceGroup and its testing.
Revision 1647 - Directory Listing
Modified Thu Jul 4 08:39:06 2013 UTC (3 years, 2 months ago) by jmduarteg
Fixing bug in jaligner: the NeedlemanWunschGotoh method used by owl.core.sequence.PairwiseSequenceAlignment had a bug causing infinite hanging when using very long sequences. The issue would happen when either of the 2 sequences to align was longer than 32768 (16 bit) and the other sequence would match it after the 32768 region, a test case is included in this commit to demonstrate it. The problem was an overflow: an array used for the traceback procedure was declared as short[] (16 bit), changing it to int[] (32 bit) the issue disappears. 
As the development in jaligner seems to be stopped I've simply downloaded the source, fixed the issue there (plus removing the loggers) and repackaged in a jar (jaligner-bugfixed.jar) that includes the sources.
Revision 1646 - Directory Listing
Modified Wed Jun 26 09:30:03 2013 UTC (3 years, 3 months ago) by jmduarteg
Now interfaces pngs have transparent background. Also changed another instance of "select resi 0" to "select none"
Revision 1645 - Directory Listing
Modified Mon Jun 24 10:25:00 2013 UTC (3 years, 3 months ago) by jmduarteg
Setting default minimum area for magenta dot displaying to 400 (was 500)
Revision 1644 - Directory Listing
Modified Mon Jun 17 14:24:45 2013 UTC (3 years, 3 months ago) by kumaran
1)Javaversion variable is added in build.xml to change the version easily. 
2)Pymol exited with error status 139 due to very long selection string written in the form of every residue(3+4+5+8+9+10). It is fixed by writing in the form of (3-5+8-10)
Revision 1643 - Directory Listing
Modified Mon Jun 17 12:46:07 2013 UTC (3 years, 3 months ago) by jmduarteg
Fixed bug CRK-128: in a non-crystallographic entry with cofactors it was crashing at getCofactors because we weren't checking for non-crystallographic entry there. The crash was a "cannot invert matrix" error, happening because the cell parameters where 0,0,0. Funnily enough this would not happen in my local machine (OpenJDK java 1.6.0_27), but it did happen in merlin (OpenJDK java1.6.0_24)
Revision 1642 - Directory Listing
Modified Thu Jun 13 10:57:42 2013 UTC (3 years, 3 months ago) by jmduarteg
Now both taxonomy and uniprot tables are read from same database
Revision 1641 - Directory Listing
Modified Thu Jun 13 09:21:02 2013 UTC (3 years, 3 months ago) by jmduarteg
Fixed bug: was null pointing on pdb files with a TER record positioned just before a HETATM record in the middle of a poly chain, now added more checks for duplicated PDB chain codes assignments which will catch that problem plus possibly others
Revision 1640 - Directory Listing
Modified Fri Apr 19 10:54:42 2013 UTC (3 years, 5 months ago) by jmduarteg
Tagging for eppic release 2.0.1
- fixed bug: can't read 'I 1 2 1' space group. Now using both main and alternative names for looking up space groups
Revision 1639 - Directory Listing
Modified Tue Apr 16 12:17:08 2013 UTC (3 years, 5 months ago) by jmduarteg
Fixed 'I 1 2 1' issue: it was actually a bug rather than a "feature", we were parsing everything in symoplib but some space groups happened to have alternative names and 'I 1 2 1' is the alternative name of 'I 2" which we were allowing. Now parsing and storing in lookup map both names.
Fixed also a bug by which the last space group in file was not added to the lookup-by-name map
Revision 1638 - Directory Listing
Modified Thu Apr 4 09:29:19 2013 UTC (3 years, 5 months ago) by jmduarteg
Changing default eclipse project name to owl
Revision 1637 - Directory Listing
Modified Wed Mar 20 09:47:07 2013 UTC (3 years, 6 months ago) by jmduarteg
Minor javadoc improvement
Revision 1636 - Directory Listing
Modified Mon Mar 18 14:06:43 2013 UTC (3 years, 6 months ago) by jmduarteg
Now will also write png files when generating chain pses.
Revision 1635 - Directory Listing
Modified Thu Mar 14 08:45:20 2013 UTC (3 years, 6 months ago) by jmduarteg
Fixed pisa oligomeric prediction behaviour when mixed assembly sizes in same assembly group
Revision 1634 - Directory Listing
Modified Wed Mar 6 11:49:39 2013 UTC (3 years, 6 months ago) by jmduarteg
Introduced a check to see if pisa server returns data or not
Revision 1633 - Directory Listing
Modified Thu Feb 28 14:39:59 2013 UTC (3 years, 6 months ago) by jmduarteg
Removing uniprot update script, doesn't belong in owl repo
Revision 1632 - Directory Listing
Modified Tue Feb 26 13:37:13 2013 UTC (3 years, 6 months ago) by jmduarteg
Now sorting the mappings in the order they happen in the PDB chain
Revision 1631 - Directory Listing
Modified Fri Feb 15 14:40:13 2013 UTC (3 years, 7 months ago) by jmduarteg
Tagging for eppic release 2.0.0
- many bug fixes, especially in cif and pdb parsers. Now hopefully a lot more robust. Cif parser was tested in whole PDB as of Feb 2013. File guesser will be more flexible with PDB files: it allows now a lot more possible first lines
- all elements added to AtomType
- better dealing with unknown elements when reading from PDB file
- fixed bug in ASA calculation: for finding neighbours we were taking default vdw radius instead of one set in setRadius
- BlastXML parser can now read both raw xml and gzipped xml blast output (autodetecting it)
Revision 1630 - Directory Listing
Modified Fri Feb 15 11:54:22 2013 UTC (3 years, 7 months ago) by jmduarteg
New feature: now blast xml parser can read either raw xml or gzipped xml files. Also HomologList will use xml.gz files only as cache files
Revision 1629 - Directory Listing
Modified Thu Feb 14 10:38:40 2013 UTC (3 years, 7 months ago) by nikhilbiyani
Removed Warnings from SiftsConnection
Revision 1628 - Directory Listing
Modified Thu Feb 14 10:28:18 2013 UTC (3 years, 7 months ago) by nikhilbiyani
Implementation of new method which returns a unique mapping of uniprot ids for all PDB chains
Revision 1627 - Directory Listing
Modified Thu Feb 14 09:54:54 2013 UTC (3 years, 7 months ago) by jmduarteg
Several fixes:
- bug fix: was always throwing exception in pdb parser for no secondary structure when not protein
- new reasonable-crystal-cell check when loading PDB entries
- safer pdb file parsing: now all substrings should be checked. For instance now swiss-model output files are parseable
Revision 1626 - Directory Listing
Modified Wed Feb 13 15:57:52 2013 UTC (3 years, 7 months ago) by jmduarteg
Another small fix related to last commit
Revision 1625 - Directory Listing
Modified Wed Feb 13 15:57:04 2013 UTC (3 years, 7 months ago) by jmduarteg
Fixed issue: now setting unknown atom type whenever we can't guess the element. If we read from PDB file and there is an unguesseable atom that we then have to write out again the code would fail because in writeAtoms we assume we have atom types for everything.
Revision 1624 - Directory Listing
Modified Wed Feb 13 15:53:22 2013 UTC (3 years, 7 months ago) by nikhilbiyani
Added AtomTypes till atomic number 110
Revision 1623 - Directory Listing
Modified Wed Feb 13 11:54:40 2013 UTC (3 years, 7 months ago) by nikhilbiyani
Bugfix: Check for nulls while reading QParams.
Revision 1622 - Directory Listing
Modified Mon Feb 11 10:57:00 2013 UTC (3 years, 7 months ago) by nikhilbiyani
BugFix: A check for protein chain introduced before initializing secondary structure. This avoids problems with pdb files not containing protein chains and still have HELIX information!!
Revision 1621 - Directory Listing
Modified Thu Feb 7 11:07:04 2013 UTC (3 years, 7 months ago) by nikhilbiyani
BugFix: While getting cofactors, do not transform an asymmetric unit if crystal cell is not present! New check introduced!
Revision 1620 - Directory Listing
Modified Wed Feb 6 17:45:07 2013 UTC (3 years, 7 months ago) by jmduarteg
Minor issue fix: now heavy water (deuterated water) treated as water, i.e. not read. Also extracted the constants to HetResidue
Revision 1619 - Directory Listing
Modified Wed Feb 6 14:55:55 2013 UTC (3 years, 7 months ago) by jmduarteg
Fixed bug in ASA calculation: was taking in finding neighbours procedure the default vdw element radius rather thatn the one set in setRadius: NOTE this changes slightly the area values we are getting.
Fixed issue in parsing of atoms when no atom type can be guessed: now whenever we can't guess we write a warning, also setRadius will use default radius if element not known (instead of null pointing)
Revision 1618 - Directory Listing
Modified Tue Feb 5 16:05:55 2013 UTC (3 years, 7 months ago) by nikhilbiyani
BugFix: Included the possibility of cell parameters being non double values.
Revision 1617 - Directory Listing
Modified Fri Feb 1 13:55:27 2013 UTC (3 years, 7 months ago) by jmduarteg
Adding more possible start for a PDB file
Revision 1616 - Directory Listing
Modified Thu Jan 31 17:45:03 2013 UTC (3 years, 7 months ago) by jmduarteg
Fixed minor issue: we were using residue 0 in order to create an empty selection but since now we use PDB residue numbers residue 0 is valid. We now use the "none" keyword used in pymol to create empty selections
Revision 1615 - Directory Listing
Modified Wed Jan 30 16:09:43 2013 UTC (3 years, 7 months ago) by jmduarteg
Included more possible first lines to guess a PDB file, plus added a better error message to hint that one should add a HEADER record
Revision 1614 - Directory Listing
Modified Wed Jan 30 10:50:26 2013 UTC (3 years, 7 months ago) by jmduarteg
Fixed small bug in PymolRunner: negative residue numbers need to be escaped
Revision 1613 - Directory Listing
Modified Wed Jan 30 09:25:07 2013 UTC (3 years, 7 months ago) by jmduarteg
Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering
Revision 1612 - Directory Listing
Modified Mon Jan 28 16:51:13 2013 UTC (3 years, 7 months ago) by jmduarteg
Fixed bug: was null pointing in parsing 2bi6 mmCIF file. It had a multi-line quoted value in a _struct_conf non-loop element. We weren't handling that correctly. 
Also added a new peptide-linked 3-letter code het residue
Revision 1611 - Directory Listing
Modified Mon Jan 28 13:55:47 2013 UTC (3 years, 7 months ago) by jmduarteg
Fix bug with resolution and rfree parsing: wasn't catching non-question-mark strings
Revision 1610 - Directory Listing
Modified Fri Jan 25 15:14:39 2013 UTC (3 years, 7 months ago) by jmduarteg
Fixed bug: very strange PDB entries can have no atoms observed in a chain at all (e.g. 1oax) or all atoms of a chain in one alt location only (e.g. 3nji). We throw now exceptions for them as in my opinion they don't follow the data-modelling standards properly.
Revision 1609 - Directory Listing
Modified Fri Jan 25 14:07:48 2013 UTC (3 years, 7 months ago) by nikhilbiyani
Complete list of of atoms, their masses, and their vdW radii's.
Revision 1608 - Directory Listing
Modified Fri Jan 25 11:13:13 2013 UTC (3 years, 8 months ago) by nikhilbiyani
Bug fix: Checks if the method is Crystallographic before getting the unit cell. The can be errors in mmCIF files, where a cell is defined but the space group is not defined for non-crystallographic methods. Hence the check needed!
Revision 1607 - Directory Listing
Modified Fri Jan 25 09:46:42 2013 UTC (3 years, 8 months ago) by nikhilbiyani
Bug fixes for 
- Rsym/RMerge not a number, Previously was handling occurrence of ? but not other characters. 
- Check for missing _pdbx_poly_seq_scheme lines in mmCIF file
Revision 1606 - Directory Listing
Modified Fri Jan 25 08:25:37 2013 UTC (3 years, 8 months ago) by jmduarteg
New method to write PDB files with pdbChainCodes
Revision 1605 - Directory Listing
Modified Thu Jan 24 10:49:45 2013 UTC (3 years, 8 months ago) by jmduarteg
Fixed bug: some cif files use double quotes (e.g. 1hhu) and we were not parsing correctly the space group for them
Revision 1604 - Directory Listing
Modified Thu Jan 24 10:11:04 2013 UTC (3 years, 8 months ago) by jmduarteg
Adding new elements found after a sample of 10000 random pdb entries
Revision 1603 - Directory Listing
Modified Tue Jan 22 14:57:37 2013 UTC (3 years, 8 months ago) by jmduarteg
Small fix to allow for underscore in blast query id
Revision 1602 - Directory Listing
Modified Tue Jan 22 10:19:21 2013 UTC (3 years, 8 months ago) by jmduarteg
Small fix: moved up the naming of blast cache file
Revision 1601 - Directory Listing
Modified Tue Jan 22 08:28:36 2013 UTC (3 years, 8 months ago) by jmduarteg
Small fix to be sure that the uniprot ver reported in error message is the actual one that the japi server returned, at the moment they seem to be having issues and 2 calls to the server return different versions!
Revision 1600 - Directory Listing
Modified Tue Nov 27 10:21:02 2012 UTC (3 years, 9 months ago) by jmduarteg
Tagging for eppic release 1.9.6.
- totally redone interface calculation: huge improvements in runtime and memory usage, explores also 2nd neighbours, uses symmetry-redundancy elimination, bugs fixed
- introduced minimum ASA threshold for considering residue at surface
- cofactors can now be used for ASA calculation in interfaces
- blast runner now chooses matrix to use based on sequence length as it is standard use in blast servers
- introduced blast+ support
- introduced clustalo support in HomologsList
- improvements and important fixes in HomologsList alignments
Revision 1599 - Directory Listing
Modified Fri Nov 16 10:02:32 2012 UTC (3 years, 10 months ago) by jmduarteg
Fixed important issues with searching and alignment of homologs: 
- ids and coverage were calculated wrongly, based on all BlastHsps for a hit. Now based on single Hsps
- fixed bug in BlastHsp.getQueryCoverage: was miscalculating the coverage by 1 unit
- the useHspsOnly parameter in alignment didn't make much sense. We need always to use the hsp segments only, extending to the full sequence is dangerous and in any case does not make sense at all if the clustering is done in hsps only
Revision 1598 - Directory Listing
Modified Thu Nov 15 10:34:15 2012 UTC (3 years, 10 months ago) by jmduarteg
New classes to parse PiQSi annotation file
Revision 1597 - Directory Listing
Modified Wed Nov 7 08:58:43 2012 UTC (3 years, 10 months ago) by jmduarteg
Several changes related to blast:
- now supporting blast+ blastp. 
- blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired
- refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+
Also updated uniprot jar.
Revision 1596 - Directory Listing
Modified Mon Nov 5 13:34:38 2012 UTC (3 years, 10 months ago) by jmduarteg
Now using makeblastdb (for blast+) and also only getting by default uniref100
Revision 1595 - Directory Listing
Modified Sun Nov 4 19:36:53 2012 UTC (3 years, 10 months ago) by jmduarteg
Added a main method to output some sifts statistics
Revision 1594 - Directory Listing
Modified Thu Nov 1 15:27:35 2012 UTC (3 years, 10 months ago) by jmduarteg
Now will also take uniprot codes as input
Revision 1593 - Directory Listing
Modified Wed Oct 31 11:43:11 2012 UTC (3 years, 10 months ago) by jmduarteg
Now supporting clustalo as well as tcoffee for alignment of homologs
Revision 1592 - Directory Listing
Modified Thu Oct 4 13:47:37 2012 UTC (3 years, 11 months ago) by jmduarteg
Another element
Revision 1591 - Directory Listing
Modified Wed Oct 3 14:57:46 2012 UTC (3 years, 11 months ago) by jmduarteg
New element added
Revision 1590 - Directory Listing
Modified Mon Oct 1 16:08:49 2012 UTC (3 years, 11 months ago) by jmduarteg
Now also checking the translation component of the SCALE matrix, and if different from (0,0,0) throwing an exception. Some entries still have a shifted origin (e.g. 1hga, 1hgb, 1hgc). Let's hope they fix this in next remediation.
Revision 1589 - Directory Listing
Modified Mon Oct 1 14:31:11 2012 UTC (3 years, 11 months ago) by jmduarteg
Now the blastp runner will automatically select a substitution matrix based on length of query, following recommendations from ncbi (http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html). Most blast web servers have this behaviour by default.
Revision 1588 - Directory Listing
Modified Thu Sep 27 13:26:00 2012 UTC (3 years, 11 months ago) by jmduarteg
New feature: now we can take cofactors into account for calculation of ASA in interfaces
Revision 1587 - Directory Listing
Modified Tue Sep 18 09:12:00 2012 UTC (4 years ago) by jmduarteg
Now using a minimum threshold value for considering a residue at surface (instead of 0 before)
Revision 1586 - Directory Listing
Modified Mon Sep 3 08:21:51 2012 UTC (4 years ago) by jmduarteg
Now using more headers for guessing PDB files, for instance modeller uses EXPDTA as first line of their output files
Revision 1585 - Directory Listing
Modified Tue Aug 28 10:03:19 2012 UTC (4 years ago) by jmduarteg
New method to create pse of chain conservation and interfaces marked with dots
Revision 1584 - Directory Listing
Modified Thu Aug 23 10:16:34 2012 UTC (4 years, 1 month ago) by jmduarteg
Now making selections for chains as well
Revision 1583 - Directory Listing
Modified Tue Aug 21 15:29:27 2012 UTC (4 years, 1 month ago) by jmduarteg
Made new CrystalTransform class serializable
Revision 1582 - Directory Listing
Modified Tue Aug 21 13:13:25 2012 UTC (4 years, 1 month ago) by jmduarteg
Important fix to interface calculation: finally total symmetry redundancy elimination is working!
- fixed a bug present since rev 1573: translation vectors of transforms were not stored properly and thus wasn't comparing the right operators
- extracted TransformIdTransform private class to new class CrystalTransform. Rationalise some of the code thanks to that (still more to be done)
- better debug output in interface calculation to show duplicates info

Revision 1581 - Directory Listing
Modified Sun Aug 19 12:54:23 2012 UTC (4 years, 1 month ago) by jmduarteg
Even less symmetry redundancy elimination, due to strange counter-example found: 2gqv
Revision 1580 - Directory Listing
Modified Sun Aug 19 12:40:46 2012 UTC (4 years, 1 month ago) by jmduarteg
Fixes to interface calculation:
- removed redundant overlap check on AUs
- introduced overlap checks at chain level, avoids the grid creation for AICgraph
- better debug output: now we show "." for non-overlap chains, "o" for empty AICgraph calculation, "x" for non-empty AICgraph calculation
Revision 1579 - Directory Listing
Modified Fri Aug 17 17:32:05 2012 UTC (4 years, 1 month ago) by jmduarteg
Another important optimisation: now the ASA calculation for the list of interfaces is a lot more efficient by only calculating uncomplexed ASAs once per chain code per transform id. 
Not supporting anymore calculation of interfaces areas with NACCESS
Revision 1578 - Directory Listing
Modified Fri Aug 17 14:57:56 2012 UTC (4 years, 1 month ago) by jmduarteg
Got rid of the ad-hoc fix to translate the sym related objects to "first cell". Now interface calculation works without it since it is done exhaustively and correctly.
Revision 1577 - Directory Listing
Modified Fri Aug 17 14:35:17 2012 UTC (4 years, 1 month ago) by jmduarteg
Important change in interface calculation:
- another massive gain in run-time and memory usage: we first use the bounding boxes translations to see if it is worth translating the whole unit cells
- thanks to that we now go to 2nd neighbors! (still performance is better than before with only 1st neighbors!). With that we fixed the long-standing bug by which we miss interfaces beyond the 1st neighbor
- included a few examples of 2nd neighbor problem in test
- re-done the symmetry redundancy elimination, it is there but it has a very little effect on overall performance. Now we only don't use an operator when we are very sure its partner was in the right place. In effect we could get rid of it because it wouldn't really affect the performance, we rather keep it as it is good to remember that there is a lot of symmetry redundancy

Revision 1576 - Directory Listing
Modified Fri Aug 17 08:13:32 2012 UTC (4 years, 1 month ago) by jmduarteg
Another important optimisation: now bounds are translated and not recalculated from scratch after translation. Fixed a bug in bounds copying (wasn't copying the boundsProtOnly boolean)
Revision 1575 - Directory Listing
Modified Thu Aug 16 16:46:13 2012 UTC (4 years, 1 month ago) by jmduarteg
A small but important fix to make sure the transformations set in the PdbAsymUnit objects are independent from those taken from the SpaceGroup objects
Revision 1574 - Directory Listing
Modified Thu Aug 16 16:05:15 2012 UTC (4 years, 1 month ago) by jmduarteg
Fixes related to last commit: now checked that cached bounds/centroid are properly reset and copied. They weren't copied at all before and not always reset
Revision 1573 - Directory Listing
Modified Thu Aug 16 13:09:48 2012 UTC (4 years, 1 month ago) by jmduarteg
IMPORTANT changes and fixes in interface calculation:
- very important bug fix: BoundingBox was not always telling properly whether 2 boxes overlap. This not only fixes the important bug but also boosts the speed of interface calculation
- optimisation of PdbChain.getAICGraph not to return an empty graph whenever no overlap of boxes is found (instead of generating empty distance matrix and checking its emptiness): this alone gives the biggest performance boost to interface calculation, around 5x faster thanks to this alone
- fine optimisation of max/min calculation in BoundingBox
- made sure that bounds caching is done properly
- introduced the right solution for symmetry redundancy elimination: operators multiplication is the identity. Before we had an ad-hoc solution that wasn't comprehensive at all
- in any case the symmetry redundancy elimination is right now almost turned off because we introduced new conditions to re-check equivalent operators to fix cases like 2gsg, 3ka0, 1vzi, 1g3p and 1eaq, where some interfaces are missed due to an equivalent operator making the molecule fall in a cell where there's no contacts
All in all this totally changes the interface calculation: 1) by a massive boost in performance 2) by making it more correct, surely there were cases with missing interfaces, we were just lucky not to find them in testing
Revision 1572 - Directory Listing
Modified Mon Aug 13 10:58:40 2012 UTC (4 years, 1 month ago) by jmduarteg
Fixed bug in PDB file parser: checking for TER records was done with a trailing space "TER ", that was fine for PDB deposited files but not for others (for instance phenix files). Because of that it was failing to parse properly some multi non-poly chains phenix files. Now removed the trailing space and problem seems to be gone. PDB parsers test passed
Revision 1571 - Directory Listing
Modified Fri Aug 10 15:47:06 2012 UTC (4 years, 1 month ago) by jmduarteg
Tagging for eppic release 1.9.5.
- better alignment in HomologsList
- better redundancy reduction in HomologList through clustering
- many bug fixes, a few of them in parsers
Revision 1570 - Directory Listing
Modified Thu Aug 9 16:07:22 2012 UTC (4 years, 1 month ago) by jmduarteg
Now logging t_coffee total runtime
Revision 1569 - Directory Listing
Modified Thu Aug 9 15:47:45 2012 UTC (4 years, 1 month ago) by jmduarteg
Fixed minor issue: phenix PDB files use lower case for double-letter atom symbols, now forcing the upper case
Revision 1568 - Directory Listing
Modified Mon Aug 6 10:21:39 2012 UTC (4 years, 1 month ago) by jmduarteg
Bug fix: was null pointing when a Deuterium atom was present in a standard amino acid (not clear anyway whether that is standard PDB practice). Now checking for unknown atoms in standard amino acids when getting their radii. Will output error and continue with their standard vdw radius.
Revision 1567 - Directory Listing
Modified Tue Jul 31 13:31:31 2012 UTC (4 years, 1 month ago) by jmduarteg
Now checking the SCALE1,2,3 PDB records when loading PDB data, in order to detect PDB entries that are not in the standard crystal frame (after remediation of 2011 only 148 non-virus entries are in nonstandard frame, marked with REMARK 285)
Revision 1566 - Directory Listing
Modified Fri Jul 27 14:20:11 2012 UTC (4 years, 1 month ago) by jmduarteg
Adding another atom type
Revision 1565 - Directory Listing
Modified Wed Jul 25 16:31:48 2012 UTC (4 years, 2 months ago) by jmduarteg
Fixing some tests to use cif file repo instead of pdbase
Revision 1564 - Directory Listing
Modified Wed Jul 25 16:12:03 2012 UTC (4 years, 2 months ago) by jmduarteg
Minor fixes in entropy calculation
Revision 1563 - Directory Listing
Modified Fri Jun 22 08:39:56 2012 UTC (4 years, 3 months ago) by jmduarteg
Fixed another small bug in cif parser: wasn't setting the sequence tags correctly
Revision 1562 - Directory Listing
Modified Wed Jun 6 09:34:00 2012 UTC (4 years, 3 months ago) by jmduarteg
Fixed bug in cif parser: wasn't setting the parent PdbAsymUnit in the PdbChains
Revision 1561 - Directory Listing
Modified Fri Jun 1 10:49:42 2012 UTC (4 years, 3 months ago) by jmduarteg
New method to calculate contact order
Revision 1560 - Directory Listing
Modified Wed May 23 10:04:05 2012 UTC (4 years, 4 months ago) by jmduarteg
Now checking that alignment from cache contains actually what we are expecting
Revision 1559 - Directory Listing
Modified Tue May 15 10:39:24 2012 UTC (4 years, 4 months ago) by jmduarteg
Method to close the connection
Revision 1558 - Directory Listing
Modified Mon May 14 14:14:13 2012 UTC (4 years, 4 months ago) by jmduarteg
Solved a couple of small issues in HomologList
Revision 1557 - Directory Listing
Modified Thu May 10 08:15:52 2012 UTC (4 years, 4 months ago) by jmduarteg
Fixed bug: for a uniref100 cluster member, was taking the representative's uniprot id/tax id instead of the member's. Database was not correctly modelled -> need also the tax  ids for cluster members (and then to query the tax ids from members and not from representative)
Revision 1556 - Directory Listing
Modified Wed May 9 12:04:21 2012 UTC (4 years, 4 months ago) by jmduarteg
New feature: now reducing redundancy via clustering with blastclust
Revision 1555 - Directory Listing
Modified Tue Apr 24 16:54:50 2012 UTC (4 years, 5 months ago) by jmduarteg
Improved a bit the skimming strategy to be a bit less naive: now it skims more from the very high identities [e.g. it seems to improve case 3b37_1, a xtal contact]
Revision 1554 - Directory Listing
Modified Tue Apr 24 13:33:47 2012 UTC (4 years, 5 months ago) by jmduarteg
Writing fasta tag with subinterval also for query
Revision 1553 - Directory Listing
Modified Tue Apr 24 13:26:04 2012 UTC (4 years, 5 months ago) by jmduarteg
Now we can do alignments using hsp regions only (instead of always full sequences)
Revision 1552 - Directory Listing
Modified Tue Apr 24 09:04:01 2012 UTC (4 years, 5 months ago) by jmduarteg
Fixed bug: redundancy (duplicate) elimination was done on whole uniprot sequences and not on HSPs
Revision 1551 - Directory Listing
Modified Tue Apr 24 08:07:13 2012 UTC (4 years, 5 months ago) by jmduarteg
Introduced identicals elimination, removed the taxonomy grouping in removeRedundancy (didn't make any sense anymore without coding sequences)
Revision 1550 - Directory Listing
Modified Mon Apr 16 15:52:28 2012 UTC (4 years, 5 months ago) by jmduarteg
Fixed bug CRK-64: was crashing in interface calculation with space group P-1. Solve by not doing redundancy elimination for non-enantiomorphic space groups.
Revision 1549 - Directory Listing
Modified Wed Mar 21 17:47:24 2012 UTC (4 years, 6 months ago) by jmduarteg
Tagging for crk release 1.9.4
Revision 1548 - Directory Listing
Modified Tue Mar 20 10:18:01 2012 UTC (4 years, 6 months ago) by jmduarteg
New target jar-core-only (now default) which will build the default and core packages only and pack all jars except for the uniprot.jar
Revision 1547 - Directory Listing
Modified Thu Mar 15 16:43:01 2012 UTC (4 years, 6 months ago) by jmduarteg
Removing test class as there is already a tester in the PymolServerOutputStream itself
Revision 1546 - Directory Listing
Modified Thu Mar 15 15:07:38 2012 UTC (4 years, 6 months ago) by jmduarteg
Removing unused class and thus JRclient dependency
Revision 1545 - Directory Listing
Modified Wed Mar 14 13:41:58 2012 UTC (4 years, 6 months ago) by jmduarteg
Better docs and clean up of core/rim calculation code
Revision 1544 - Directory Listing
Modified Tue Mar 6 10:10:06 2012 UTC (4 years, 6 months ago) by jmduarteg
Changed how uniprotver is read
Revision 1543 - Directory Listing
Modified Thu Mar 1 18:23:02 2012 UTC (4 years, 6 months ago) by jmduarteg
Now can sort the blast hit list by evalue ascending
Revision 1542 - Directory Listing
Modified Wed Feb 29 17:37:21 2012 UTC (4 years, 6 months ago) by jmduarteg
Fixed issues with homologs with a uniparc id as reference, now the reference can be either uniprot or uniparc
Revision 1541 - Directory Listing
Modified Tue Feb 28 15:01:00 2012 UTC (4 years, 6 months ago) by jmduarteg
Fixed bug: version 4.0 was using "UniProt ID" attribute tags and "representativeMember" tags. That was a mix of oldest and newer formats, now fixed for all
Revision 1540 - Directory Listing
Modified Tue Feb 28 14:18:48 2012 UTC (4 years, 6 months ago) by jmduarteg
Fixed bug in uniref xml parser: was not taking the right uniprot representative for old style (e.g. ver 1.0) xml files. They also contain several uniprot ids sometimes: first one being the active representative and the remaining being the inactive ones.
Revision 1539 - Directory Listing
Modified Mon Feb 27 13:58:44 2012 UTC (4 years, 6 months ago) by jmduarteg
New code to dump local uniprot db into a fasta file that can be use to formatdb and blast
Revision 1538 - Directory Listing
Modified Sun Feb 26 15:12:05 2012 UTC (4 years, 6 months ago) by jmduarteg
Implemented retrieval of uniprot KB data from local database
Revision 1537 - Directory Listing
Modified Sat Feb 25 17:55:47 2012 UTC (4 years, 7 months ago) by jmduarteg
Changed naming convention of uniprot db/tables
Revision 1536 - Directory Listing
Modified Fri Feb 24 17:23:03 2012 UTC (4 years, 7 months ago) by jmduarteg
New class for extracting information from a local Uniprot KB database. Not tested yet.
Revision 1535 - Directory Listing
Modified Fri Feb 24 13:29:26 2012 UTC (4 years, 7 months ago) by jmduarteg
Restructured how the UniprotConnection is used. Now all uniprot connection stuff done within the class
Revision 1534 - Directory Listing
Modified Thu Feb 23 17:55:08 2012 UTC (4 years, 7 months ago) by jmduarteg
Now the reference entry in HomologList is also a UnirefEntry. Not using anymore UniprotEntry
Revision 1533 - Directory Listing
Modified Thu Feb 23 16:31:32 2012 UTC (4 years, 7 months ago) by jmduarteg
Major change: Homolog and HomologList are now using the new class UnirefEntry. Removed a lot of the code related to Ka/Ks calculation and EMBL CDS retrieval
Revision 1532 - Directory Listing
Modified Thu Feb 23 14:01:55 2012 UTC (4 years, 7 months ago) by jmduarteg
Fixed bug: for members of clusters there's also inactive uniprot ids in rare cases, now only taking the active uniprot id for the member and ignoring the inactives
Revision 1531 - Directory Listing
Modified Thu Feb 23 11:37:40 2012 UTC (4 years, 7 months ago) by jmduarteg
More complete parsing: cluster members and inactive ids
Revision 1530 - Directory Listing
Modified Thu Feb 23 08:43:35 2012 UTC (4 years, 7 months ago) by jmduarteg
Some refactoring
Revision 1529 - Directory Listing
Modified Wed Feb 22 17:07:14 2012 UTC (4 years, 7 months ago) by jmduarteg
A new parser for uniref xml files
Revision 1528 - Directory Listing
Modified Tue Feb 21 14:05:30 2012 UTC (4 years, 7 months ago) by jmduarteg
Tagging for crk version 1.9.3
Revision 1527 - Directory Listing
Modified Fri Feb 17 13:28:03 2012 UTC (4 years, 7 months ago) by jmduarteg
Added atom type
Revision 1526 - Directory Listing
Modified Fri Feb 17 09:59:08 2012 UTC (4 years, 7 months ago) by jmduarteg
Now printing warnings if Hydrogens present when calculating interfaces
Revision 1525 - Directory Listing
Modified Thu Feb 16 15:42:08 2012 UTC (4 years, 7 months ago) by jmduarteg
Fixed important bug in tests: wasn't calling removeHatoms before calculating interfaces
Revision 1524 - Directory Listing
Modified Thu Feb 9 15:34:10 2012 UTC (4 years, 7 months ago) by jmduarteg
New classes for Grid Engine job querying
Revision 1523 - Directory Listing
Modified Wed Feb 8 10:46:23 2012 UTC (4 years, 7 months ago) by jmduarteg
Implemented caching of alignment files
Revision 1522 - Directory Listing
Modified Tue Feb 7 08:58:41 2012 UTC (4 years, 7 months ago) by jmduarteg
Relaxed the tolerance thresholds for testing of interfaces
Revision 1521 - Directory Listing
Modified Mon Feb 6 17:00:30 2012 UTC (4 years, 7 months ago) by jmduarteg
Fixed issue: was only considering axes in a, b, c. Now we properly check whether two operators are in same axis, by storing in a HashMap all operator ids per axis. Was affecting some exotic space groups like P 2 3.
Revision 1520 - Directory Listing
Modified Mon Feb 6 16:21:48 2012 UTC (4 years, 7 months ago) by jmduarteg
More improvements and another exclude list
Revision 1519 - Directory Listing
Modified Mon Feb 6 11:54:21 2012 UTC (4 years, 7 months ago) by jmduarteg
Improved the symmetry redundancy elimination test and added exclude list for a special case
Revision 1518 - Directory Listing
Modified Mon Jan 30 09:33:28 2012 UTC (4 years, 7 months ago) by jmduarteg
Updating uniprot japi
Revision 1517 - Directory Listing
Modified Fri Jan 27 16:32:26 2012 UTC (4 years, 7 months ago) by jmduarteg
A couple of fixes to the new test 
Revision 1516 - Directory Listing
Modified Thu Jan 26 17:12:57 2012 UTC (4 years, 7 months ago) by jmduarteg
New test for interface finder with/without redundancy elimination
Revision 1515 - Directory Listing
Modified Thu Jan 26 09:41:51 2012 UTC (4 years, 8 months ago) by jmduarteg
Implemented some more symmetry redundancy elimination: now also removing redundancy in some of the 3,4,6-fold axes. We still need a more general rule, but this is better than nothing

Revision 1514 - Directory Listing
Modified Wed Jan 25 17:55:10 2012 UTC (4 years, 8 months ago) by jmduarteg
Implemented some more symmetry redundancy elimination: now also removing redundancy in 2-fold axes

Revision 1513 - Directory Listing
Modified Wed Jan 25 11:37:32 2012 UTC (4 years, 8 months ago) by jmduarteg
Implemented some basic symmetry redundancy elimination in interfaces search. Moved interfaces-search to a separate class.
New pymol output file in enumerateInterfaces with all interfaces in a single session
Revision 1512 - Directory Listing
Modified Fri Jan 20 16:22:57 2012 UTC (4 years, 8 months ago) by jmduarteg
Fixed bug: was not setting the transl member of ChainInterface
Revision 1511 - Directory Listing
Modified Thu Dec 22 10:07:14 2011 UTC (4 years, 9 months ago) by jmduarteg
Improved pymol interface coloring: no showing sticks for whole interface but different colors only for core residues
Revision 1510 - Directory Listing
Modified Mon Dec 19 16:03:42 2011 UTC (4 years, 9 months ago) by jmduarteg
Fixed bug: was crashing with some NMR entries containing cell constants in cif file but with a "?" value (e.g. 1fmm)
Revision 1509 - Directory Listing
Modified Thu Dec 15 11:17:22 2011 UTC (4 years, 9 months ago) by jmduarteg
Now producing space group algebraic strings with fractions
Revision 1508 - Directory Listing
Modified Tue Dec 13 15:59:12 2011 UTC (4 years, 9 months ago) by jmduarteg
Adding flag to use uniparc or not
Revision 1507 - Directory Listing
Modified Tue Dec 13 14:47:32 2011 UTC (4 years, 9 months ago) by jmduarteg
Now supporting both uniprot and uniparc entries in HomologList
Revision 1506 - Directory Listing
Modified Mon Dec 12 10:54:04 2011 UTC (4 years, 9 months ago) by jmduarteg
New methods for filtering by domain of life
Revision 1505 - Directory Listing
Modified Wed Dec 7 17:30:05 2011 UTC (4 years, 9 months ago) by jmduarteg
Now UniprotHomologList contains a full list and a filtered list, making it more flexible
Revision 1504 - Directory Listing
Modified Wed Dec 7 10:35:38 2011 UTC (4 years, 9 months ago) by jmduarteg
Now catching OutOfMemory errors and continuing in redundancy removal procedure
Revision 1503 - Directory Listing
Modified Wed Dec 7 08:43:11 2011 UTC (4 years, 9 months ago) by jmduarteg
New method to produce statistics of the sequence entropies variability
Revision 1502 - Directory Listing
Modified Tue Dec 6 11:29:25 2011 UTC (4 years, 9 months ago) by jmduarteg
Tagging version for crk 1.9.2
Revision 1501 - Directory Listing
Modified Tue Dec 6 11:02:46 2011 UTC (4 years, 9 months ago) by jmduarteg
Fixed minor issue: now specifying what we print in tabular info
Revision 1500 - Directory Listing
Modified Tue Dec 6 08:10:12 2011 UTC (4 years, 9 months ago) by jmduarteg
Switching off surface rendering
Revision 1499 - Directory Listing
Modified Mon Dec 5 15:57:36 2011 UTC (4 years, 9 months ago) by jmduarteg
Fixed bug: slight miscalculation in query coverage (by one unit per hsp), would have affected very short entries
Revision 1498 - Directory Listing
Modified Mon Dec 5 11:31:10 2011 UTC (4 years, 9 months ago) by jmduarteg
Fixed minor bug: now will re-blast only if maxNumSeqs above 500 and more hits requested
Revision 1497 - Directory Listing
Modified Sat Dec 3 16:12:05 2011 UTC (4 years, 9 months ago) by jmduarteg
New feature: now can specify a subinterval in UniprotHomologList
Revision 1496 - Directory Listing
Modified Wed Nov 30 13:39:15 2011 UTC (4 years, 9 months ago) by jmduarteg
New method for getting sequence with MSEs as METs
Revision 1495 - Directory Listing
Modified Wed Nov 30 11:29:36 2011 UTC (4 years, 9 months ago) by jmduarteg
Fixed issue with uniparc and uniprot isoform ids
Revision 1494 - Directory Listing
Modified Tue Nov 29 18:00:50 2011 UTC (4 years, 9 months ago) by jmduarteg
New method
Revision 1493 - Directory Listing
Modified Fri Nov 25 10:48:53 2011 UTC (4 years, 10 months ago) by jmduarteg
Modified the uniref regex to also capture uniprot isoforms identifiers
Revision 1492 - Directory Listing
Modified Fri Nov 18 10:48:57 2011 UTC (4 years, 10 months ago) by jmduarteg
Improved the blast cache checking
Revision 1491 - Directory Listing
Modified Thu Nov 17 14:56:11 2011 UTC (4 years, 10 months ago) by jmduarteg
Now can pass option -v to blast (max number of hits reported)
Revision 1490 - Directory Listing
Modified Thu Nov 17 14:51:43 2011 UTC (4 years, 10 months ago) by jmduarteg
Updated uniprot japi jar to november's one
Revision 1489 - Directory Listing
Modified Wed Nov 16 14:26:57 2011 UTC (4 years, 10 months ago) by jmduarteg
Fixed logging and error handling of tcoffee: now it will really log errors to log file, temp files won't be deleted when exit!=0, command line is logged
Revision 1488 - Directory Listing
Modified Wed Nov 16 11:42:28 2011 UTC (4 years, 10 months ago) by jmduarteg
Fixed minor issue: wasn't logging an error through logger
Revision 1487 - Directory Listing
Modified Wed Nov 16 10:49:18 2011 UTC (4 years, 10 months ago) by jmduarteg
More logging
Revision 1486 - Directory Listing
Modified Wed Nov 16 08:20:28 2011 UTC (4 years, 10 months ago) by jmduarteg
Now blasting against uniref also supported in UniprotHomologList
Revision 1485 - Directory Listing
Modified Tue Nov 15 10:24:40 2011 UTC (4 years, 10 months ago) by jmduarteg
Adding downloading of uniref100
Revision 1484 - Directory Listing
Modified Fri Nov 11 16:06:07 2011 UTC (4 years, 10 months ago) by jmduarteg
Now explicitely specifying number of threads in TcoffeeRunner
Revision 1483 - Directory Listing
Modified Wed Nov 9 07:01:47 2011 UTC (4 years, 10 months ago) by jmduarteg
Fixed bug CRK-29: wasn't calculating interfaces for electron crystallography or neutron diffraction entries
Revision 1482 - Directory Listing
Modified Wed Oct 26 15:36:05 2011 UTC (4 years, 11 months ago) by jmduarteg
Now we consider pisa gray predictions as well
Revision 1481 - Directory Listing
Modified Mon Oct 24 08:54:36 2011 UTC (4 years, 11 months ago) by jmduarteg
Updated uniprot japi jars
Revision 1480 - Directory Listing
Modified Tue Oct 18 08:43:32 2011 UTC (4 years, 11 months ago) by jmduarteg
Minor fix
Revision 1479 - Directory Listing
Modified Fri Oct 14 09:26:13 2011 UTC (4 years, 11 months ago) by jmduarteg
Improved pisa assembly parsing and implemented a oligomeric predictor to automatically call the oligomeric assembly type from the PISA output
Revision 1478 - Directory Listing
Modified Thu Oct 13 08:29:22 2011 UTC (4 years, 11 months ago) by jmduarteg
New feature: pisa assembly parsing
Revision 1477 - Directory Listing
Modified Thu Oct 6 13:10:49 2011 UTC (4 years, 11 months ago) by jmduarteg
Fixed bug: isSecondProtein() was not calling the right molecule
Revision 1476 - Directory Listing
Modified Thu Oct 6 10:02:09 2011 UTC (4 years, 11 months ago) by jmduarteg
Introduced alternative parsing mode for PDB files: if no SEQRES present now two modes of parsing possible, one where the sequence is padded with Xs based on numbering and one where sequence is taken as is in ATOM lines whatever the numbering
Revision 1475 - Directory Listing
Modified Fri Sep 30 06:44:26 2011 UTC (4 years, 11 months ago) by jmduarteg
Fixed bug: interface calculation for NMR structures was not done correctly. NMR structures do have a dummy CRYST1 record, so we have to force avoid using it when exp method is not X-RAY.
Revision 1474 - Directory Listing
Modified Fri Sep 30 06:21:26 2011 UTC (4 years, 11 months ago) by jmduarteg
Fixed minor space group issue: some very weird PDB entries (racemic mixtures) are in space group P -1, unusually PDB use for it the non-standard name P 1-
Revision 1473 - Directory Listing
Modified Thu Sep 29 08:34:06 2011 UTC (4 years, 11 months ago) by jmduarteg
A few more atom types
Revision 1472 - Directory Listing
Modified Wed Sep 28 15:06:19 2011 UTC (4 years, 11 months ago) by jmduarteg
Fixed a couple of problems with ScopConnection. Added another atom type.
Revision 1471 - Directory Listing
Modified Thu Sep 8 09:19:09 2011 UTC (5 years ago) by jmduarteg
Introduced some more experimental code for enumeration of assemblies. BEWARE many things are UNFINISHED, namely in InterfaceGraph class the code to find induced and symmetry related interfaces is just a draft. There are many fundamental issues not solved yet. Be careful especially with implementations of equals and hashCode methods in InterfaceGraph, SubunitId, InterfaceGraphEdge etc. They alter "quietly" the behaviour of everything.
Revision 1470 - Directory Listing
Modified Thu Sep 8 08:12:47 2011 UTC (5 years ago) by jmduarteg
Removing some fields to do with zooming and refactoring
Revision 1469 - Directory Listing
Modified Thu Sep 8 07:56:48 2011 UTC (5 years ago) by jmduarteg
Tagging version for crk 1.9.1
Revision 1468 - Directory Listing
Modified Wed Sep 7 16:15:49 2011 UTC (5 years ago) by jmduarteg
Fixed bug: was not getting correctly the chain if it happened to appear only as the second member of the interface
Revision 1467 - Directory Listing
Modified Mon Sep 5 16:53:40 2011 UTC (5 years ago) by jmduarteg
New method for getting URL of uniprot entry
Revision 1466 - Directory Listing
Modified Mon Sep 5 16:21:32 2011 UTC (5 years ago) by jmduarteg
Some improvements to PymolRunner, including reading color mappings from properties file
Revision 1465 - Directory Listing
Modified Fri Sep 2 08:27:59 2011 UTC (5 years ago) by jmduarteg
New method to find all residues in surface that belong to no interface
Revision 1464 - Directory Listing
Modified Thu Sep 1 16:22:01 2011 UTC (5 years ago) by jmduarteg
New methods for transforming vectors to orthonormal or to crystal basis
Revision 1463 - Directory Listing
Modified Wed Aug 31 09:06:39 2011 UTC (5 years ago) by jmduarteg
Updating common-maths jar to latest stable release 2.2 (from 1.2)
Revision 1462 - Directory Listing
Modified Tue Aug 30 16:20:36 2011 UTC (5 years ago) by jmduarteg
Fixed issues with mixed nucleic acid/protein entries and getAllInterfaces and calculation of ASAs in DNA
Revision 1461 - Directory Listing
Modified Mon Aug 29 10:46:35 2011 UTC (5 years ago) by jmduarteg
Now really fixed the bug with DNA/RNA ASA calculations (there were a few other issues with atom nomenclature)
Revision 1460 - Directory Listing
Modified Mon Aug 29 08:29:57 2011 UTC (5 years ago) by jmduarteg
Fixed bug: was nullpointing when calculating ASA of DNA/RNA. Atom codes have a '*' in the naccess vdw.radii file, now converting them to proper PDB format
Revision 1459 - Directory Listing
Modified Fri Aug 26 07:00:03 2011 UTC (5 years, 1 month ago) by jmduarteg
New method to get the chain2repchain map
Revision 1458 - Directory Listing
Modified Wed Aug 24 14:43:45 2011 UTC (5 years, 1 month ago) by jmduarteg
Adapted to changes in PymolRunner
Revision 1457 - Directory Listing
Modified Wed Aug 24 13:30:58 2011 UTC (5 years, 1 month ago) by jmduarteg
Some more modified aminoacids
Revision 1456 - Directory Listing
Modified Mon Aug 22 14:52:42 2011 UTC (5 years, 1 month ago) by jmduarteg
Tidied up PymolRunner and made a bit faster by merging png and pse/pml creation for interfaces
Revision 1455 - Directory Listing
Modified Mon Aug 22 14:51:20 2011 UTC (5 years, 1 month ago) by jmduarteg
Committing test case file that was missing since a few revisions
Revision 1454 - Directory Listing
Modified Mon Aug 22 13:05:34 2011 UTC (5 years, 1 month ago) by jmduarteg
More features for PymolRunner to display fancy pymol interface representations
Revision 1453 - Directory Listing
Modified Fri Aug 19 16:15:51 2011 UTC (5 years, 1 month ago) by jmduarteg
Got rid of -p option when executing pymol
Revision 1452 - Directory Listing
Modified Fri Aug 19 14:46:44 2011 UTC (5 years, 1 month ago) by jmduarteg
Now using grey for symmetry related partners in interface thumbnails 
Revision 1451 - Directory Listing
Modified Fri Aug 19 13:02:25 2011 UTC (5 years, 1 month ago) by jmduarteg
Methods for asa and bsa of rim/core
Revision 1450 - Directory Listing
Modified Fri Aug 19 12:50:00 2011 UTC (5 years, 1 month ago) by jmduarteg
Another peptide-linked HET residue
Revision 1449 - Directory Listing
Modified Fri Aug 19 12:38:59 2011 UTC (5 years, 1 month ago) by jmduarteg
New method getBSA
Revision 1448 - Directory Listing
Modified Thu Aug 18 15:23:57 2011 UTC (5 years, 1 month ago) by jmduarteg
Fixed bug in PDB file parsing: wasn't parsing correctly PDB files with no TER records and non-poly HETATMs. They were both merged together into one chain.
Revision 1447 - Directory Listing
Modified Thu Aug 18 11:51:33 2011 UTC (5 years, 1 month ago) by jmduarteg
Removing duplicate entry
Revision 1446 - Directory Listing
Modified Thu Aug 18 10:55:24 2011 UTC (5 years, 1 month ago) by jmduarteg
Another removed entry, this time  a mismatch of titles PDB vs CIF
Revision 1445 - Directory Listing
Modified Thu Aug 18 10:29:42 2011 UTC (5 years, 1 month ago) by jmduarteg
Removed another strange entry (after july 2011 remediation) from test list
Revision 1444 - Directory Listing
Modified Thu Aug 18 09:56:40 2011 UTC (5 years, 1 month ago) by jmduarteg
Removed a strange entry (after july 2011 remediation) from test list
Revision 1443 - Directory Listing
Modified Thu Aug 18 08:50:54 2011 UTC (5 years, 1 month ago) by jmduarteg
Converted table names to capitals and extracted constants. Original pdbase has capitals, it worked at mpi mg because we were using mysql in case insensitive mode.
Revision 1442 - Directory Listing
Modified Thu Aug 18 08:11:46 2011 UTC (5 years, 1 month ago) by jmduarteg
Removing manifest file, now in build.xml
Revision 1441 - Directory Listing
Modified Thu Aug 18 08:09:04 2011 UTC (5 years, 1 month ago) by jmduarteg
Added manifest info to build.xml script. Removed obsolete shell build script
Revision 1440 - Directory Listing
Modified Thu Aug 18 07:03:28 2011 UTC (5 years, 1 month ago) by jmduarteg
Tagging from bug fix branch for bug fixed version of CMView 1.9.4 (released as 1.1.1). Important bug fix of DaliRunner
Revision 1439 - Directory Listing
Modified Wed Aug 17 12:36:42 2011 UTC (5 years, 1 month ago) by jmduarteg
An ant script for owl!
Revision 1438 - Directory Listing
Modified Wed Aug 17 12:35:52 2011 UTC (5 years, 1 month ago) by jmduarteg
An ant script for owl!
Revision 1437 - Directory Listing
Modified Wed Aug 17 10:07:33 2011 UTC (5 years, 1 month ago) by jmduarteg
Removed not needed jar (only cmview needs this one)
Revision 1436 - Directory Listing
Modified Wed Aug 17 10:06:53 2011 UTC (5 years, 1 month ago) by jmduarteg
Removed not needed jar (only cmview needs this one)
Revision 1435 - Directory Listing
Modified Tue Aug 16 16:03:09 2011 UTC (5 years, 1 month ago) by jmduarteg
Fixed bugs in DaliRunner
- it wouldn't run from cmview when the two chains had same pdb code and pdb chain code
- it wouldn't work with newer versions of DaliLite as apparently the output file names and formats changed 
Revision 1434 - Directory Listing
Modified Tue Aug 16 16:02:34 2011 UTC (5 years, 1 month ago) by jmduarteg
Fixed bugs in DaliRunner
- it wouldn't run from cmview when the two chains had same pdb code and pdb chain code
- it wouldn't work with newer versions of DaliLite as apparently the output file names and formats changed 
Revision 1433 - Directory Listing
Modified Tue Aug 16 15:36:21 2011 UTC (5 years, 1 month ago) by jmduarteg
Creating owl branch from tag owl-1.9.3 for bug fixes of cmview (release 1.1). To go together with branch cmview-1.9 
Revision 1432 - Directory Listing
Modified Fri Aug 5 14:44:41 2011 UTC (5 years, 1 month ago) by jmduarteg
New element
Revision 1431 - Directory Listing
Modified Mon Aug 1 15:04:21 2011 UTC (5 years, 1 month ago) by jmduarteg
Changed behaviour of getId() in ChainInterfaceList, now uses the same ids as the interfaces, i.e. starts counting from 1 and not from 0.
New graph classes for storing interface topology
Revision 1430 - Directory Listing
Modified Thu Jul 28 06:50:37 2011 UTC (5 years, 1 month ago) by jmduarteg
Fixed bug: title was parsing line until char 80, but sometimes (non PDB deposited) files are trimmed of spaces
Revision 1429 - Directory Listing
Modified Fri Jul 15 15:44:57 2011 UTC (5 years, 2 months ago) by jmduarteg
Introduced calculation of relative ASAs. 
A few new methods to calculate rim/core of interfaces using alternative definitions.
Revision 1428 - Directory Listing
Modified Fri Jul 8 13:42:10 2011 UTC (5 years, 2 months ago) by jmduarteg
Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation
Revision 1427 - Directory Listing
Modified Wed Jul 6 12:34:13 2011 UTC (5 years, 2 months ago) by jmduarteg
Fixed bug in pdb file parsing. Wasn't checking properly for atom serials in ascending order (was checking across chains and needs to be within chains only)
Revision 1426 - Directory Listing
Modified Tue Jun 21 17:25:37 2011 UTC (5 years, 3 months ago) by jmduarteg
Two more atom types
Revision 1425 - Directory Listing
Modified Tue Jun 21 10:49:33 2011 UTC (5 years, 3 months ago) by jmduarteg
Another atom type
Revision 1424 - Directory Listing
Modified Mon Jun 20 14:35:43 2011 UTC (5 years, 3 months ago) by jmduarteg
Minor fix: to avoid nullpointers when calculating radii and atom unknown
Revision 1423 - Directory Listing
Modified Mon Jun 20 14:29:00 2011 UTC (5 years, 3 months ago) by jmduarteg
Another atom type
Revision 1422 - Directory Listing
Modified Mon Jun 20 12:11:06 2011 UTC (5 years, 3 months ago) by jmduarteg
New atom type
Revision 1421 - Directory Listing
Modified Thu Jun 16 16:57:37 2011 UTC (5 years, 3 months ago) by jmduarteg
Fixed bug: was not checking that atom type actually exists
Revision 1420 - Directory Listing
Modified Thu Jun 16 14:59:14 2011 UTC (5 years, 3 months ago) by jmduarteg
Adding element
Revision 1419 - Directory Listing
Modified Thu Jun 16 13:34:25 2011 UTC (5 years, 3 months ago) by jmduarteg
Improvements mainly to ChainInterface and associated classes: now can detect a lot more specific interactions in interface: disulfides, hydrogen bonds, any other kind of close interactions
Revision 1418 - Directory Listing
Modified Fri Jun 10 09:14:26 2011 UTC (5 years, 3 months ago) by jmduarteg
Tagging version 1.9.5. Many bug fixes after introduction of hetatoms, especially with regards to read/write of PDB files. First tag with hetatoms-support.
Revision 1417 - Directory Listing
Modified Fri Jun 10 08:31:42 2011 UTC (5 years, 3 months ago) by jmduarteg
Some improvements and fixes to enumerateInterfaces
Revision 1416 - Directory Listing
Modified Thu Jun 9 18:46:06 2011 UTC (5 years, 3 months ago) by jmduarteg
Fixed bug: was nullpointing when trying to get radius of unknown atom in het aminoacid
Revision 1415 - Directory Listing
Modified Thu Jun 9 13:52:54 2011 UTC (5 years, 3 months ago) by jmduarteg
Better doc
Revision 1414 - Directory Listing
Modified Tue Jun 7 15:19:08 2011 UTC (5 years, 3 months ago) by jmduarteg
Minor fix: now writing the serialized file only once per interface list
Revision 1413 - Directory Listing
Modified Tue Jun 7 15:14:35 2011 UTC (5 years, 3 months ago) by jmduarteg
New option to output interfaces serialized file
Revision 1412 - Directory Listing
Modified Tue Jun 7 13:36:00 2011 UTC (5 years, 3 months ago) by jmduarteg
Now outputs core sizes as well
Revision 1411 - Directory Listing
Modified Tue Jun 7 12:15:51 2011 UTC (5 years, 3 months ago) by jmduarteg
Fixed bug: was not using full path of the given pymol executable
Revision 1410 - Directory Listing
Modified Mon Jun 6 08:52:03 2011 UTC (5 years, 3 months ago) by jmduarteg
Fixed bug: was not setting the actually used bsaToAsa cutoff when zooming
Revision 1409 - Directory Listing
Modified Fri Jun 3 14:05:44 2011 UTC (5 years, 3 months ago) by jmduarteg
Fixed minor bug: was outputting duplicate TER records when writing ChainInterface PDB files.
Revision 1408 - Directory Listing
Modified Fri Jun 3 08:22:56 2011 UTC (5 years, 3 months ago) by jmduarteg
Updated uniprot jar
Revision 1407 - Directory Listing
Modified Thu Jun 2 16:34:08 2011 UTC (5 years, 3 months ago) by jmduarteg
New methods and script to calculate mass of a protein/chain.
Revision 1406 - Directory Listing
Modified Mon May 30 14:08:31 2011 UTC (5 years, 3 months ago) by jmduarteg
Some new methods for disulfide detection and other minor things
Revision 1405 - Directory Listing
Modified Thu May 26 15:56:12 2011 UTC (5 years, 4 months ago) by jmduarteg
Now can calculate interfaces also for non-polymer chains, introduced new parameter to do only polymer chains or both poly/non-poly.
Revision 1404 - Directory Listing
Modified Thu May 26 10:24:55 2011 UTC (5 years, 4 months ago) by jmduarteg
Introduced some more checks in PDB file parser, now should be even more robust with badly formatted files.
Added some more atom types.
Revision 1403 - Directory Listing
Modified Wed May 25 09:03:49 2011 UTC (5 years, 4 months ago) by jmduarteg
Fixed a few bugs:
- PdbChain: copy() was missing some important fields, PDB file writing method was printing SEQRES for nonpoly chains too
- naccess BSA calculation had a few problems
- PdbAsymUnit: a few important issues with PDB/CIF chain codes
Revision 1402 - Directory Listing
Modified Tue May 24 17:07:49 2011 UTC (5 years, 4 months ago) by jmduarteg
Fixed minor bug: seq identical group string was wrong when only one member in group.
Revision 1401 - Directory Listing
Modified Tue May 24 12:34:36 2011 UTC (5 years, 4 months ago) by jmduarteg
Minor fix to writing of pdb files from ChainInterface
Revision 1400 - Directory Listing
Modified Tue May 24 12:24:01 2011 UTC (5 years, 4 months ago) by jmduarteg
Fixed some issues with writing of pdb files and wrote a test for write/read pdb files.
Revision 1399 - Directory Listing
Modified Tue May 24 09:06:15 2011 UTC (5 years, 4 months ago) by jmduarteg
Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
Revision 1398 - Directory Listing
Modified Mon May 23 16:48:37 2011 UTC (5 years, 4 months ago) by jmduarteg
Minor fix: was not printing het residues in ChainInterface print methods.
Revision 1397 - Directory Listing
Modified Mon May 23 15:55:38 2011 UTC (5 years, 4 months ago) by jmduarteg
Now using hetatoms for testing interfaces against pisa
Revision 1396 - Directory Listing
Modified Mon May 23 15:03:02 2011 UTC (5 years, 4 months ago) by jmduarteg
New method to produce strings with chain codes of sequence identical chains
Revision 1395 - Directory Listing
Modified Fri May 20 13:30:33 2011 UTC (5 years, 4 months ago) by jmduarteg
Now can calculate interfaces (only of AU) in cases when no crystal info is available
Revision 1394 - Directory Listing
Modified Thu May 19 14:56:08 2011 UTC (5 years, 4 months ago) by jmduarteg
Removed obsolete classes to analyse histone. Moved some useful methods for inertia moment calculation to GeometryTools
Revision 1393 - Directory Listing
Modified Thu May 19 14:41:29 2011 UTC (5 years, 4 months ago) by jmduarteg
Tagging version 1.9.4 before major change: support for HETATMs
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (5 years, 4 months ago) by jmduarteg
MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Revision 1391 - Directory Listing
Modified Fri May 13 17:08:44 2011 UTC (5 years, 4 months ago) by jmduarteg
Now throwing separate exceptions as before
Revision 1390 - Directory Listing
Modified Fri May 13 17:06:19 2011 UTC (5 years, 4 months ago) by jmduarteg
Fixed bug: pymol was hanging sometimes when running the script through stdin piping. Now using the -d mode it's more stable.
Revision 1389 - Directory Listing
Modified Fri May 6 12:56:04 2011 UTC (5 years, 4 months ago) by jmduarteg
Added many atoms + corrected masses. Now the mass is the standard mass rather than before (wrongly) the mass of the lightest isotope.
Revision 1388 - Directory Listing
Modified Tue Apr 12 08:05:10 2011 UTC (5 years, 5 months ago) by jmduarteg
Unzip method
Revision 1387 - Directory Listing
Modified Sun Apr 10 11:10:30 2011 UTC (5 years, 5 months ago) by hstehr
adding package-info for owl.mutanom
Revision 1386 - Directory Listing
Modified Thu Apr 7 15:09:48 2011 UTC (5 years, 5 months ago) by jmduarteg
Changed constant name after change in kraken api
Revision 1385 - Directory Listing
Modified Thu Apr 7 14:55:45 2011 UTC (5 years, 5 months ago) by jmduarteg
New uniprot japi version
Revision 1384 - Directory Listing
Modified Wed Apr 6 07:59:43 2011 UTC (5 years, 5 months ago) by stehr
System.out.println(cmdline) is commented out.
Revision 1383 - Directory Listing
Modified Tue Apr 5 14:15:39 2011 UTC (5 years, 5 months ago) by stehr
tmp files will be written to the static disk.
Revision 1382 - Directory Listing
Modified Mon Apr 4 14:37:28 2011 UTC (5 years, 5 months ago) by jmduarteg
Documented the -t option 
Revision 1381 - Directory Listing
Modified Fri Apr 1 15:48:30 2011 UTC (5 years, 5 months ago) by jmduarteg
Improved javadocs
Revision 1380 - Directory Listing
Modified Fri Apr 1 07:53:32 2011 UTC (5 years, 5 months ago) by stehr
Going back to old version of PolyposeRunner because new version was way too slow
Revision 1379 - Directory Listing
Modified Thu Mar 31 14:28:20 2011 UTC (5 years, 5 months ago) by stehr
Fixed another problem with persistent temp files
Revision 1378 - Directory Listing
Modified Thu Mar 31 09:13:13 2011 UTC (5 years, 5 months ago) by jmduarteg
More debug output
Revision 1377 - Directory Listing
Modified Thu Mar 31 09:11:08 2011 UTC (5 years, 5 months ago) by stehr
Fix: Now deleting polypose temp files which were polluting /tmp directory
Revision 1376 - Directory Listing
Modified Thu Mar 31 07:59:09 2011 UTC (5 years, 5 months ago) by jmduarteg
Another test
Revision 1375 - Directory Listing
Modified Thu Mar 31 07:41:36 2011 UTC (5 years, 5 months ago) by jmduarteg
Fixed bug in finding unique and rep chains.
Revision 1374 - Directory Listing
Modified Wed Mar 30 16:30:42 2011 UTC (5 years, 5 months ago) by jmduarteg
Adding Serializable interface to some classes
Revision 1373 - Directory Listing
Modified Wed Mar 30 10:23:48 2011 UTC (5 years, 5 months ago) by jmduarteg
Now PdbChain also implements Iterable
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (5 years, 5 months ago) by jmduarteg
MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
Revision 1371 - Directory Listing
Modified Wed Mar 30 07:34:06 2011 UTC (5 years, 5 months ago) by jmduarteg
Tagging owl-1.9.3 before major interface change.
Revision 1370 - Directory Listing
Modified Tue Mar 29 18:29:16 2011 UTC (5 years, 5 months ago) by hstehr
Updated some JavaDocs
Revision 1369 - Directory Listing
Modified Tue Mar 29 16:20:18 2011 UTC (5 years, 5 months ago) by jmduarteg
tagging owl-1.9.2 to match CMView-1.9.2-released-as-1.1rc5
Revision 1368 - Directory Listing
Modified Tue Mar 29 16:12:26 2011 UTC (5 years, 5 months ago) by jmduarteg
Removing tag owl-1.9.2 because it doesn't include some minor fixes.
Revision 1367 - Directory Listing
Modified Mon Mar 28 17:49:23 2011 UTC (5 years, 5 months ago) by hstehr
Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
Revision 1366 - Directory Listing
Modified Mon Mar 28 17:46:49 2011 UTC (5 years, 5 months ago) by hstehr
preparing for adding 'mutanom' package: adding dependencies to jars dir
Revision 1365 - Directory Listing
Modified Mon Mar 28 16:51:55 2011 UTC (5 years, 5 months ago) by hstehr
tagging owl-1.9.2 to match CMView-1.9.2-released-as-1.1rc5
Revision 1364 - Directory Listing
Modified Mon Mar 28 16:49:11 2011 UTC (5 years, 5 months ago) by hstehr
removing tag owl-1.9.2 which contained wrong contents (copy of all tags instead of trunk)
Revision 1363 - Directory Listing
Modified Mon Mar 28 16:35:43 2011 UTC (5 years, 5 months ago) by jmduarteg
New class BoundingBox for bounds. Added bounds caching also to PdbAsymUnit. Fixed some issues with it in Pdb. Everything looks a lot cleaner thanks to new class.
Revision 1362 - Directory Listing
Modified Mon Mar 28 10:53:47 2011 UTC (5 years, 5 months ago) by jmduarteg
Fixed bug: wasn't resetting bounds whenever the coordinates were transformed.
Revision 1361 - Directory Listing
Modified Mon Mar 28 10:43:32 2011 UTC (5 years, 5 months ago) by jmduarteg
Fixed bug: now caching bounds properly.
Revision 1360 - Directory Listing
Modified Mon Mar 28 10:21:06 2011 UTC (5 years, 5 months ago) by jmduarteg
Minor fix: now forcing lower case in pdb code so that we can grab the cif file if input is upper case.
Revision 1359 - Directory Listing
Modified Mon Mar 28 10:15:49 2011 UTC (5 years, 5 months ago) by jmduarteg
New option -d
Revision 1358 - Directory Listing
Modified Mon Mar 28 09:32:42 2011 UTC (5 years, 5 months ago) by jmduarteg
More optimisation on geometric hashing algorithm.
Revision 1357 - Directory Listing
Modified Sat Mar 26 16:29:27 2011 UTC (5 years, 6 months ago) by jmduarteg
Some more optimisation, not sure if this really improves run time.
Revision 1356 - Directory Listing
Modified Fri Mar 25 14:59:41 2011 UTC (5 years, 6 months ago) by jmduarteg
More optimisation and simplification of geometric hashing algorithm. Runs very slightly faster.
Revision 1355 - Directory Listing
Modified Fri Mar 25 11:30:15 2011 UTC (5 years, 6 months ago) by hstehr
Fixed some conflicts when running multiple instances of this on the same machine
Revision 1354 - Directory Listing
Modified Fri Mar 25 09:28:23 2011 UTC (5 years, 6 months ago) by jmduarteg
Another (very minor) optimisation in geometric hashing algorithm
Revision 1353 - Directory Listing
Modified Thu Mar 24 19:37:52 2011 UTC (5 years, 6 months ago) by jmduarteg
Optimised and simplified the geometric hashing algorithm implementation, now runs slightly faster.
Revision 1352 - Directory Listing
Modified Tue Mar 22 18:18:36 2011 UTC (5 years, 6 months ago) by jmduarteg
tagging version 1.9.2 to match CMView-1.9.2-released-as-1.1rc5
Revision 1351 - Directory Listing
Modified Tue Mar 22 16:02:05 2011 UTC (5 years, 6 months ago) by hstehr
unnecessary codes removed
Revision 1350 - Directory Listing
Modified Tue Mar 22 15:51:13 2011 UTC (5 years, 6 months ago) by hstehr
add -O to dump observed sequences
Revision 1349 - Directory Listing
Modified Mon Mar 21 18:28:31 2011 UTC (5 years, 6 months ago) by hstehr
moving info about reduced alphabets from main() to printReducedAlphabetInfo()
Revision 1348 - Directory Listing
Modified Mon Mar 21 18:20:14 2011 UTC (5 years, 6 months ago) by hstehr
adding some missing documentation
Revision 1347 - Directory Listing
Modified Mon Mar 21 10:38:06 2011 UTC (5 years, 6 months ago) by hstehr
moving project CCCP to this repository
Revision 1346 - Directory Listing
Modified Fri Mar 18 08:25:07 2011 UTC (5 years, 6 months ago) by jmduarteg
Now detecting type of sequence: protein/nucleotide
Revision 1345 - Directory Listing
Modified Thu Mar 17 13:58:32 2011 UTC (5 years, 6 months ago) by jmduarteg
Now the colors of chains of pymol generated images are consistent with the letter codes (given a chain letter code the color will always be the same for it for all images generated)
Revision 1344 - Directory Listing
Modified Wed Mar 16 18:29:35 2011 UTC (5 years, 6 months ago) by hstehr

Revision 1343 - Directory Listing
Modified Wed Mar 16 18:29:19 2011 UTC (5 years, 6 months ago) by hstehr

Revision 1342 - Directory Listing
Modified Wed Mar 16 17:53:02 2011 UTC (5 years, 6 months ago) by hstehr

Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (5 years, 6 months ago) by jmduarteg
Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit
Revision 1340 - Directory Listing
Modified Sun Mar 13 17:44:18 2011 UTC (5 years, 6 months ago) by hstehr
Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta
Revision 1339 - Directory Listing
Modified Sun Mar 13 14:50:37 2011 UTC (5 years, 6 months ago) by hstehr
new script to convert clustalW to fasta format
Revision 1338 - Directory Listing
Modified Fri Mar 11 16:53:33 2011 UTC (5 years, 6 months ago) by jmduarteg
Fixed bug. Pymol was blocking
Revision 1337 - Directory Listing
Modified Fri Mar 11 08:47:52 2011 UTC (5 years, 6 months ago) by jmduarteg
Changing file names of contact map test files, windows didn't like the ':' in the file names
Revision 1336 - Directory Listing
Modified Wed Mar 9 11:05:05 2011 UTC (5 years, 6 months ago) by jmduarteg
New runner for pymol
Revision 1335 - Directory Listing
Modified Wed Mar 9 08:38:35 2011 UTC (5 years, 6 months ago) by jmduarteg
Now throwing InterruptedException. Refactor BlastErro to BlastException
Revision 1334 - Directory Listing
Modified Wed Mar 9 08:13:04 2011 UTC (5 years, 6 months ago) by jmduarteg
Refactoring xxxError to xxxException
Revision 1333 - Directory Listing
Modified Tue Mar 8 18:21:32 2011 UTC (5 years, 6 months ago) by jmduarteg
Important change: for maximum compatibility in no-SEQRES case we are now back to using the existing numbering if there's nothing wrong with it (no negatives or ins codes). If there's something wrong with numbering then we set the SEQRES to be the observed sequence and renumber. 
Now behaviour is as it was before revision 1329. With the difference that a lot more PDB files can be read. 
Revision 1332 - Directory Listing
Modified Tue Mar 8 15:00:46 2011 UTC (5 years, 6 months ago) by jmduarteg
Another fix to PdbfilePdb parser. Now it is more robust with bad formatting, tested on a whole tar ball of CASP predictions. Added the CASP predictions test set to tests.
Revision 1331 - Directory Listing
Modified Tue Mar 8 11:23:46 2011 UTC (5 years, 6 months ago) by jmduarteg
Another improvement to PdbfilePdb parsing: now we can also detect some ambiguous cases in alignments by checking the contiguity of the 3D chain. This fixes 2 cases from our test data set: 1dki and 2ofz. Now only 2 warnings for the whole dataset (both because of ambiguous assignment in HIS tags, safe to ignore. Could even be that CIF got them wrong)
Revision 1330 - Directory Listing
Modified Tue Mar 8 09:11:34 2011 UTC (5 years, 6 months ago) by jmduarteg
Now the re-numbering of residue serials in PDB files has been improved. Instead of aligning the sequences whenever the serials don't match SEQRES, we first try to see if there is a shift in the serials with respect to SEQRES (happens in many cases). Only if we can't find a shift that fully matches SEQRES we proceed to re-aligning. We also treat properly now the ins codes. Mapping is as close to CIF as possible. The parsers test passes for the whole cullpdb20. For some entries like 2ofz the mapping does not coincide 100% with CIF as there are ambiguities in the alignment.
Revision 1329 - Directory Listing
Modified Sat Mar 5 15:38:12 2011 UTC (5 years, 6 months ago) by jmduarteg
Important change: now the PDB file reader will try to read and fix the numbering of PDB files. Whenever the alignment is wrong it will realign and renumber using the jaligner package. The result of reading original PDB files now will be the same as that of reading CIF files, including proper mapping of classical PDB numbers to SEQRES residue serials (as in CIF). 
There is one change of behaviour in comparison to before: when no SEQRES present the sequence is taken to be that of ATOM lines instead of padding it with Xs.
Still in this version the re-alignment is not perfect as there are some times when ambiguities occur and they are not solved (e.g. in 2nwr where alignment in an unobserved loop can be at two possible places for a GLY). That is anyway a rather minor problem (coordinates are still fine, just the chain is not ordered correctly at 1 or 2 points) and rare (~1% of files)
Revision 1328 - Directory Listing
Modified Thu Mar 3 15:45:42 2011 UTC (5 years, 6 months ago) by jmduarteg
Removed two exception classes that were only used privately, didn't make much sense. Now using PdbLoadException
Revision 1327 - Directory Listing
Modified Thu Mar 3 14:33:29 2011 UTC (5 years, 6 months ago) by jmduarteg
Some more atoms seen in pdb files
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (5 years, 6 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1325 - Directory Listing
Modified Thu Mar 3 13:09:55 2011 UTC (5 years, 6 months ago) by jmduarteg
Now pdb file type guessing will guess correctly also with files starting with CRYST1 or SEQRES.
PdbAsymUnit now works with pdb files like those 2 and also with ATOM line only ones
Revision 1324 - Directory Listing
Modified Thu Mar 3 10:55:54 2011 UTC (5 years, 6 months ago) by jmduarteg
A few bug fixes and improvements in pdb data parsing.
- bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files
- improved very slightly the cif file parser moving out of loops the index getters
- drop fullLength as a field in Pdb, now we have only getFullLength()
- pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster)
- now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before

Revision 1323 - Directory Listing
Modified Sat Feb 26 11:17:51 2011 UTC (5 years, 6 months ago) by hstehr
tagging version 1.9.1 to match CMView-1.9.1-released-as-1.1rc4
Revision 1322 - Directory Listing
Modified Thu Feb 24 10:35:11 2011 UTC (5 years, 7 months ago) by hstehr
New method hasChain(String): boolean
Revision 1321 - Directory Listing
Modified Wed Feb 23 11:16:13 2011 UTC (5 years, 7 months ago) by jmduarteg
New enum for nucleotides
Revision 1320 - Directory Listing
Modified Wed Feb 23 10:45:32 2011 UTC (5 years, 7 months ago) by jmduarteg
Added atom types that appear in HET residues and details to docs
Revision 1319 - Directory Listing
Modified Thu Feb 17 09:01:05 2011 UTC (5 years, 7 months ago) by jmduarteg
Removed the serialize/deserialize methods (now in Goodies)
Revision 1318 - Directory Listing
Modified Thu Feb 17 08:58:55 2011 UTC (5 years, 7 months ago) by jmduarteg
Methods to serialize/deserialize from file
Revision 1317 - Directory Listing
Modified Wed Feb 9 17:41:17 2011 UTC (5 years, 7 months ago) by jmduarteg
Catching if the server returns non-requested records and throwin IOException for it.
Revision 1316 - Directory Listing
Modified Wed Feb 9 15:55:49 2011 UTC (5 years, 7 months ago) by jmduarteg
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
Revision 1315 - Directory Listing
Modified Wed Feb 9 11:46:03 2011 UTC (5 years, 7 months ago) by jmduarteg
Removed a now unused method
Revision 1314 - Directory Listing
Modified Wed Feb 9 11:36:04 2011 UTC (5 years, 7 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1313 - Directory Listing
Modified Wed Feb 9 10:28:56 2011 UTC (5 years, 7 months ago) by jmduarteg
Now taking paths from owl_test_paths.dat file
Revision 1312 - Directory Listing
Modified Mon Feb 7 15:00:47 2011 UTC (5 years, 7 months ago) by jmduarteg
Put back the parsing of score p values (was commented out)
Revision 1311 - Directory Listing
Modified Tue Feb 1 13:44:30 2011 UTC (5 years, 7 months ago) by jmduarteg
Now can do all chains of a given pdb codes instead of only the first one
Revision 1310 - Directory Listing
Modified Mon Jan 31 16:49:11 2011 UTC (5 years, 7 months ago) by jmduarteg
Fixed bug: was not checking whether the uniprot japi was actually returning all requested records for ids given when using getMultipleEntries. Now checking, logging it and removing the not-found ids from the homolog list.
Revision 1309 - Directory Listing
Modified Mon Jan 31 11:46:02 2011 UTC (5 years, 7 months ago) by jmduarteg
New jar for uniprot JAPI
Revision 1308 - Directory Listing
Modified Fri Jan 28 18:44:21 2011 UTC (5 years, 7 months ago) by jmduarteg
Fixed important bug that broke the reconstruction programs. Tinker output files don't contain occupancy/bfactors. Thus we have to make their parsing optional. Added a test case for this.
Revision 1307 - Directory Listing
Modified Wed Jan 26 10:32:20 2011 UTC (5 years, 8 months ago) by jmduarteg
Methods to serialize/deserialize from file ChainInterface
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (5 years, 8 months ago) by jmduarteg
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (5 years, 8 months ago) by jmduarteg
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
Revision 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (5 years, 8 months ago) by jmduarteg
Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
Revision 1303 - Directory Listing
Modified Fri Jan 14 20:21:03 2011 UTC (5 years, 8 months ago) by hstehr
tagging version 1.9.0 matching CMView 1.9.0 released as 1.1rc3
Revision 1302 - Directory Listing
Modified Fri Jan 14 18:15:38 2011 UTC (5 years, 8 months ago) by hstehr
adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
Revision 1301 - Directory Listing
Modified Fri Jan 14 16:24:16 2011 UTC (5 years, 8 months ago) by hstehr
overwriting default contactTypes.dat with the one needed for CMView release versions (only contains standard contact types). The old version with all esoteric contact types is renamed to contactTypes.all.dat
Revision 1300 - Directory Listing
Modified Wed Jan 12 10:22:15 2011 UTC (5 years, 8 months ago) by jmduarteg
Better docs
Revision 1299 - Directory Listing
Modified Tue Jan 11 17:38:33 2011 UTC (5 years, 8 months ago) by hstehr
adding Model-It server files to repository
Revision 1298 - Directory Listing
Modified Tue Jan 11 14:35:17 2011 UTC (5 years, 8 months ago) by jmduarteg
Now storing the query coverage cutoff.
Revision 1297 - Directory Listing
Modified Fri Jan 7 18:08:37 2011 UTC (5 years, 8 months ago) by jmduarteg
New methods to get sequence identical chains
Revision 1296 - Directory Listing
Modified Fri Jan 7 11:16:43 2011 UTC (5 years, 8 months ago) by jmduarteg
Bringing back the PISA classes for interface, molecule and residues. We store things first into them and only then convert to our own ChainInterface if needed. This is a much better approach less prone to errors. Tests pass.
Revision 1295 - Directory Listing
Modified Tue Dec 21 13:30:46 2010 UTC (5 years, 9 months ago) by jmduarteg
Now using Rsym whenever Rmerge and Rsym disagree
Revision 1294 - Directory Listing
Modified Mon Dec 20 10:32:31 2010 UTC (5 years, 9 months ago) by jmduarteg
Fixed bug: now copying the new fields (exp method, resolution, R free, Rsym) in the copy method
Revision 1293 - Directory Listing
Modified Mon Dec 20 09:35:49 2010 UTC (5 years, 9 months ago) by jmduarteg
Now parsing experimental method, resolution, R free and R sym.
Revision 1292 - Directory Listing
Modified Fri Dec 17 18:21:05 2010 UTC (5 years, 9 months ago) by cvehlow
Control database access! for CGAP
Revision 1291 - Directory Listing
Modified Fri Dec 17 16:38:25 2010 UTC (5 years, 9 months ago) by cvehlow
Control database access! for CGAP
Revision 1290 - Directory Listing
Modified Fri Dec 17 14:09:48 2010 UTC (5 years, 9 months ago) by cvehlow
add setParametersDB
Revision 1289 - Directory Listing
Modified Wed Dec 15 11:57:49 2010 UTC (5 years, 9 months ago) by jmduarteg
Introduced constant for formatdb executable
Revision 1288 - Directory Listing
Modified Fri Dec 10 15:23:40 2010 UTC (5 years, 9 months ago) by matt4077
adding java help to jars collection which is not really needed for building OWL but for building CMView
Revision 1287 - Directory Listing
Modified Fri Dec 10 15:17:04 2010 UTC (5 years, 9 months ago) by matt4077

Revision 1286 - Directory Listing
Modified Fri Dec 10 11:34:13 2010 UTC (5 years, 9 months ago) by hstehr
calling readStructureOrNull was exiting rather than returning null
Revision 1285 - Directory Listing
Modified Thu Dec 2 11:03:18 2010 UTC (5 years, 9 months ago) by jmduarteg
Now throwing MatchNotFound exception instead of catching it.
Revision 1284 - Directory Listing
Modified Mon Nov 29 10:06:28 2010 UTC (5 years, 9 months ago) by cvehlow
Overrides removed
Revision 1283 - Directory Listing
Modified Tue Nov 23 14:29:37 2010 UTC (5 years, 10 months ago) by jmduarteg
New getName method.
Revision 1282 - Directory Listing
Modified Thu Nov 18 09:24:15 2010 UTC (5 years, 10 months ago) by jmduarteg
Fixed formatting of the exception message
Revision 1281 - Directory Listing
Modified Wed Nov 17 13:45:09 2010 UTC (5 years, 10 months ago) by jmduarteg
Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.
Revision 1280 - Directory Listing
Modified Mon Nov 15 15:57:25 2010 UTC (5 years, 10 months ago) by jmduarteg
Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.
Revision 1279 - Directory Listing
Modified Mon Nov 15 15:12:44 2010 UTC (5 years, 10 months ago) by jmduarteg
Now asa calc done with our own implementation (was still using naccess)
Revision 1278 - Directory Listing
Modified Wed Nov 10 09:59:37 2010 UTC (5 years, 10 months ago) by jmduarteg
Fixed the rim/core zooming which wasn't working after redesign of things
Revision 1277 - Directory Listing
Modified Tue Nov 9 14:22:53 2010 UTC (5 years, 10 months ago) by jmduarteg
Forgot to fix 2 problems in last commit.
Revision 1276 - Directory Listing
Modified Tue Nov 9 13:58:05 2010 UTC (5 years, 10 months ago) by jmduarteg
More methods to report on interfaces clashes. Extracted clash distance constant.
Revision 1275 - Directory Listing
Modified Wed Nov 3 14:17:53 2010 UTC (5 years, 10 months ago) by jmduarteg
New uniprot japi 2010_11
Revision 1274 - Directory Listing
Modified Fri Oct 29 10:14:41 2010 UTC (5 years, 10 months ago) by jmduarteg
Fixed bug: was writing out PDB files of interfaces with mixed PDB/cif chain codes. Now they are always PDB chain codes. Got rid of ugly method setChainCode in Pdb
Revision 1273 - Directory Listing
Modified Thu Oct 28 13:56:03 2010 UTC (5 years, 10 months ago) by jmduarteg
Fixed buf: EMBL DB fetch returns sequences now in upper case, we were not converting properly to lower case in one place, now should be fixed.
Revision 1272 - Directory Listing
Modified Thu Oct 28 09:54:32 2010 UTC (5 years, 10 months ago) by jmduarteg
New method to get number of interfaces above a certain area
Revision 1271 - Directory Listing
Modified Tue Oct 26 16:20:14 2010 UTC (5 years, 11 months ago) by jmduarteg
New method to check clashes
Revision 1270 - Directory Listing
Modified Tue Oct 26 15:28:24 2010 UTC (5 years, 11 months ago) by jmduarteg
Fixed bug: was still not converting well algebraic transformations to matrix: was failing for transformations with terms like "X-Y+1/3"
Revision 1269 - Directory Listing
Modified Tue Oct 26 13:42:40 2010 UTC (5 years, 11 months ago) by jmduarteg
Fixed bug in SpaceGroupTest. Now it works and test passes.
Introduced checking for clashes in interfaces. Added it to the PdbAsymUnitTest
Revision 1268 - Directory Listing
Modified Fri Oct 22 17:07:57 2010 UTC (5 years, 11 months ago) by jmduarteg
Fixed some bugs with parsing symop.lib and conversion of transformations. Properly testing SpaceGroups and parsing now. Still one test (transpose equal inverse) does not work for trigonal and hexagonal groups.
Revision 1267 - Directory Listing
Modified Thu Oct 21 16:26:54 2010 UTC (5 years, 11 months ago) by jmduarteg
Now possible to not retrieve any CDS data
Revision 1266 - Directory Listing
Modified Thu Oct 21 15:26:35 2010 UTC (5 years, 11 months ago) by jmduarteg
Now throwing IOException when the server returns an error (happens for example when it is down)
Revision 1265 - Directory Listing
Modified Wed Oct 20 08:01:41 2010 UTC (5 years, 11 months ago) by jmduarteg
Now keeping track of ASA calc method
Revision 1264 - Directory Listing
Modified Tue Oct 19 16:58:00 2010 UTC (5 years, 11 months ago) by jmduarteg
Added printing of rim and core residues methods.
Revision 1263 - Directory Listing
Modified Mon Oct 18 13:12:10 2010 UTC (5 years, 11 months ago) by jmduarteg
Some restructuring of code to improve the crk application
Revision 1262 - Directory Listing
Modified Thu Oct 14 08:27:45 2010 UTC (5 years, 11 months ago) by jmduarteg
Fixed bug: some PDB files (like those output by phenix) don't write the Z number at the end of the CRYST1 record, thus not having enough trailing spaces, we have to take care of this.
Revision 1261 - Directory Listing
Modified Wed Oct 13 08:38:40 2010 UTC (5 years, 11 months ago) by jmduarteg
Added option to compile specific revision
Revision 1260 - Directory Listing
Modified Fri Oct 8 15:00:58 2010 UTC (5 years, 11 months ago) by jmduarteg
Using the new UniprotVerMismatchException instead of IOException
Revision 1259 - Directory Listing
Modified Fri Oct 8 13:45:56 2010 UTC (5 years, 11 months ago) by jmduarteg
New exception for mismatching uniprot versions
Revision 1258 - Directory Listing
Modified Fri Oct 8 13:15:13 2010 UTC (5 years, 11 months ago) by jmduarteg
Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators.
Added a test for SpaceGroup to test for proper parsing of algebraic strings
Revision 1257 - Directory Listing
Modified Thu Oct 7 18:34:46 2010 UTC (5 years, 11 months ago) by hstehr
updating jars for Uniprot release 2010_10
Revision 1256 - Directory Listing
Modified Thu Oct 7 17:04:32 2010 UTC (5 years, 11 months ago) by jmduarteg
Now reporting on percent burial too
Revision 1255 - Directory Listing
Modified Thu Oct 7 09:37:55 2010 UTC (5 years, 11 months ago) by jmduarteg
Minor changes to the test.
Revision 1254 - Directory Listing
Modified Thu Oct 7 08:38:10 2010 UTC (5 years, 11 months ago) by jmduarteg
Made conf file path a resource path so that it is readable from jar file too.
Revision 1253 - Directory Listing
Modified Wed Oct 6 17:01:19 2010 UTC (5 years, 11 months ago) by jmduarteg
Some minor updates
Revision 1252 - Directory Listing
Modified Wed Oct 6 14:22:03 2010 UTC (5 years, 11 months ago) by jmduarteg
Implemented some parallelisation in ASA calculation. It doesn't scale very well (could measure x2 speed-up with 4 CPUs in a Core2 Quad) but at least we have it, now this is starting to be better than NACCESS!
Revision 1251 - Directory Listing
Modified Tue Oct 5 12:46:24 2010 UTC (5 years, 11 months ago) by jmduarteg
Some more complete tests.
Revision 1250 - Directory Listing
Modified Mon Oct 4 16:23:26 2010 UTC (5 years, 11 months ago) by jmduarteg
Putting back number of sphere points parameter to Bosco's default, the other one was too inaccurate
Revision 1249 - Directory Listing
Modified Mon Oct 4 14:30:40 2010 UTC (5 years, 11 months ago) by jmduarteg
Some optimisation of the asa code, run time improved substantially.
Revision 1248 - Directory Listing
Modified Fri Oct 1 14:50:24 2010 UTC (5 years, 11 months ago) by jmduarteg
Now using our own ASA calculation instead of NACCESS for the interface areas calculation. We are slower than NACCESS but at least don't depend on it anymore, old NACCESS methods can still be used.
Revision 1247 - Directory Listing
Modified Fri Oct 1 12:53:40 2010 UTC (5 years, 11 months ago) by jmduarteg
Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
Revision 1246 - Directory Listing
Modified Thu Sep 30 16:19:58 2010 UTC (5 years, 11 months ago) by jmduarteg
Some minor improvements: now populating ids of ChainInterfaces, now interface area is half to match pisa's. 
Fixed bug in getAllInterfaces tester, wasn't comparing properly in small values. 
Revision 1245 - Directory Listing
Modified Thu Sep 30 10:44:38 2010 UTC (5 years, 11 months ago) by gmueller
does most of the job SparseMatrix did before
Revision 1244 - Directory Listing
Modified Thu Sep 30 09:09:36 2010 UTC (5 years, 11 months ago) by jmduarteg
Finally ASA/BSA comparison to PISA test passes. Have to exclude one case where slight difference interface area values led to different sorting and so comparsion doesn't work. This will still be a problem whenever that happens (whenever different sorting of PISA vs ours)
Revision 1243 - Directory Listing
Modified Thu Sep 30 08:34:46 2010 UTC (5 years, 11 months ago) by gmueller
some methods removed and added to a new class, other simplified
Revision 1242 - Directory Listing
Modified Wed Sep 29 15:22:49 2010 UTC (5 years, 11 months ago) by jmduarteg
Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).
Revision 1241 - Directory Listing
Modified Tue Sep 21 17:08:36 2010 UTC (6 years ago) by jmduarteg
Fixed bug: the bsa values of residues of the different interfaces were being updated on the same references, we have to copy before creating ChainInterface objects in getAllInterfaces.
Implemented interface pdb file outputting in enumerateInterfaces
Still interfaces tests don't pass because of 2 problems: a) order of first/second molecule not necessarily same as PISA (and in case of same chain codes can't catch it with chain codes), b) in many cases there are many minor discrepancies, usually associated to a lot of small negative bsa values.
Revision 1240 - Directory Listing
Modified Tue Sep 21 12:12:07 2010 UTC (6 years ago) by hstehr
suppressing two warnings
Revision 1239 - Directory Listing
Modified Tue Sep 21 12:01:35 2010 UTC (6 years ago) by gmueller
sparse matrix exception
Revision 1238 - Directory Listing
Modified Tue Sep 21 09:43:32 2010 UTC (6 years ago) by jmduarteg
Fixed minor bug in test, was not comparing properly the interface count of pisa vs ours.
Revision 1237 - Directory Listing
Modified Tue Sep 21 09:17:50 2010 UTC (6 years ago) by cvehlow
commit latest version
Revision 1236 - Directory Listing
Modified Mon Sep 13 11:03:14 2010 UTC (6 years ago) by cvehlow
variable 2D csv-files loadable
Revision 1235 - Directory Listing
Modified Fri Sep 10 14:39:45 2010 UTC (6 years ago) by cvehlow
Color scale class moved from gmbp to owl
Revision 1234 - Directory Listing
Modified Thu Sep 9 13:36:28 2010 UTC (6 years ago) by hstehr
New method to get PDB cross refs for a Uniprot entry
Revision 1233 - Directory Listing
Modified Thu Sep 9 11:36:44 2010 UTC (6 years ago) by hstehr
Renaming UniprotPdbRef to UniProtPdbRef to be consistent with UniProtConnection
Revision 1232 - Directory Listing
Modified Thu Sep 9 11:27:45 2010 UTC (6 years ago) by hstehr
Merging (yet again) my personal UniProtConnection with owl.core.connections.UniProtConnection; new features: Methods for retrieving cross references for PDB and PhosphoSitePlus
Revision 1231 - Directory Listing
Modified Thu Sep 9 11:26:08 2010 UTC (6 years ago) by hstehr
Adding class PhosphoSiteConnection
Revision 1230 - Directory Listing
Modified Wed Sep 8 16:30:40 2010 UTC (6 years ago) by jmduarteg
Fixed bug: bsa values were wrongly calculated. 
Now sort of interfaces is always descending.
Some more testing for individual residues asa and bsa values. 
Still an issue: individual bsas are not matching pisa's even though total interface areas are fine.
Revision 1229 - Directory Listing
Modified Wed Sep 8 09:24:54 2010 UTC (6 years ago) by jmduarteg
New method for finding identical sequences (entities)
Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (6 years ago) by jmduarteg
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
Revision 1227 - Directory Listing
Modified Tue Sep 7 09:47:02 2010 UTC (6 years ago) by gmueller
new methods added
-method, takes care of row and column index maps (refreshMatrix())
-methods, adding or removing entries, without refreshing index mapping
-norm methods(norm1(), norm2(), normInf()) as well as a special innerProduct() method

Revision 1226 - Directory Listing
Modified Mon Sep 6 10:15:25 2010 UTC (6 years ago) by hstehr
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
Revision 1225 - Directory Listing
Modified Wed Sep 1 15:57:23 2010 UTC (6 years ago) by jmduarteg
Now elimination of redundant interfaces not based only on count of edges, but also on identity of each of the contacts (atom's serials, atom codes, residue serials, residue types). Added more test cases. Seems to be working fine.
Revision 1224 - Directory Listing
Modified Wed Sep 1 14:30:52 2010 UTC (6 years ago) by cvehlow
added methods
Revision 1223 - Directory Listing
Modified Wed Sep 1 14:26:00 2010 UTC (6 years ago) by hstehr
updated classes for evaluating our CASP predictions
Revision 1222 - Directory Listing
Modified Wed Sep 1 14:23:40 2010 UTC (6 years ago) by hstehr
please don't check in Mac specific constants
Revision 1221 - Directory Listing
Modified Wed Sep 1 14:21:58 2010 UTC (6 years ago) by hstehr
updating annotations to get rid of warnings
Revision 1220 - Directory Listing
Modified Wed Sep 1 14:20:44 2010 UTC (6 years ago) by hstehr
deleting two classes which were making problems
Revision 1219 - Directory Listing
Modified Wed Sep 1 13:35:16 2010 UTC (6 years ago) by hstehr
added some javadoc
Revision 1218 - Directory Listing
Modified Wed Sep 1 13:02:18 2010 UTC (6 years ago) by jmduarteg
Fixed bug: was null pointing in parsing NMR cif files because they don't have crystal parameter fields. Now skipping that properly. Added NMR test entry to test cases.
Revision 1217 - Directory Listing
Modified Tue Aug 31 17:11:30 2010 UTC (6 years ago) by jmduarteg
First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.
Revision 1216 - Directory Listing
Modified Tue Aug 31 15:02:53 2010 UTC (6 years ago) by jmduarteg
Committing a version that 1st) properly places the symoped generated units of the first unit cell in the first unit cell (and not elsewhere like before) 2nd) does not miss any interfaces because of just doing half of the neighbours (e.g. in 7odc it wouldn't work). Now no interfaces are missing but lots of duplicates are found. So not a fully working version yet.
Revision 1215 - Directory Listing
Modified Fri Aug 27 17:03:45 2010 UTC (6 years ago) by jmduarteg
Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side.
Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa.
Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct.
Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.
Revision 1214 - Directory Listing
Modified Fri Aug 27 09:43:03 2010 UTC (6 years, 1 month ago) by jmduarteg
Faster BSA calculation by avoiding redundant runs of NACCESS.
Revision 1213 - Directory Listing
Modified Fri Aug 27 09:07:13 2010 UTC (6 years, 1 month ago) by jmduarteg
Changed default cutoff to coincide with PISA, entry 1pmm was a good clue (one interface has a 1 atom contact with 6 cutoff). 
Now going to the negative side (instead of positive) when translating the unit cell to coincide with PISA operators.
Revision 1212 - Directory Listing
Modified Thu Aug 26 15:52:49 2010 UTC (6 years, 1 month ago) by jmduarteg
First fully working implementation of interface enumeration!! WAn exact copy of PISA's interface enumeration! (only tested with very few examples so far)
Revision 1211 - Directory Listing
Modified Thu Aug 26 08:21:24 2010 UTC (6 years, 1 month ago) by jmduarteg
First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point. 
Revision 1210 - Directory Listing
Modified Wed Aug 25 11:28:14 2010 UTC (6 years, 1 month ago) by cvehlow
Changes to select certain Secondary Structure Type for Traces extraction!
Revision 1209 - Directory Listing
Modified Mon Aug 23 12:25:36 2010 UTC (6 years, 1 month ago) by jmduarteg
Fixed bug: was missing one operator in getTransformations
Revision 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (6 years, 1 month ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1207 - Directory Listing
Modified Mon Aug 23 12:09:04 2010 UTC (6 years, 1 month ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1206 - Directory Listing
Modified Fri Aug 20 13:29:09 2010 UTC (6 years, 1 month ago) by jmduarteg
Moved getTransformations method to Pdb and PdbAsymUnit where it really belongs.
Revision 1205 - Directory Listing
Modified Fri Aug 20 10:49:13 2010 UTC (6 years, 1 month ago) by jmduarteg
Now all crystal transformations work properly: doing the crystal to orthonormal basis conversion properly.
Revision 1204 - Directory Listing
Modified Thu Aug 19 15:06:01 2010 UTC (6 years, 1 month ago) by jmduarteg
Implemented some methods to do translations properly along crystal axes.
Revision 1203 - Directory Listing
Modified Thu Aug 19 10:52:46 2010 UTC (6 years, 1 month ago) by hstehr
renamed class benchmarkAll to createResultWebPages
Revision 1202 - Directory Listing
Modified Thu Aug 19 10:21:08 2010 UTC (6 years, 1 month ago) by hstehr
suppress "method not used" warning
Revision 1201 - Directory Listing
Modified Thu Aug 19 10:18:59 2010 UTC (6 years, 1 month ago) by hstehr
deleting KendallsTau class (even if it already deleted on the server)
Revision 1200 - Directory Listing
Modified Thu Aug 19 10:16:06 2010 UTC (6 years, 1 month ago) by hstehr
removed some bad characters
Revision 1199 - Directory Listing
Modified Thu Aug 19 10:14:54 2010 UTC (6 years, 1 month ago) by hstehr
added some debug output (commented out)
Revision 1198 - Directory Listing
Modified Thu Aug 19 10:11:45 2010 UTC (6 years, 1 month ago) by cvehlow
classes moved
Revision 1197 - Directory Listing
Modified Thu Aug 19 10:08:52 2010 UTC (6 years, 1 month ago) by hstehr
Adding some javadoc
Revision 1196 - Directory Listing
Modified Thu Aug 19 10:06:15 2010 UTC (6 years, 1 month ago) by hstehr
new class for scoring all casp7/casp8/casp9 server models in terms of GDT_TS and Acc/Cov of the contact map
Revision 1195 - Directory Listing
Modified Thu Aug 19 09:56:51 2010 UTC (6 years, 1 month ago) by cvehlow
classes moved
Revision 1194 - Directory Listing
Modified Thu Aug 19 09:56:40 2010 UTC (6 years, 1 month ago) by cvehlow
classes moved
Revision 1193 - Directory Listing
Modified Thu Aug 19 09:46:03 2010 UTC (6 years, 1 month ago) by hstehr
Created a stub method for KendalsTau in owl.core.util.Statistics
Revision 1192 - Directory Listing
Modified Thu Aug 12 15:23:53 2010 UTC (6 years, 1 month ago) by jmduarteg
Committing test class for AICGraph
Revision 1191 - Directory Listing
Modified Thu Aug 12 15:18:44 2010 UTC (6 years, 1 month ago) by jmduarteg
Considerable clean up of Pdb. Now the algorithm for calculating atom contacts is all under new class Grid (also refactored Box to GridCell). Tests for graph calculations passed.
Revision 1190 - Directory Listing
Modified Thu Aug 12 12:45:24 2010 UTC (6 years, 1 month ago) by jmduarteg
Fixed bug: now properly also including OXTs in inter-chain atom interaction graph calculation.
Revision 1189 - Directory Listing
Modified Thu Aug 12 12:24:04 2010 UTC (6 years, 1 month ago) by jmduarteg
Implemented inter-chain contact calculation (using same hashing algorithm as in intra-chain).
Revision 1188 - Directory Listing
Modified Wed Aug 11 15:33:22 2010 UTC (6 years, 1 month ago) by jmduarteg
New class PdbAsymUnit (which should be called Pdb, but we can't for obvious reasons). 
Fixed bug in Pdb.copy(), wasn't copying the new fields crystalCell and spaceGroup
Revision 1187 - Directory Listing
Modified Wed Aug 11 14:46:34 2010 UTC (6 years, 1 month ago) by cvehlow
Implementation of class for Check for Correctness of Casp server model files
Revision 1186 - Directory Listing
Modified Wed Aug 11 14:28:33 2010 UTC (6 years, 1 month ago) by cvehlow
max Cluster Path two possibilities (Mac Unix)
Revision 1185 - Directory Listing
Modified Wed Aug 11 13:34:13 2010 UTC (6 years, 1 month ago) by cvehlow
Method added which returns complete result in TreeMap
Revision 1184 - Directory Listing
Modified Wed Aug 11 13:13:50 2010 UTC (6 years, 1 month ago) by hstehr
deleting scoreGeomOfPdbSets which had compilation errors because it was checkid in accidentally
Revision 1183 - Directory Listing
Modified Wed Aug 11 13:05:09 2010 UTC (6 years, 1 month ago) by cvehlow
bug removed nullpointer?!
Revision 1182 - Directory Listing
Modified Wed Aug 11 10:17:32 2010 UTC (6 years, 1 month ago) by cvehlow
Implementation of class for KendallsTau Correlation Calculation
Implementation of class for Check for Correctness of Casp server model files
Implementation of class for Calculation of geometric scoring
Revision 1181 - Directory Listing
Modified Tue Aug 10 15:51:11 2010 UTC (6 years, 1 month ago) by jmduarteg
Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.
Revision 1180 - Directory Listing
Modified Tue Aug 10 10:48:23 2010 UTC (6 years, 1 month ago) by jmduarteg
Now correctly parsing the right short name field
Revision 1179 - Directory Listing
Modified Tue Aug 10 09:26:16 2010 UTC (6 years, 1 month ago) by jmduarteg
New classes to parse and store crystallographic space groups info.
Revision 1178 - Directory Listing
Modified Mon Aug 9 07:48:56 2010 UTC (6 years, 1 month ago) by cvehlow
actual methods 
Revision 1177 - Directory Listing
Modified Mon Aug 9 07:44:15 2010 UTC (6 years, 1 month ago) by cvehlow
actual version
Revision 1176 - Directory Listing
Modified Fri Aug 6 10:03:26 2010 UTC (6 years, 1 month ago) by jmduarteg
Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
Revision 1175 - Directory Listing
Modified Fri Aug 6 09:21:33 2010 UTC (6 years, 1 month ago) by cvehlow
Method to get translated and rotated coordinates.
Revision 1174 - Directory Listing
Modified Thu Aug 5 14:47:11 2010 UTC (6 years, 1 month ago) by jmduarteg
New method setChainCode
Revision 1173 - Directory Listing
Modified Wed Aug 4 15:27:40 2010 UTC (6 years, 1 month ago) by hstehr
minor modifications to casp benchmarking script
Revision 1172 - Directory Listing
Modified Wed Aug 4 15:26:03 2010 UTC (6 years, 1 month ago) by jmduarteg
Now using apache commons logging
Revision 1171 - Directory Listing
Modified Wed Aug 4 10:47:28 2010 UTC (6 years, 1 month ago) by hstehr
small update for compatibility with Casp9 data (changing baker group name string)
Revision 1170 - Directory Listing
Modified Wed Aug 4 10:43:52 2010 UTC (6 years, 1 month ago) by hstehr
adding secondary structure functions to RIGEnsemble and GraphAverager: GraphAverager can now use DSSP to get consensus secondary structure from underlying structures.
Revision 1169 - Directory Listing
Modified Mon Aug 2 17:29:07 2010 UTC (6 years, 1 month ago) by hstehr
some more fixes for doing benchmarking on Casp9 targets
Revision 1168 - Directory Listing
Modified Mon Aug 2 16:47:37 2010 UTC (6 years, 1 month ago) by jmduarteg
Now catching the case when the best translation contains stop codons. This is usually due to a wrong genetic code, but for the moment it's still very difficult to know the genetic code from encoding organelle+organism taxonomy, so this is the temporary solution.
Revision 1167 - Directory Listing
Modified Mon Aug 2 14:42:36 2010 UTC (6 years, 1 month ago) by hstehr
updated casp benchmarking classes for Casp9, still missing: update group suffix
Revision 1166 - Directory Listing
Modified Fri Jul 30 14:58:26 2010 UTC (6 years, 1 month ago) by jmduarteg
Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)
Revision 1165 - Directory Listing
Modified Fri Jul 30 11:03:57 2010 UTC (6 years, 1 month ago) by cvehlow
HahpMap keytype changed to Pair instead of String
Revision 1164 - Directory Listing
Modified Fri Jul 30 09:56:39 2010 UTC (6 years, 1 month ago) by jmduarteg
Now returning null for the representative CDS when the gene encoding organelle is not nucleus/plasmid. Before the whole program would stop, which wasn't ideal. Eventually we will need to use the proper genetic code when needed.
Revision 1163 - Directory Listing
Modified Wed Jul 28 12:56:41 2010 UTC (6 years, 1 month ago) by jmduarteg
Got rid of german text (was causing a warning in compilation), anyway there shouldn't be any german... unless we start i8nsing.
Revision 1162 - Directory Listing
Modified Wed Jul 28 09:15:19 2010 UTC (6 years, 1 month ago) by jmduarteg
Allowing plasmids as gene encoding organelles without having to treat them especially as they don't have a different genetic code.
Revision 1161 - Directory Listing
Modified Tue Jul 27 09:56:30 2010 UTC (6 years, 2 months ago) by cvehlow
slight changes
Revision 1160 - Directory Listing
Modified Fri Jul 23 15:11:40 2010 UTC (6 years, 2 months ago) by jmduarteg
Updating to latest uniprot 2010_08
Revision 1159 - Directory Listing
Modified Fri Jul 23 14:56:35 2010 UTC (6 years, 2 months ago) by jmduarteg
Reverting change made in last revision. It intended to fix a bug for a particular test case (don't know anymore which one!) but it actually broke most other cases.
Revision 1158 - Directory Listing
Modified Wed Jul 21 11:00:08 2010 UTC (6 years, 2 months ago) by cvehlow
print function
Revision 1157 - Directory Listing
Modified Wed Jul 7 15:31:14 2010 UTC (6 years, 2 months ago) by jmduarteg
Fixed bug, wasn't computing the nucleotide alignment correctly (was missing the last codon)
Revision 1156 - Directory Listing
Modified Wed Jul 7 13:18:24 2010 UTC (6 years, 2 months ago) by jmduarteg
More fixes to build script
Revision 1155 - Directory Listing
Modified Wed Jul 7 13:15:06 2010 UTC (6 years, 2 months ago) by jmduarteg
Implemented a simple skimming strategy. Put back some debug level logging to info level, logging aint' easy!
Revision 1154 - Directory Listing
Modified Wed Jul 7 10:39:28 2010 UTC (6 years, 2 months ago) by jmduarteg
And all other amiguous codons
Revision 1153 - Directory Listing
Modified Wed Jul 7 08:46:37 2010 UTC (6 years, 2 months ago) by jmduarteg
Another ambiguous nucleotide letter
Revision 1152 - Directory Listing
Modified Tue Jul 6 17:44:28 2010 UTC (6 years, 2 months ago) by jmduarteg
Fixed make script for new structure of owl
Revision 1151 - Directory Listing
Modified Tue Jul 6 16:58:04 2010 UTC (6 years, 2 months ago) by jmduarteg
Fixed bug: was null pointing with null cache file (which is a valid value)
Revision 1150 - Directory Listing
Modified Tue Jul 6 10:46:50 2010 UTC (6 years, 2 months ago) by cvehlow
PrintOut method ion RIGGeometry
Revision 1149 - Directory Listing
Modified Mon Jul 5 16:46:57 2010 UTC (6 years, 2 months ago) by jmduarteg
Changed level of some logging messages

Revision 1148 - Directory Listing
Modified Mon Jul 5 16:16:44 2010 UTC (6 years, 2 months ago) by jmduarteg
New removeRedundancy method
Revision 1147 - Directory Listing
Modified Mon Jul 5 08:35:15 2010 UTC (6 years, 2 months ago) by jmduarteg
Implemented logging with log4j library
Revision 1146 - Directory Listing
Modified Fri Jul 2 09:54:46 2010 UTC (6 years, 2 months ago) by jmduarteg
Now can write sequences with or without query
Revision 1145 - Directory Listing
Modified Thu Jul 1 16:05:26 2010 UTC (6 years, 2 months ago) by jmduarteg
Now can filter also on query coverage
Revision 1144 - Directory Listing
Modified Thu Jul 1 10:09:55 2010 UTC (6 years, 2 months ago) by jmduarteg
Changed the order of checks in isReferenceSeqPositionReliable
Revision 1143 - Directory Listing
Modified Thu Jul 1 10:02:53 2010 UTC (6 years, 2 months ago) by jmduarteg
New methods to check for reliability of positions with respect of the CDS matching
Revision 1142 - Directory Listing
Modified Wed Jun 30 09:55:27 2010 UTC (6 years, 2 months ago) by jmduarteg
Now nucleotide alignment contains reference sequence as well. Moved entropy and kaks calc methods to UniprotHomologList.
Revision 1141 - Directory Listing
Modified Tue Jun 29 12:56:41 2010 UTC (6 years, 2 months ago) by cvehlow
methods by saurabh included
Revision 1140 - Directory Listing
Modified Tue Jun 29 08:49:34 2010 UTC (6 years, 2 months ago) by jmduarteg
Fixed bug: now nucleotide alignment is in same order as protein alignment
Revision 1139 - Directory Listing
Modified Mon Jun 28 17:44:19 2010 UTC (6 years, 2 months ago) by jmduarteg
Fixed bug: when retrieving (or reading from cache) embl cds sequences and embl dbfetch doesn't have a certain identifier, then we were adding nulls to the list of emblcds sequences of the UniprotHomologList (resulting in a null pointer down the line)
Revision 1138 - Directory Listing
Modified Mon Jun 28 14:51:24 2010 UTC (6 years, 2 months ago) by cvehlow
Getter for Atoms-TreeMap.
Revision 1137 - Directory Listing
Modified Mon Jun 28 13:38:32 2010 UTC (6 years, 2 months ago) by jmduarteg
Now checking the sequence identity of the representative CDS to be above a minimum value.
Revision 1136 - Directory Listing
Modified Mon Jun 28 12:49:31 2010 UTC (6 years, 2 months ago) by jmduarteg
New ambiguous nucleotide w.
Revision 1135 - Directory Listing
Modified Fri Jun 25 13:40:27 2010 UTC (6 years, 3 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1134 - Directory Listing
Modified Fri Jun 25 13:39:57 2010 UTC (6 years, 3 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1133 - Directory Listing
Modified Fri Jun 25 13:36:03 2010 UTC (6 years, 3 months ago) by jmduarteg
Fixed bug: getNucleotideAlignment was nullpointing when encountering a null return from getRepresentativeCDS() (which happens whenever there is no representative CDS for the particular UniprotEntry). Now checking for nulls before using the homolog in the alignment.
Revision 1132 - Directory Listing
Modified Fri Jun 25 13:01:53 2010 UTC (6 years, 3 months ago) by jmduarteg
New SelectonRunner class. More taxonomy information retrieved from uniprot.
Revision 1131 - Directory Listing
Modified Thu Jun 24 09:46:24 2010 UTC (6 years, 3 months ago) by cvehlow
Changes: use different db for traces!
Revision 1130 - Directory Listing
Modified Thu Jun 24 09:42:57 2010 UTC (6 years, 3 months ago) by cvehlow
Rotation and translation procedure version 2 available in class Gmbp_Geom. Will be extended by Saurabh.
Revision 1129 - Directory Listing
Modified Wed Jun 23 10:24:30 2010 UTC (6 years, 3 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1128 - Directory Listing
Modified Wed Jun 23 10:23:44 2010 UTC (6 years, 3 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (6 years, 3 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1126 - Directory Listing
Modified Tue Jun 22 12:19:07 2010 UTC (6 years, 3 months ago) by jmduarteg
New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.
Revision 1125 - Directory Listing
Modified Mon Jun 21 15:39:04 2010 UTC (6 years, 3 months ago) by cvehlow
Rotation and translation procedure transfered into extra class GmbpGeometry
Revision 1124 - Directory Listing
Modified Mon Jun 21 15:38:09 2010 UTC (6 years, 3 months ago) by cvehlow
GmbpGeometry class implements rotation and translation invariant framework.
Revision 1123 - Directory Listing
Modified Mon Jun 21 12:50:54 2010 UTC (6 years, 3 months ago) by jmduarteg
Improved the selection of representative CDS
Revision 1122 - Directory Listing
Modified Mon Jun 21 10:48:05 2010 UTC (6 years, 3 months ago) by jmduarteg
Some refactoring
Revision 1121 - Directory Listing
Modified Fri Jun 18 16:02:55 2010 UTC (6 years, 3 months ago) by jmduarteg
Now implementing HasFeatures
Revision 1120 - Directory Listing
Modified Fri Jun 18 13:29:34 2010 UTC (6 years, 3 months ago) by jmduarteg
New class UniprotEntry. Things make a lot more sense now...
Revision 1119 - Directory Listing
Modified Fri Jun 18 11:55:46 2010 UTC (6 years, 3 months ago) by jmduarteg
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
Revision 1118 - Directory Listing
Modified Fri Jun 18 10:34:00 2010 UTC (6 years, 3 months ago) by cvehlow
RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.
Revision 1117 - Directory Listing
Modified Thu Jun 17 09:52:30 2010 UTC (6 years, 3 months ago) by jmduarteg
Now checking codon length before translating
Revision 1116 - Directory Listing
Modified Thu Jun 17 09:48:22 2010 UTC (6 years, 3 months ago) by jmduarteg
Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.
Revision 1115 - Directory Listing
Modified Wed Jun 16 15:10:16 2010 UTC (6 years, 3 months ago) by cvehlow
Changes in edge-cluster direction!
Revision 1114 - Directory Listing
Modified Wed Jun 16 10:26:22 2010 UTC (6 years, 3 months ago) by jmduarteg
New feature: code for dna to protein translation
Revision 1113 - Directory Listing
Modified Wed Jun 16 10:26:00 2010 UTC (6 years, 3 months ago) by jmduarteg
Replacing uniprot japi jar after new uniprot release 2010_07
Revision 1112 - Directory Listing
Modified Tue Jun 15 08:44:52 2010 UTC (6 years, 3 months ago) by jmduarteg
Now getting also gene encoding organelle from uniprot api
Revision 1111 - Directory Listing
Modified Mon Jun 14 15:50:46 2010 UTC (6 years, 3 months ago) by jmduarteg
Now getPdbResSerFromResSer and getResSerFromPdbResSer will return null/-1 whenever there's no mapping. Allows then for checking from the caller.
Revision 1110 - Directory Listing
Modified Mon Jun 14 13:21:49 2010 UTC (6 years, 3 months ago) by cvehlow
Methods added to Save and Load settings of SphoxelMap_Traces_View.
Revision 1109 - Directory Listing
Modified Thu Jun 10 16:29:42 2010 UTC (6 years, 3 months ago) by jmduarteg
Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.
Revision 1108 - Directory Listing
Modified Thu Jun 10 16:27:48 2010 UTC (6 years, 3 months ago) by jmduarteg
Now parsing the symmetry operators.
Revision 1107 - Directory Listing
Modified Thu Jun 10 10:20:35 2010 UTC (6 years, 3 months ago) by jmduarteg
Fixed bug: was nullpointing with empty cache files
Revision 1106 - Directory Listing
Modified Thu Jun 10 09:24:30 2010 UTC (6 years, 3 months ago) by jmduarteg
Implemented caching of blast in UniprotHomologList
Revision 1105 - Directory Listing
Modified Thu Jun 10 09:23:41 2010 UTC (6 years, 3 months ago) by jmduarteg
Our own copy file method! :-)
Revision 1104 - Directory Listing
Modified Wed Jun 9 17:04:36 2010 UTC (6 years, 3 months ago) by jmduarteg
Now reading uniprot version from reldate.txt and checking against the uniprot api version
Revision 1103 - Directory Listing
Modified Wed Jun 9 16:11:18 2010 UTC (6 years, 3 months ago) by jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision 1102 - Directory Listing
Modified Wed Jun 9 14:59:42 2010 UTC (6 years, 3 months ago) by cvehlow
Cluster-edge direction evaluated.
Revision 1101 - Directory Listing
Modified Wed Jun 9 09:26:27 2010 UTC (6 years, 3 months ago) by jmduarteg
Now serializable (to be able to write them to file)
Revision 1100 - Directory Listing
Modified Tue Jun 8 17:30:26 2010 UTC (6 years, 3 months ago) by cvehlow
Implementation of class that performs clustering on the nbhStringNodes.
Revision 1099 - Directory Listing
Modified Tue Jun 8 09:56:17 2010 UTC (6 years, 3 months ago) by jmduarteg
Some fixes to the help string
Revision 1098 - Directory Listing
Modified Tue Jun 8 09:10:32 2010 UTC (6 years, 3 months ago) by jmduarteg
Fixed bug: was nullpointing at retrieveUniprotKBData because of a single uniprot id can have multiple blast hits and was using the uni ids as unique identifiers => the lookup map was failing. Now the lookup map is from uniIds to lists of homologs(hits)
Revision 1097 - Directory Listing
Modified Mon Jun 7 10:17:58 2010 UTC (6 years, 3 months ago) by jmduarteg
Now explicitely specifying output dnd file in tcoffee so it can be removed by the calling program.
Revision 1096 - Directory Listing
Modified Fri Jun 4 14:48:12 2010 UTC (6 years, 3 months ago) by jmduarteg
Minor doc fix
Revision 1095 - Directory Listing
Modified Wed Jun 2 15:06:46 2010 UTC (6 years, 3 months ago) by jmduarteg
Fixed bug: was nullpointing when the letter encountered in counting the column was unknown.
Revision 1094 - Directory Listing
Modified Wed Jun 2 13:19:21 2010 UTC (6 years, 3 months ago) by jmduarteg
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Revision 1093 - Directory Listing
Modified Wed Jun 2 08:34:04 2010 UTC (6 years, 3 months ago) by hstehr
checking in some of Michael's example files
Revision 1092 - Directory Listing
Modified Wed Jun 2 08:07:50 2010 UTC (6 years, 3 months ago) by lappe
Contact Map for server prediction directory evaluation added
Revision 1091 - Directory Listing
Modified Tue Jun 1 15:56:12 2010 UTC (6 years, 3 months ago) by cvehlow
Class OptimalSingleEnv for scoring of different substrings.
Revision 1090 - Directory Listing
Modified Tue Jun 1 12:16:52 2010 UTC (6 years, 3 months ago) by matt4077
little contact map example done
Revision 1089 - Directory Listing
Modified Tue Jun 1 11:14:05 2010 UTC (6 years, 3 months ago) by matt4077
added a package for example scripts using the library
Revision 1088 - Directory Listing
Modified Tue Jun 1 09:14:19 2010 UTC (6 years, 3 months ago) by cvehlow
max number of traces
Revision 1087 - Directory Listing
Modified Mon May 31 15:41:25 2010 UTC (6 years, 3 months ago) by jmduarteg
Improved the getRimAndCore method
Revision 1086 - Directory Listing
Modified Mon May 31 15:41:16 2010 UTC (6 years, 3 months ago) by cvehlow
Extract maximum number of traces!
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (6 years, 3 months ago) by jmduarteg
Some new methods
Revision 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (6 years, 3 months ago) by matt4077
renamed  conflicting ContactMap class.
Revision 1083 - Directory Listing
Modified Mon May 31 13:31:23 2010 UTC (6 years, 3 months ago) by hstehr
fixed bug in printf statement because pdbResSer has changed from int to String
Revision 1082 - Directory Listing
Modified Fri May 28 15:00:31 2010 UTC (6 years, 3 months ago) by jmduarteg
Fixed bug in getRimAndCore, now we do end the loop correctly at the hard cutoff value.
Revision 1081 - Directory Listing
Modified Fri May 28 14:51:46 2010 UTC (6 years, 3 months ago) by jmduarteg
Fixed bug with '-' embl cds identifiers.
Revision 1080 - Directory Listing
Modified Fri May 28 12:55:41 2010 UTC (6 years, 3 months ago) by jmduarteg
Undoing some stuff commited by error in last commit
Revision 1079 - Directory Listing
Modified Fri May 28 12:52:31 2010 UTC (6 years, 3 months ago) by jmduarteg
Improved the rim and core calculation. The pdb res serial is now a String in PisaResidue (because of insertion codes)
Revision 1078 - Directory Listing
Modified Thu May 27 10:33:41 2010 UTC (6 years, 4 months ago) by jmduarteg
Now parsing the seq_num residue number.
Revision 1077 - Directory Listing
Modified Thu May 27 09:51:50 2010 UTC (6 years, 4 months ago) by jmduarteg
Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes
Revision 1076 - Directory Listing
Modified Wed May 26 10:10:06 2010 UTC (6 years, 4 months ago) by jmduarteg
Now using UK mirror
Revision 1075 - Directory Listing
Modified Fri May 21 17:33:34 2010 UTC (6 years, 4 months ago) by jmduarteg
PISA connection and xml interfaces description parser
Revision 1074 - Directory Listing
Modified Fri May 21 10:02:24 2010 UTC (6 years, 4 months ago) by jmduarteg
Implemented profile counting and entropy calculation for alignment.
Revision 1073 - Directory Listing
Modified Thu May 20 15:21:10 2010 UTC (6 years, 4 months ago) by jmduarteg
Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()
Revision 1072 - Directory Listing
Modified Thu May 20 13:59:25 2010 UTC (6 years, 4 months ago) by jmduarteg
Implemented methods to run a tcoffee alignment. Now also retrieving uniprot sequences via the uniprot api.
Revision 1071 - Directory Listing
Modified Thu May 20 12:46:11 2010 UTC (6 years, 4 months ago) by cvehlow
Histogram for different sstypes --> number of nodes per trace.
Revision 1070 - Directory Listing
Modified Wed May 19 16:20:42 2010 UTC (6 years, 4 months ago) by jmduarteg
Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
Revision 1069 - Directory Listing
Modified Tue May 18 14:53:34 2010 UTC (6 years, 4 months ago) by jmduarteg
New methods to retrieve uniprot data and embl cds for a single homolog
Revision 1068 - Directory Listing
Modified Tue May 18 09:31:39 2010 UTC (6 years, 4 months ago) by cvehlow
HandOverThetaPhiRanges
Revision 1067 - Directory Listing
Modified Wed May 12 16:36:24 2010 UTC (6 years, 4 months ago) by hstehr
fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()
Revision 1066 - Directory Listing
Modified Wed May 12 12:00:11 2010 UTC (6 years, 4 months ago) by hstehr
new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
Revision 1065 - Directory Listing
Modified Tue May 11 15:14:45 2010 UTC (6 years, 4 months ago) by hstehr
reverting changes to .project and .classpath which were accidentally committed
Revision 1064 - Directory Listing
Modified Tue May 11 14:57:20 2010 UTC (6 years, 4 months ago) by hstehr
fixed a bug in GraphAverager.getGraphWithTopContacts() which caused a null pointer exception in jung.SparseGraph.addEdge(), this may even be a bug in jung
Revision 1063 - Directory Listing
Modified Mon May 10 10:23:03 2010 UTC (6 years, 4 months ago) by stehr
Creating constructor which was apparently lost during some previous refactoring but which was needed by class cccp.testGraphAverager
Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (6 years, 4 months ago) by stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision 1061 - Directory Listing
Modified Fri May 7 14:13:07 2010 UTC (6 years, 4 months ago) by hstehr
Adding the possibility to set the timeout for a JPredConnection. Next step is to add this as a user variable to CMView
Revision 1060 - Directory Listing
Modified Fri May 7 11:53:13 2010 UTC (6 years, 4 months ago) by hstehr
New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
Revision 1059 - Directory Listing
Modified Wed May 5 14:28:19 2010 UTC (6 years, 4 months ago) by jmduarteg
Fixed java doc
Revision 1058 - Directory Listing
Modified Mon May 3 16:57:21 2010 UTC (6 years, 4 months ago) by cvehlow
Load from zip-file!
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (6 years, 4 months ago) by matt4077
add psi/phi constraints from secondary structure to tinker reconstructions
Revision 1056 - Directory Listing
Modified Fri Apr 30 11:31:45 2010 UTC (6 years, 4 months ago) by stehr
New example implementation of ResidueContactScoringFunction
Revision 1055 - Directory Listing
Modified Wed Apr 28 15:08:53 2010 UTC (6 years, 4 months ago) by jmduarteg
Removed code left over from debugging.
Revision 1054 - Directory Listing
Modified Wed Apr 28 13:37:00 2010 UTC (6 years, 4 months ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1053 - Directory Listing
Modified Wed Apr 28 10:58:18 2010 UTC (6 years, 4 months ago) by jmduarteg
New script to maintain a local copy of blastable uniprot sequences db.
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (6 years, 5 months ago) by hstehr
Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph
Revision 1051 - Directory Listing
Modified Tue Apr 27 15:34:38 2010 UTC (6 years, 5 months ago) by jmduarteg
Minor fix to java docs
Revision 1050 - Directory Listing
Modified Tue Apr 27 12:39:52 2010 UTC (6 years, 5 months ago) by cvehlow
Load precalc sphoxel data if possible.
Revision 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (6 years, 5 months ago) by hstehr
removing @Override annotations which were causing compilation errors for me
Revision 1048 - Directory Listing
Modified Tue Apr 27 08:24:18 2010 UTC (6 years, 5 months ago) by jmduarteg
New classes UniprotHomolog and UniprotHomologList to contain a set of homologs of a given sequence, including the blast hit data, embl cds coding sequences etc.
Revision 1047 - Directory Listing
Modified Mon Apr 26 16:13:36 2010 UTC (6 years, 5 months ago) by jmduarteg
SecondaryStructure now implements Iterable after refactoring of getIterator
Revision 1046 - Directory Listing
Modified Mon Apr 26 15:26:59 2010 UTC (6 years, 5 months ago) by hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision 1045 - Directory Listing
Modified Mon Apr 26 12:55:28 2010 UTC (6 years, 5 months ago) by jmduarteg
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
Revision 1044 - Directory Listing
Modified Mon Apr 26 10:37:14 2010 UTC (6 years, 5 months ago) by hstehr
New interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.
Revision 1043 - Directory Listing
Modified Thu Apr 22 12:21:37 2010 UTC (6 years, 5 months ago) by jmduarteg
Fixed blast parsing bug: was parsing the Hit_def tag instead of the Hit_id tag for the subject id. When formatdb is run with option "-o T" then indices are properly generated and Hit_id contains the correct tag.
Revision 1042 - Directory Listing
Modified Wed Apr 21 16:11:08 2010 UTC (6 years, 5 months ago) by jmduarteg
New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
Revision 1041 - Directory Listing
Modified Wed Apr 21 13:24:18 2010 UTC (6 years, 5 months ago) by hstehr
New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.
Revision 1040 - Directory Listing
Modified Wed Apr 21 10:44:19 2010 UTC (6 years, 5 months ago) by jmduarteg
New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
Revision 1039 - Directory Listing
Modified Tue Apr 20 10:19:32 2010 UTC (6 years, 5 months ago) by cvehlow
New class gmbp for handling (saving) angle (theta-phi) ranges for certain contacts (iNum-jNum combinations);
Revision 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (6 years, 5 months ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (6 years, 5 months ago) by matt4077
adding phi/psi constraints to edges
Revision 1036 - Directory Listing
Modified Mon Apr 19 14:27:11 2010 UTC (6 years, 5 months ago) by jmduarteg
Changed return type of addFeature to boolean to match the java Collection interface
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (6 years, 5 months ago) by jmduarteg
Extracted the EC data parsing code to its own connection class.
Revision 1034 - Directory Listing
Modified Mon Apr 19 12:42:21 2010 UTC (6 years, 5 months ago) by jmduarteg
Extracted Scop parsing code to its own connection class.
Revision 1033 - Directory Listing
Modified Mon Apr 19 12:26:22 2010 UTC (6 years, 5 months ago) by jmduarteg
Extracted the CSA parsing code to its own connection class.
Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (6 years, 5 months ago) by jmduarteg
Extracted the calc-vol and calc-surf runner code to its own Runner class.
Revision 1031 - Directory Listing
Modified Mon Apr 19 10:00:34 2010 UTC (6 years, 5 months ago) by jmduarteg
Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon. Oligomeric state should be implemented as some kind of feature.
Revision 1030 - Directory Listing
Modified Mon Apr 19 09:39:07 2010 UTC (6 years, 5 months ago) by jmduarteg
Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.
Revision 1029 - Directory Listing
Modified Mon Apr 19 09:01:51 2010 UTC (6 years, 5 months ago) by jmduarteg
Fixed hard-coded resources paths broken since major restructuring of project.
Revision 1028 - Directory Listing
Modified Fri Apr 16 13:21:40 2010 UTC (6 years, 5 months ago) by cvehlow
Faster SQL queries
Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (6 years, 5 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1026 - Directory Listing
Modified Thu Apr 15 15:28:29 2010 UTC (6 years, 5 months ago) by cvehlow
changes
Revision 1025 - Directory Listing
Modified Thu Apr 15 09:28:23 2010 UTC (6 years, 5 months ago) by jmduarteg
Remove hard-coded MySQL parameters. Please use always .my.cnf files for MySQL parameters!
Revision 1024 - Directory Listing
Modified Wed Apr 14 15:59:13 2010 UTC (6 years, 5 months ago) by cvehlow

Revision 1023 - Directory Listing
Modified Tue Apr 13 17:14:22 2010 UTC (6 years, 5 months ago) by cvehlow
FloatPairSet first commit
Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (6 years, 5 months ago) by stehr
new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)
Revision 1021 - Directory Listing
Modified Fri Apr 9 15:30:15 2010 UTC (6 years, 5 months ago) by hstehr
adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()
Revision 1020 - Directory Listing
Modified Fri Apr 9 15:22:20 2010 UTC (6 years, 5 months ago) by cvehlow
Classes for sphoxel and nbhstraces handling. csv handling
Revision 1019 - Directory Listing
Modified Fri Apr 9 13:16:07 2010 UTC (6 years, 5 months ago) by cvehlow
First version of class for sphoxel computation.
Revision 1018 - Directory Listing
Modified Fri Apr 9 10:40:29 2010 UTC (6 years, 5 months ago) by hstehr
removing a warning in owl.embed.contactmaps.Demes
Revision 1017 - Directory Listing
Modified Fri Apr 9 09:42:32 2010 UTC (6 years, 5 months ago) by jmduarteg
New methods for random sampling a RIGraph and randomly adding noise. The code was already somewhere in the embed package but here seems more convenient.
Revision 1016 - Directory Listing
Modified Fri Apr 9 09:18:35 2010 UTC (6 years, 5 months ago) by jmduarteg
Added a supresswarnings tag (it's simply unused code)
Revision 1015 - Directory Listing
Modified Fri Apr 9 09:16:04 2010 UTC (6 years, 5 months ago) by jmduarteg
Fixed import (was a compile error)
Revision 1014 - Directory Listing
Modified Thu Apr 8 16:34:26 2010 UTC (6 years, 5 months ago) by gmueller
cone peeling algorithm as implemented in sathyas classes, does not contain any public constructors, must use public statics
Revision 1013 - Directory Listing
Modified Thu Apr 1 10:49:30 2010 UTC (6 years, 5 months ago) by matt4077
resolving conflicts
Revision 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (6 years, 5 months ago) by hstehr
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
Revision 1011 - Directory Listing
Modified Wed Mar 31 20:21:01 2010 UTC (6 years, 5 months ago) by jmduarteg
Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 
Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (6 years, 5 months ago) by hstehr
refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (6 years, 5 months ago) by hstehr
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
Revision 1008 - Directory Listing
Modified Wed Mar 31 14:03:27 2010 UTC (6 years, 5 months ago) by hstehr
refactoring: adapting test packages to match new package structure
Revision 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (6 years, 5 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
Revision 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (6 years, 5 months ago) by hstehr
refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (6 years, 5 months ago) by hstehr
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 1004 - Directory Listing
Modified Wed Mar 31 11:59:33 2010 UTC (6 years, 5 months ago) by hstehr
starting refactoring: first creating packages owl and owl.core
Revision 1003 - Directory Listing
Modified Wed Mar 31 11:54:57 2010 UTC (6 years, 5 months ago) by hstehr
tagging OWL 1.2.0 in sync with CMView 1.2.0 before major refactoring
Revision 1002 - Directory Listing
Modified Tue Mar 30 11:22:07 2010 UTC (6 years, 5 months ago) by gmueller
latest version of gabriel (embed.contactmaps)
Revision 1001 - Directory Listing
Modified Tue Mar 30 11:09:04 2010 UTC (6 years, 5 months ago) by gmueller
latest version of gabriel
Revision 1000 - Directory Listing
Modified Mon Mar 29 10:20:38 2010 UTC (6 years, 5 months ago) by jmduarteg
Now DsspRunner is purely static (makes more sense)
Revision 999 - Directory Listing
Modified Mon Mar 29 10:06:42 2010 UTC (6 years, 5 months ago) by jmduarteg
Fixed the dsspRunner call (now it's static).
Revision 998 - Directory Listing
Modified Mon Mar 29 10:04:04 2010 UTC (6 years, 5 months ago) by jmduarteg
Minor refactoring and comment fixes
Revision 997 - Directory Listing
Modified Mon Mar 29 09:41:31 2010 UTC (6 years, 5 months ago) by lappe
Turns the RIGraph into a GMatrix 
public void convert2GMatrix( GMatrix A)
Revision 996 - Directory Listing
Modified Thu Mar 25 12:07:41 2010 UTC (6 years, 6 months ago) by matt4077
reconstruct: added an option -c to add phi/psi constraints from a psipred secondary structure prediction.  
Revision 995 - Directory Listing
Modified Thu Mar 25 11:48:27 2010 UTC (6 years, 6 months ago) by jmduarteg
Removed the executable property
Revision 994 - Directory Listing
Modified Wed Mar 24 15:09:16 2010 UTC (6 years, 6 months ago) by hstehr
new method AminoAcid.valuesInOrderOfHydrophobicity()
Revision 993 - Directory Listing
Modified Mon Mar 22 14:14:10 2010 UTC (6 years, 6 months ago) by jmduarteg
Removing the svn:executable properties from jars that didn't need it
Revision 992 - Directory Listing
Modified Mon Mar 22 14:10:34 2010 UTC (6 years, 6 months ago) by jmduarteg
Removed unneeded code
Revision 991 - Directory Listing
Modified Mon Mar 22 14:07:56 2010 UTC (6 years, 6 months ago) by jmduarteg
Setting the svn:executable property of make-owl.sh so that when it is checked out it will be set to executable.
Revision 990 - Directory Listing
Modified Mon Mar 22 12:00:54 2010 UTC (6 years, 6 months ago) by jmduarteg
Now classpath passed with -cp instead of using env variable. Hopefully this is more compatible with other platforms (i.e. maybe it will work on Macs)
Revision 989 - Directory Listing
Modified Fri Mar 19 09:00:00 2010 UTC (6 years, 6 months ago) by hstehr
adding a method RIGraph.getOrderedNeighbors(Node) because the default method getNeighbors(Node) returns the neighbours in non-deterministic order(!) which caused me lots of trouble
Revision 988 - Directory Listing
Modified Thu Mar 18 12:02:13 2010 UTC (6 years, 6 months ago) by jmduarteg
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.

Revision 987 - Directory Listing
Modified Thu Mar 18 11:08:58 2010 UTC (6 years, 6 months ago) by jmduarteg
New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class)
Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!)
Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.

Revision 986 - Directory Listing
Modified Wed Mar 17 11:45:59 2010 UTC (6 years, 6 months ago) by matt4077
fixing a bug where floats in CASP RR files are rendered with comma for those unfortunate people stuck on german computers. 
Revision 985 - Directory Listing
Modified Tue Mar 16 13:47:40 2010 UTC (6 years, 6 months ago) by hstehr
Adding new package owl.connections with connector classes to online databases and services. Starting with PhosphoSitePlusConnection for accessing a database of posttranslational modifications and PDomainsConnection for accessing a very useful webservice which calculates structural domains using a variety of methods including Scop, Cath, DomainParser, ProteinDomainParser and others.
Revision 984 - Directory Listing
Modified Tue Mar 16 13:24:35 2010 UTC (6 years, 6 months ago) by hstehr
Commiting an old change of some constant in PolyposeRunner. I forgot what this does but it must be good :)
Revision 983 - Directory Listing
Modified Tue Mar 16 13:22:26 2010 UTC (6 years, 6 months ago) by hstehr
adding some convenience methods to IntervalSet
Revision 982 - Directory Listing
Modified Tue Mar 16 13:01:01 2010 UTC (6 years, 6 months ago) by hstehr
Restoring deleted class Pair because it is needed by one of my programs. 
Revision 981 - Directory Listing
Modified Tue Mar 16 12:53:13 2010 UTC (6 years, 6 months ago) by hstehr
Introducing new StructuralDomainFeature for structural domains as defined by SCOP, CATH, DomainParser etc.
Revision 980 - Directory Listing
Modified Tue Feb 23 20:32:01 2010 UTC (6 years, 7 months ago) by duarte
Changed project name to owl
Revision 979 - Directory Listing
Modified Tue Feb 23 19:03:30 2010 UTC (6 years, 7 months ago) by duarte
Fixed some issues
Revision 978 - Directory Listing
Modified Tue Feb 23 18:57:24 2010 UTC (6 years, 7 months ago) by duarte
Moved all reconstruct scripts and config files to reconstruct directory. 
Modified scripts accordingly
Revision 977 - Directory Listing
Modified Tue Feb 23 17:41:08 2010 UTC (6 years, 7 months ago) by duarte
Better error message for no tinker paths set up
Revision 976 - Directory Listing
Modified Tue Feb 23 17:36:23 2010 UTC (6 years, 7 months ago) by duarte
Renamed script and fixed bug
Revision 975 - Directory Listing
Modified Tue Feb 23 17:30:54 2010 UTC (6 years, 7 months ago) by duarte
Moved scripts to scripts directory.
New scripts for packaging the reconstruct executable for distribution.
Revision 974 - Directory Listing
Modified Tue Feb 23 14:50:07 2010 UTC (6 years, 7 months ago) by duarte
Adding license files
Revision 973 - Directory Listing
Modified Tue Feb 23 14:32:00 2010 UTC (6 years, 7 months ago) by duarte
Moving the CASP project into OWL as the casp package.
Revision 972 - Directory Listing
Modified Tue Feb 23 12:13:13 2010 UTC (6 years, 7 months ago) by duarte
Adding back removal of temp files
Revision 971 - Directory Listing
Modified Tue Feb 23 12:10:43 2010 UTC (6 years, 7 months ago) by duarte
CLASSPATH not hard-coded any more. Now taking the jars list from svn.
Revision 970 - Directory Listing
Modified Tue Feb 23 11:47:05 2010 UTC (6 years, 7 months ago) by duarte
Now PDB data will be loaded from online PDB's ftp if no PDBASE_DB specified in config file
Revision 969 - Directory Listing
Modified Tue Feb 23 11:20:32 2010 UTC (6 years, 7 months ago) by duarte
Now configuration (tinker paths) is read from config file.
Revision 968 - Directory Listing
Modified Mon Feb 22 16:03:45 2010 UTC (6 years, 7 months ago) by duarte
Updated make-aglappe script (and renamed to make-owl).
Changed aglappe strings to OWL (following new name of library)
Revision 967 - Directory Listing
Modified Thu Feb 18 15:53:18 2010 UTC (6 years, 7 months ago) by duarte
Forgot to really add the libraries in the last commit!
Revision 966 - Directory Listing
Modified Thu Feb 18 15:51:56 2010 UTC (6 years, 7 months ago) by duarte
Updated jung jars to version 2.0.1 (finally the release version, not alpha or beta!)
Revision 965 - Directory Listing
Modified Thu Feb 18 15:25:10 2010 UTC (6 years, 7 months ago) by duarte
Fixed paths of tests (was missing the src directory since we moved everything under src)
Revision 964 - Directory Listing
Modified Tue Feb 16 12:01:40 2010 UTC (6 years, 7 months ago) by gmueller
new class for sparse double matrices
Revision 963 - Directory Listing
Modified Tue Feb 16 12:00:55 2010 UTC (6 years, 7 months ago) by gmueller
some new classes
Revision 962 - Directory Listing
Modified Tue Feb 16 11:51:18 2010 UTC (6 years, 7 months ago) by gmueller
minor changes, that now fit into the renewed version
Revision 961 - Directory Listing
Modified Mon Feb 15 11:55:40 2010 UTC (6 years, 7 months ago) by duarte
Now analyseHistone will output the coordinates of the side chains of ARGs (NH1 atom) and LYSs (NZ atom) instead of the CA atoms.
Some new methods in Pdb
Revision 960 - Directory Listing
Modified Fri Feb 12 15:34:09 2010 UTC (6 years, 7 months ago) by duarte
New executable class from my workspace.
Revision 959 - Directory Listing
Modified Fri Feb 12 15:25:33 2010 UTC (6 years, 7 months ago) by duarte
Moved IntervalTest class to test.tools package
Revision 958 - Directory Listing
Modified Fri Feb 12 15:22:36 2010 UTC (6 years, 7 months ago) by duarte
Moved Interval* and IntPair* classes to tools package
Revision 957 - Directory Listing
Modified Fri Feb 12 15:06:04 2010 UTC (6 years, 7 months ago) by duarte
Added some useful tools to the default package from my workspace. More clean up.
Revision 956 - Directory Listing
Modified Fri Feb 12 14:46:46 2010 UTC (6 years, 7 months ago) by duarte
Removed some obsolete classes.
Revision 955 - Directory Listing
Modified Tue Feb 9 10:44:24 2010 UTC (6 years, 7 months ago) by duarte
Now removed variable and put back code that shouldn't have been commented out
Revision 954 - Directory Listing
Modified Tue Feb 9 10:43:02 2010 UTC (6 years, 7 months ago) by duarte
Commented out some unused variables to get rid of warnings
Revision 953 - Directory Listing
Modified Mon Feb 8 15:36:45 2010 UTC (6 years, 7 months ago) by duarte
Refactoring of inconsistently named methods in RIGraph
Revision 952 - Directory Listing
Modified Fri Feb 5 16:41:47 2010 UTC (6 years, 7 months ago) by duarte
Added some new prediction measures for DecoyScoreSet: rank, delta rmsd, n% enrichment value
Extended the range of the distance bins.
Revision 951 - Directory Listing
Modified Fri Jan 29 16:12:34 2010 UTC (6 years, 7 months ago) by duarte
Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
Revision 950 - Directory Listing
Modified Fri Jan 29 11:57:38 2010 UTC (6 years, 7 months ago) by duarte
Major refactoring and clean-up.
Most important changes are some methods in Pdb class: get_graph->getRIGraph and dump2pdb->writeToPDBFile
Removed all specific FileFormatError exception classes, now using only the generic FileFormatError.
All tests passed.
Revision 949 - Directory Listing
Modified Thu Jan 28 16:11:34 2010 UTC (6 years, 7 months ago) by duarte
Tagging version 1.1.2 before major refactoring.
Revision 948 - Directory Listing
Modified Thu Jan 28 13:33:08 2010 UTC (6 years, 7 months ago) by duarte
New test for rmsd on intervals
Revision 947 - Directory Listing
Modified Thu Jan 28 11:39:27 2010 UTC (6 years, 7 months ago) by duarte
New rmsd method to calculate rmsd on residue intervals instead of whole chain.
Fixed bug: checkScop was throwing exception when it was called on a PdbfilePdb that didn't have a PDB code
Revision 946 - Directory Listing
Modified Wed Jan 27 17:06:12 2010 UTC (6 years, 7 months ago) by duarte
Now passing db explicitely instead of using the db from the connection.
Revision 945 - Directory Listing
Modified Wed Jan 27 16:49:49 2010 UTC (6 years, 7 months ago) by duarte
Added new scoring method: atom distance based scoring (scoring based on multiple distance bins, instead of just on contacts)
Revision 944 - Directory Listing
Modified Fri Jan 22 17:47:21 2010 UTC (6 years, 8 months ago) by duarte
Fixed bug (hopefully, didn't test!) introduced in last revision. Wasn't initialising properly the maps
Revision 943 - Directory Listing
Modified Fri Jan 22 16:11:43 2010 UTC (6 years, 8 months ago) by winkelma
contact map rainbows
Revision 942 - Directory Listing
Modified Fri Jan 22 14:03:44 2010 UTC (6 years, 8 months ago) by duarte
Moved up to Scorer initResMap and initAtomMap
Revision 941 - Directory Listing
Modified Fri Jan 15 17:48:27 2010 UTC (6 years, 8 months ago) by winkelma
delta rank
Revision 940 - Directory Listing
Modified Thu Jan 7 19:01:26 2010 UTC (6 years, 8 months ago) by winkelma
Delta Rank
Revision 939 - Directory Listing
Modified Thu Jan 7 14:35:48 2010 UTC (6 years, 8 months ago) by duarte
Fixed bug with notifier (only used from CMView). Now if null it will be skipped.
Revision 938 - Directory Listing
Modified Tue Jan 5 15:47:39 2010 UTC (6 years, 8 months ago) by stehr
fixed bugs in getDescription()
Revision 937 - Directory Listing
Modified Thu Dec 17 14:42:16 2009 UTC (6 years, 9 months ago) by gmueller

Revision 936 - Directory Listing
Modified Thu Dec 17 13:45:02 2009 UTC (6 years, 9 months ago) by gmueller
fields changed to private
Revision 935 - Directory Listing
Modified Thu Dec 17 13:44:20 2009 UTC (6 years, 9 months ago) by gmueller
fields changed to private
Revision 934 - Directory Listing
Modified Thu Dec 17 13:41:36 2009 UTC (6 years, 9 months ago) by gmueller
all fields to private
Revision 933 - Directory Listing
Modified Thu Dec 17 13:35:48 2009 UTC (6 years, 9 months ago) by gmueller
some methods modifiers were changed from protected to public, since classes of the sub package rely on those
Revision 932 - Directory Listing
Modified Thu Dec 17 13:34:07 2009 UTC (6 years, 9 months ago) by gmueller
all classes for evolution, correlation function, neighborhood string converter etc.
Revision 931 - Directory Listing
Modified Thu Dec 17 12:18:57 2009 UTC (6 years, 9 months ago) by gmueller
full package, with all classes

Revision 930 - Directory Listing
Modified Tue Dec 8 14:39:55 2009 UTC (6 years, 9 months ago) by gmueller
minor changes
Revision 929 - Directory Listing
Modified Tue Dec 8 14:38:46 2009 UTC (6 years, 9 months ago) by gmueller
final version, might still contain bugs, but seems consistent so far
Revision 928 - Directory Listing
Modified Fri Nov 27 15:58:42 2009 UTC (6 years, 9 months ago) by gmueller
the older version still had a bug in the setNbhStringMaps(String,String) method
Revision 927 - Directory Listing
Modified Fri Nov 27 15:38:31 2009 UTC (6 years, 9 months ago) by gmueller
a class that gets neighborhood Strings and queries them
Revision 926 - Directory Listing
Modified Tue Nov 17 13:38:29 2009 UTC (6 years, 10 months ago) by gmueller
helper class
Revision 925 - Directory Listing
Modified Mon Oct 26 14:32:37 2009 UTC (6 years, 11 months ago) by winkelma
merged tinker changes into trunk
Revision 924 - Directory Listing
Modified Mon Oct 26 14:20:16 2009 UTC (6 years, 11 months ago) by winkelma
merged trunk into branch
Revision 923 - Directory Listing
Modified Mon Oct 26 14:18:25 2009 UTC (6 years, 11 months ago) by winkelma
DALI alignment correction
Revision 922 - Directory Listing
Modified Mon Oct 26 14:08:42 2009 UTC (6 years, 11 months ago) by winkelma
Tinker
Revision 921 - Directory Listing
Modified Mon Oct 26 14:08:19 2009 UTC (6 years, 11 months ago) by winkelma
Tinker
Revision 920 - Directory Listing
Modified Thu Oct 22 17:07:34 2009 UTC (6 years, 11 months ago) by winkelma
Tinker Runner Details
Revision 919 - Directory Listing
Modified Tue Oct 20 16:55:17 2009 UTC (6 years, 11 months ago) by duarte
Fixed bug: was not handling correctly sequences with 'X' in reconstruction
Fixed bug: Pdb.getPhi/Psi were failing because hasCoordinates(int,String) was NullPointing for unobserved residues. 
Added test case for getAllPhiPsi
Revision 918 - Directory Listing
Modified Tue Oct 20 15:55:18 2009 UTC (6 years, 11 months ago) by winkelma
more Tinker 
Revision 917 - Directory Listing
Modified Tue Oct 20 15:53:30 2009 UTC (6 years, 11 months ago) by stehr
bugfix for last checkin (null pointer exception)
Revision 916 - Directory Listing
Modified Tue Oct 20 13:13:19 2009 UTC (6 years, 11 months ago) by stehr
New convenience methods in MySQLConnection for simple retrieval of String, Integer and Double arrays from an SQL query. Some documentation clean-up.
Revision 915 - Directory Listing
Modified Tue Oct 20 12:38:56 2009 UTC (6 years, 11 months ago) by stehr
fixed an interesting bug where a recursive function call would lead to a stack overflow exception
Revision 914 - Directory Listing
Modified Tue Oct 20 12:37:40 2009 UTC (6 years, 11 months ago) by stehr
updated constant LATEST_VERSION to CSA version 2.2.11 (of 7th August 2009)
Revision 913 - Directory Listing
Modified Mon Oct 19 16:27:29 2009 UTC (6 years, 11 months ago) by winkelma
Tinker integration
Revision 912 - Directory Listing
Modified Fri Oct 16 14:51:49 2009 UTC (6 years, 11 months ago) by winkelma
TINKER
Revision 911 - Directory Listing
Modified Thu Oct 15 20:28:24 2009 UTC (6 years, 11 months ago) by winkelma
Branch for tinker integration
Revision 910 - Directory Listing
Modified Wed Oct 14 17:10:41 2009 UTC (6 years, 11 months ago) by winkelma
tolerate unobserved residues in DALI alignments
Revision 909 - Directory Listing
Modified Tue Oct 13 10:27:15 2009 UTC (6 years, 11 months ago) by stehr
Added DALI Alignment option
Revision 908 - Directory Listing
Modified Wed Sep 30 13:23:13 2009 UTC (6 years, 11 months ago) by stehr
new feature type PhosphoSitePlusFeature (for post-translational modifications)
Revision 907 - Directory Listing
Modified Wed Sep 30 08:54:22 2009 UTC (6 years, 11 months ago) by stehr
new method getDoubleFromDb()
Revision 906 - Directory Listing
Modified Tue Sep 22 13:25:42 2009 UTC (7 years ago) by duarte
New classes for triplet scoring.
Revision 905 - Directory Listing
Modified Sun Sep 6 10:43:03 2009 UTC (7 years ago) by duarte
Now printing some more rmsd stats (numbers of structs below certain rmsd cutoffs).

Revision 904 - Directory Listing
Modified Thu Sep 3 15:34:21 2009 UTC (7 years ago) by duarte
Moved all decoy scoring stuff to its own package.
Split CombinedScorer into two classes AtomCombinedScorer and ResCombinedScorer. Made combined scorer more efficient: now loading only once the graphs.
Revision 903 - Directory Listing
Modified Thu Sep 3 12:10:25 2009 UTC (7 years ago) by duarte
Now writing rmsd ranges to stats files
Revision 902 - Directory Listing
Modified Thu Sep 3 10:28:43 2009 UTC (7 years ago) by duarte
New CombinedScorer class to combined type+count scoring. Now scoreDecoys doesn't take anymore a minSeqSep, it will be taken instead from the scoring matrices meta data.
Revision 901 - Directory Listing
Modified Tue Sep 1 17:02:30 2009 UTC (7 years ago) by duarte
Added method to get the scoring type
Revision 900 - Directory Listing
Modified Tue Sep 1 12:31:30 2009 UTC (7 years ago) by duarte
One more field in DecoyScoreSet: the decoy group to which the decoy set belongs. Writing it to db too.
Revision 899 - Directory Listing
Modified Tue Sep 1 12:30:22 2009 UTC (7 years ago) by duarte
Fixed bug: parse() was not closing file when throwing an exception. The bug surfaced when parsing a dir with a lot of decoys that were somehow malformed PDB files, sometimes it would throw a FileNotFoundException with message "Too many open files".
Revision 898 - Directory Listing
Modified Tue Sep 1 10:11:20 2009 UTC (7 years ago) by duarte
Now writing more complete info to score files. New feature: can also write decoy score results to database.
Revision 897 - Directory Listing
Modified Mon Aug 31 08:53:06 2009 UTC (7 years ago) by duarte
Increased number of neighbor-count bins. For higher cutoffs the number of bins go up dramatically.
Revision 896 - Directory Listing
Modified Sun Aug 30 16:36:04 2009 UTC (7 years ago) by duarte
New class DecoyScoreSetGroup to represent a set of DecoySets. Now scoreDecoys much clearer.
Revision 895 - Directory Listing
Modified Fri Aug 28 10:57:23 2009 UTC (7 years ago) by duarte
Got rid of redundant class DecoySetStats, its members were all just properties of DecoyScoreSet. Modified accordingly scoreDecoys.
Revision 894 - Directory Listing
Modified Fri Aug 28 10:01:01 2009 UTC (7 years ago) by duarte
New classes to score decoys based on contact counts (residue or atom contacts). New superclass for all scorer classes Scorer. 
Revision 893 - Directory Listing
Modified Wed Aug 26 14:45:39 2009 UTC (7 years, 1 month ago) by duarte
New executable scoreDecoys to score sets of decoy sets. 
Revision 892 - Directory Listing
Modified Wed Aug 26 13:06:03 2009 UTC (7 years, 1 month ago) by duarte
Added isAllAtom to Pdb and getNumHeavyAtoms to Pdb and Residue. Fixed some docs that were still not properly clarifying about hydrogens.
Added complete main methods to AtomTypeScorer and ResTypeScorer with command line options and defaults.
Revision 891 - Directory Listing
Modified Tue Aug 25 14:38:45 2009 UTC (7 years, 1 month ago) by duarte
New classes for scoring protein structures based on residue/atom type empirical potentials.
Revision 890 - Directory Listing
Modified Tue Aug 25 09:31:46 2009 UTC (7 years, 1 month ago) by duarte
Bug fixes in pdb file parser. Was throwing string out of bounds exception with some pdb files.
Revision 889 - Directory Listing
Modified Tue Aug 25 09:29:33 2009 UTC (7 years, 1 month ago) by duarte
New spearman method
Revision 888 - Directory Listing
Modified Thu Aug 20 10:30:16 2009 UTC (7 years, 1 month ago) by stehr
New methods for mean and (sample-) standard deviation
Revision 887 - Directory Listing
Modified Mon Aug 17 16:18:14 2009 UTC (7 years, 1 month ago) by stehr
rewrote method getPerAtomDistances such that atom serials do not need to match between the two structures (matching corresponding atoms based in resser)
Revision 886 - Directory Listing
Modified Fri Aug 14 10:47:15 2009 UTC (7 years, 1 month ago) by stehr
New executable writePerAtomDistancesToBFactor (see doc for details), new method Pdb.getPerAtomDistances(Pdb referencePdb), made Atom.DEFAULT_B_FACTOR public.
Revision 885 - Directory Listing
Modified Fri Aug 14 10:37:31 2009 UTC (7 years, 1 month ago) by duarte
Major change: now hydrogens are read in Pdb and subclasses
New getChirality method in Residue.
Added some more unit tests.
Revision 884 - Directory Listing
Modified Tue Aug 11 16:01:00 2009 UTC (7 years, 1 month ago) by duarte
Major commit: 
- change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors
- added many tests and test files for Pdb (and merged some already existing tests from the default package)
- removed obsolete classes related to msd
- bug fix: PdbfilePdb now properly reads files with alt codes
- all tests passed
Revision 883 - Directory Listing
Modified Tue Aug 11 14:37:16 2009 UTC (7 years, 1 month ago) by stehr
some cosmetic changes
Revision 882 - Directory Listing
Modified Tue Aug 11 13:10:08 2009 UTC (7 years, 1 month ago) by stehr
updated version to 1.2.0 (forgot to change version number in last tag)
Revision 881 - Directory Listing
Modified Tue Aug 11 12:49:20 2009 UTC (7 years, 1 month ago) by duarte
Tagging 1.1.1 before major changes
Revision 880 - Directory Listing
Modified Fri Aug 7 13:47:15 2009 UTC (7 years, 1 month ago) by stehr
deleting obsolete package proteinstructure.features
Revision 879 - Directory Listing
Modified Fri Aug 7 13:45:06 2009 UTC (7 years, 1 month ago) by stehr
moving all classes in proteinstructure.features to features
Revision 878 - Directory Listing
Modified Fri Aug 7 13:41:45 2009 UTC (7 years, 1 month ago) by stehr
preparing to move package 'proteinstructure.features' to 'features'
Revision 877 - Directory Listing
Modified Fri Aug 7 13:39:18 2009 UTC (7 years, 1 month ago) by stehr
Testing package-info.java for adding javadoc comment at the package level
Revision 876 - Directory Listing
Modified Fri Aug 7 13:35:42 2009 UTC (7 years, 1 month ago) by stehr
New methods for writing sequence in Fasta format
Revision 875 - Directory Listing
Modified Fri Aug 7 13:33:42 2009 UTC (7 years, 1 month ago) by stehr
new method getUniprotTypeName()
Revision 874 - Directory Listing
Modified Fri Aug 7 13:32:06 2009 UTC (7 years, 1 month ago) by stehr
updated static convenience methods for loading Pdb objects
Revision 873 - Directory Listing
Modified Fri Aug 7 13:30:09 2009 UTC (7 years, 1 month ago) by stehr
adding main method for testing
Revision 872 - Directory Listing
Modified Fri Aug 7 13:26:20 2009 UTC (7 years, 1 month ago) by stehr
adding compareTo method to compare two IntervalSets
Revision 871 - Directory Listing
Modified Wed Aug 5 12:29:50 2009 UTC (7 years, 1 month ago) by stehr
New and updates feature types (UniprotFeature, PrositeFeature, CsaFeature)
Revision 870 - Directory Listing
Modified Wed Aug 5 12:28:42 2009 UTC (7 years, 1 month ago) by stehr
New classes for scanning Prosite Database
Revision 869 - Directory Listing
Modified Mon Aug 3 14:18:02 2009 UTC (7 years, 1 month ago) by stehr
HasFeatures.addFeature() now throws OverlappingFeatureException and new InvalidFeatureCooordinatesException
Revision 868 - Directory Listing
Modified Mon Aug 3 14:11:43 2009 UTC (7 years, 1 month ago) by stehr
New package proteinstructure.features with basic interfaces and classes for a general feature mechanism which could eventuelly replace classes like Scop, ScopRegion, ECRegion, CatalyticSite, CatalyticSiteSet and the corresponding variables in the Pdb class.
Revision 867 - Directory Listing
Modified Tue Jul 28 17:28:21 2009 UTC (7 years, 1 month ago) by duarte
New class Atom. Not doing anything yet. Now only need it so that Residue class can compile.
Revision 866 - Directory Listing
Modified Tue Jul 21 17:09:31 2009 UTC (7 years, 2 months ago) by duarte
Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
Revision 865 - Directory Listing
Modified Tue Jul 21 15:45:07 2009 UTC (7 years, 2 months ago) by duarte
Minor changes: added comments, docs, reorganized
Revision 864 - Directory Listing
Modified Tue Jul 21 10:44:34 2009 UTC (7 years, 2 months ago) by duarte
Extracted constants. Written a basic test for consurf parsing.
Revision 863 - Directory Listing
Modified Mon Jul 20 10:21:59 2009 UTC (7 years, 2 months ago) by duarte
New check in PdbfilePdb parser. New test for pdb file parsing in PdbParsersTest.
Revision 862 - Directory Listing
Modified Thu Jul 16 08:42:00 2009 UTC (7 years, 2 months ago) by duarte
Adapted PdbasePdb and CiffilePdb to new mmCIF format (introduced in new remediated release in Feb 2009). Now the atom_sites_alt table is gone so we have to read alt locs from atom_site instead. All tests passed (PdbParsersTest)
Revision 861 - Directory Listing
Modified Fri Jun 5 09:13:01 2009 UTC (7 years, 3 months ago) by duarte
Fixed +1 issues
Revision 860 - Directory Listing
Modified Fri May 29 15:55:47 2009 UTC (7 years, 3 months ago) by gmueller
class to estimate the correlation function to a given error function, deals onlz with Population arrays
Revision 859 - Directory Listing
Modified Fri May 29 15:46:56 2009 UTC (7 years, 3 months ago) by duarte
Fixed docs, now removing some temp files that weren't been removed
Revision 858 - Directory Listing
Modified Fri May 29 15:44:06 2009 UTC (7 years, 3 months ago) by gmueller
new class to deal with arrays of Individuals class, provides methods to generate new arrays of Individuals
Revision 857 - Directory Listing
Modified Fri May 29 15:41:56 2009 UTC (7 years, 3 months ago) by gmueller
major bugs removed and documentation added, couple of method removed to new classes, i.g. Population class and CorrelationFunction class
Revision 856 - Directory Listing
Modified Thu Apr 30 15:21:32 2009 UTC (7 years, 4 months ago) by gmueller
fixed randomSets method
Revision 855 - Directory Listing
Modified Thu Apr 30 14:21:59 2009 UTC (7 years, 4 months ago) by gmueller
new class for some evolution
Revision 854 - Directory Listing
Modified Wed Apr 8 16:42:35 2009 UTC (7 years, 5 months ago) by duarte
New methods copy() and translate()
Revision 853 - Directory Listing
Modified Tue Apr 7 12:47:24 2009 UTC (7 years, 5 months ago) by gmueller
distance map and contact map error function
Revision 852 - Directory Listing
Modified Fri Apr 3 10:41:56 2009 UTC (7 years, 5 months ago) by duarte
Now aligning x-axis with reference residue ARG G42. Now theta values in [-pi,pi].
Revision 851 - Directory Listing
Modified Fri Apr 3 09:33:53 2009 UTC (7 years, 5 months ago) by duarte
Now Polymer can read also DNA. analyseHistone now uses DNA as well: axis calculated with DNA, outputting z/theta stats for phosphates of DNA.
Revision 850 - Directory Listing
Modified Wed Apr 1 13:20:37 2009 UTC (7 years, 5 months ago) by duarte
New classes to perform analysis of histone lateral surface.
Revision 849 - Directory Listing
Modified Thu Mar 19 09:30:44 2009 UTC (7 years, 6 months ago) by stehr
updated documentation
Revision 848 - Directory Listing
Modified Thu Mar 19 09:29:31 2009 UTC (7 years, 6 months ago) by stehr
New class PdbSet providing convenience methods to load sets of PDB objects from list files, directories, ...
Revision 847 - Directory Listing
Modified Thu Mar 19 09:21:19 2009 UTC (7 years, 6 months ago) by stehr
new executable for pairwise (global) sequence alignment
Revision 846 - Directory Listing
Modified Thu Mar 19 09:18:30 2009 UTC (7 years, 6 months ago) by stehr
Adding a symbol for a stop codon (*, STP)
Revision 845 - Directory Listing
Modified Mon Mar 16 13:26:35 2009 UTC (7 years, 6 months ago) by duarte
Move the scoring methods to their own class as statics. Did a bit of refactoring.
Revision 844 - Directory Listing
Modified Tue Mar 10 10:39:08 2009 UTC (7 years, 6 months ago) by duarte
New script to mirror a pdb
Revision 843 - Directory Listing
Modified Fri Mar 6 16:31:07 2009 UTC (7 years, 6 months ago) by duarte
One more command line argument: contact percent sampling
Revision 842 - Directory Listing
Modified Tue Feb 17 18:03:34 2009 UTC (7 years, 7 months ago) by duarte
New method to filter on minWeight
Revision 841 - Directory Listing
Modified Tue Feb 17 17:42:17 2009 UTC (7 years, 7 months ago) by duarte
Fixed bug: copy() was throwing NullPointer when the RIGraph had a null SecondaryStructure annotation.
Revision 840 - Directory Listing
Modified Tue Feb 17 16:07:29 2009 UTC (7 years, 7 months ago) by duarte
New method getMotifNoGaps

Revision 839 - Directory Listing
Modified Tue Feb 17 15:51:59 2009 UTC (7 years, 7 months ago) by stehr
added option to keep pymol script
Revision 838 - Directory Listing
Modified Mon Feb 16 16:47:58 2009 UTC (7 years, 7 months ago) by duarte
New class in tools: RegexFileFilter, a convenient FileFilter based on regex, amazingly java doesn't provide this!
Revision 837 - Directory Listing
Modified Thu Jan 29 14:34:10 2009 UTC (7 years, 7 months ago) by duarte
Changed the value of the unobserved residue constant from "?" to "X". This is to fix CMView that had a lot of problems with it.
Revision 836 - Directory Listing
Modified Thu Jan 29 13:20:29 2009 UTC (7 years, 7 months ago) by duarte
Fixed bug (an old one!): the atomser2coord and atomser2resser maps contained also hydrogen atoms whilst the resset_atom2atomserial map contained only non-H atoms. Now all contain only non-H. The "bug" only surfaced after the rewrite of the Pdb.writeAtoms method: writing the atom lines would give a NullPointer when encountering a Hydrogen (if the read pdb entry contained Hyrdrogens).
Revision 835 - Directory Listing
Modified Mon Jan 26 13:38:34 2009 UTC (7 years, 7 months ago) by duarte
Changed scoring: from sum(upi-ui)2 to sum of max(0,upi-ui).
New methods to write subsets to files in table (tab delimited) format.
Now main() writes out all scores/subsets to two files instead of only outputting best, worse and ensemble of bests.
Moved ScoreSet to its own file, new static methods to read subsets from db.
Revision 834 - Directory Listing
Modified Sat Jan 24 10:20:39 2009 UTC (7 years, 8 months ago) by duarte
Now using file name as id for reports when reconstructing from cm files.
Revision 833 - Directory Listing
Modified Wed Jan 21 10:24:20 2009 UTC (7 years, 8 months ago) by duarte
New method to get an ensemble RIG from a group of best scoring sets.
Revision 832 - Directory Listing
Modified Tue Jan 20 12:01:34 2009 UTC (7 years, 8 months ago) by duarte
Changed the scoring so that is an error function: now it is the average sum square upper bounds deviation from the contact map. A perfect fit to the contact maps is err=0.
Cleaned up, refactored and documented.
Revision 831 - Directory Listing
Modified Mon Jan 19 17:09:04 2009 UTC (7 years, 8 months ago) by duarte
New experimental class Distiller
Revision 830 - Directory Listing
Modified Mon Jan 19 10:04:43 2009 UTC (7 years, 8 months ago) by stehr
now outputting a png image highlighting structure center, catalytic residues and mutated residues
Revision 829 - Directory Listing
Modified Mon Jan 19 10:00:38 2009 UTC (7 years, 8 months ago) by stehr
updated to latest CSA version, added toString() methods
Revision 828 - Directory Listing
Modified Mon Jan 19 09:55:42 2009 UTC (7 years, 8 months ago) by stehr
New static methods for conveniently loading PDB objects without needing to deal with exceptions (loadStructureOrExit, loadStructureOrNull)
Revision 827 - Directory Listing
Modified Mon Jan 19 09:47:19 2009 UTC (7 years, 8 months ago) by stehr
New class GeometryTools for simple geometric operations (currently implemented: torsion angles)
Revision 826 - Directory Listing
Modified Fri Jan 16 18:26:07 2009 UTC (7 years, 8 months ago) by duarte
Now printing statistics for both lower and upper violations.
Revision 825 - Directory Listing
Modified Fri Jan 16 12:03:14 2009 UTC (7 years, 8 months ago) by duarte
Fixed bug: this time really fixed bug from last revision. Now references of the bounds arrays are properly handled (hopefully!). Tests seem correct: now the output models when metrizing seem not to be correlated anymore
Revision 824 - Directory Listing
Modified Thu Jan 15 18:19:27 2009 UTC (7 years, 8 months ago) by duarte
Fixed bug: was reusing the same bounds after every metrization in reconstruct(), now restarting from the initial bounds for each metrization.
In metrize() final sampled matrix is now always reinitialising seed.

Revision 823 - Directory Listing
Modified Thu Jan 15 16:09:59 2009 UTC (7 years, 8 months ago) by duarte
Now printing restrains viols and bounds viols.
Revision 822 - Directory Listing
Modified Wed Jan 14 16:08:19 2009 UTC (7 years, 8 months ago) by duarte
Now Reconstructer can also take RIGraphs with "unobserved" residues (i.e. with missing nodes).
Model pdb files that Reconstructer creates now contain strictly only CA atoms.
Revision 821 - Directory Listing
Modified Tue Jan 13 18:52:50 2009 UTC (7 years, 8 months ago) by duarte
New classes Reconstructer and ModelPdb. Reconstructer is a one-stop solution for reconstructing from contact maps (RIGraph) using BoundsSmoother and Embedder. At the moment doesn't support reconstruction of contact maps with non-observed residues.
Revision 820 - Directory Listing
Modified Fri Jan 9 10:35:07 2009 UTC (7 years, 8 months ago) by duarte
Removing vecmath package which was not in use.
Revision 819 - Directory Listing
Modified Tue Jan 6 10:31:47 2009 UTC (7 years, 8 months ago) by stehr
new command line tools for visualizing surface accessibility and for printing information about a mutated site in a protein structure
Revision 818 - Directory Listing
Modified Tue Jan 6 10:24:07 2009 UTC (7 years, 8 months ago) by stehr
added method getTypeDescription to output a string representation of the secondary structure type (currently not distinguishing between different numbers of states)
Revision 817 - Directory Listing
Modified Tue Jan 6 10:21:58 2009 UTC (7 years, 8 months ago) by stehr
fixed bug in runAccess : temporary file could not be created when pdb code was not known, now using '1xxx' in this case
Revision 816 - Directory Listing
Modified Tue Jan 6 10:20:16 2009 UTC (7 years, 8 months ago) by stehr
New enum class AminoAcid
Revision 815 - Directory Listing
Modified Thu Dec 18 13:41:37 2008 UTC (7 years, 9 months ago) by stehr
new executables for pairwise all-against-all sequence alignments (pairwiseSeqId) and for calculating surface accessibilities and writing them to the b-factor column
Revision 814 - Directory Listing
Modified Thu Dec 18 13:40:07 2008 UTC (7 years, 9 months ago) by stehr
added methods to set b-factor values; updated writeAtomLines to write b-factors if set (currently b-factors are not being read when creating a pdb object); added method getAtomSersFromResSer(); added writeAtomLines method with simpler interface
Revision 813 - Directory Listing
Modified Tue Dec 16 11:11:39 2008 UTC (7 years, 9 months ago) by duarte
Fixed runNaccess to use unique file names and documented it. Wrote also a junit test case for it.
Revision 812 - Directory Listing
Modified Fri Nov 28 11:13:24 2008 UTC (7 years, 9 months ago) by duarte
Fixed bug: in check of input of intervals wasn't checking ig intervals was null.
Revision 811 - Directory Listing
Modified Thu Nov 27 15:11:53 2008 UTC (7 years, 9 months ago) by duarte
New options -e and -i in reconstruct (for forcing angle constraints)
Revision 810 - Directory Listing
Modified Thu Nov 27 13:50:14 2008 UTC (7 years, 9 months ago) by duarte
Two new statics: to get phi/psi constraints for intervals of one given structure.
Revision 809 - Directory Listing
Modified Mon Nov 24 11:21:01 2008 UTC (7 years, 10 months ago) by duarte
Introduced some more checks for validity of contact types.
Revision 808 - Directory Listing
Modified Fri Nov 21 15:39:19 2008 UTC (7 years, 10 months ago) by duarte
Introduced a delay between runProtein and runXyzpdb in reconstruct to make sure when we run xyzpdb the file is there: we try to find xyzFile a few times with a delay between retries.
Revision 807 - Directory Listing
Modified Fri Nov 21 13:46:35 2008 UTC (7 years, 10 months ago) by duarte
Fixed bug: wasn't checking exit value of protein, xyzpdb and pdbxyz. Now throwing exception when exit value not 0.
Revision 806 - Directory Listing
Modified Thu Nov 20 14:29:04 2008 UTC (7 years, 10 months ago) by duarte
New method contains().
Revision 805 - Directory Listing
Modified Thu Nov 20 11:31:56 2008 UTC (7 years, 10 months ago) by duarte
Added debug option in reconstruct: at the moment just prints some of the stack traces.
Revision 804 - Directory Listing
Modified Tue Nov 18 17:49:17 2008 UTC (7 years, 10 months ago) by duarte
Made Bound[][] bounds a member, thus changing the signature of most methods. Refactored getBoundsAllPairs(bounds) to better name computeTriangleInequality: now it uses as input the bounds member variable and updates it as output.
Revision 803 - Directory Listing
Modified Tue Nov 18 13:21:34 2008 UTC (7 years, 10 months ago) by duarte
Fisrt full implementation of metrization 
Revision 802 - Directory Listing
Modified Mon Nov 17 18:27:21 2008 UTC (7 years, 10 months ago) by duarte
Some big changes: now internally we use the data structure Bound[][] for all steps. We only use graphs for when we need to calculate shortest paths.
Define some static functions for printing info.
Made the scaling method an option passed as an argument to embed()
Extracted to separate file the Bound class.
Drafted an implementation of metrize
Revision 801 - Directory Listing
Modified Mon Nov 17 13:40:10 2008 UTC (7 years, 10 months ago) by duarte
Fixed bug: was not doing correctly the sanity checks in getAlignmentFullSeqs
Revision 800 - Directory Listing
Modified Fri Nov 14 17:20:56 2008 UTC (7 years, 10 months ago) by duarte
Introduced scaling of the embedded coordinates (first good embedding ever!!)
Make the random generation more consistent. Also introduced for debugging a fixed seed.
Revision 799 - Directory Listing
Modified Thu Nov 13 17:56:16 2008 UTC (7 years, 10 months ago) by duarte
Fixed in BoundsSmoother: now the lower bound will be set to the triangle inequality value only if the newly found lower bound is bigger than the hard spheres bound.
Now we also introduce contiguous CA distance constraints (3.8)
In main now checking for violations to the full bounds matrix.
New method in Pdb for getting distance matrix as Jama object
Revision 798 - Directory Listing
Modified Thu Nov 13 11:31:06 2008 UTC (7 years, 10 months ago) by duarte
New method in Pdb to set atoms for all coordinates of a given atom. Used in BoundsSmoother and Embedder mains.
Changed slightly how parameters are passed in BoundsSmoother.
Revision 797 - Directory Listing
Modified Wed Nov 12 16:13:39 2008 UTC (7 years, 10 months ago) by duarte
Lower bounds bounds-smoothing now also implemented (using Dijkstra's shortest path algorithm and offsetting to avoid negative weights).
Revision 796 - Directory Listing
Modified Tue Nov 11 10:01:20 2008 UTC (7 years, 10 months ago) by duarte
First implementation of BoundsSmoother. Does only bounds smoothing through triangle inequality for the upper bounds (for lower bounds just takes a hard-spheres distance value)
Revision 795 - Directory Listing
Modified Fri Nov 7 14:45:58 2008 UTC (7 years, 10 months ago) by duarte
Fixed bug (hopefully): was not closing drmaa session after every runParallelDistgeom, only in the shutdown hook. We need to close it always in case there is more than one run within the same instance of the JVM.
Revision 794 - Directory Listing
Modified Thu Nov 6 14:17:12 2008 UTC (7 years, 10 months ago) by duarte
Got rid of hard coded mysql server references in scripts.
Revision 793 - Directory Listing
Modified Tue Nov 4 10:21:49 2008 UTC (7 years, 10 months ago) by duarte
Cleaned up and updated the testPdb example code.
Revision 792 - Directory Listing
Modified Tue Nov 4 09:23:59 2008 UTC (7 years, 10 months ago) by duarte
Cleaned up and updated the mysql connection example
Revision 791 - Directory Listing
Modified Mon Nov 3 15:44:41 2008 UTC (7 years, 10 months ago) by filippis
white TO talyn
Revision 790 - Directory Listing
Modified Mon Nov 3 15:27:18 2008 UTC (7 years, 10 months ago) by filippis
white TO talyn
Revision 789 - Directory Listing
Modified Mon Nov 3 15:21:53 2008 UTC (7 years, 10 months ago) by filippis
white TO talyn
Revision 788 - Directory Listing
Modified Mon Nov 3 15:13:59 2008 UTC (7 years, 10 months ago) by filippis
white TO talyn
Revision 787 - Directory Listing
Modified Mon Nov 3 14:17:04 2008 UTC (7 years, 10 months ago) by duarte
First implementation of the embedding part of the EMBED algorithm by Havel: from an exact complete distance matrix gives 3d coordinates for the embedding.
Revision 786 - Directory Listing
Modified Fri Oct 31 10:40:30 2008 UTC (7 years, 10 months ago) by duarte
Implemented a more robust approach to failure of jobs in parallel distgeom. Now we send 1.1*n jobs and require that only n of them finish successfully. These solves many issues: even if 0.1*n jobs fail the whole thing will be successful, if a jobs hangs forever we will not wait for it to finish.
Revision 785 - Directory Listing
Modified Thu Oct 30 16:07:54 2008 UTC (7 years, 10 months ago) by duarte
Fixed bug: now parallel distgeom works even if a relative path  specified in caller script.
Revision 784 - Directory Listing
Modified Thu Oct 30 15:25:43 2008 UTC (7 years, 10 months ago) by duarte
Minor change in help string
Revision 783 - Directory Listing
Modified Thu Oct 30 12:52:46 2008 UTC (7 years, 10 months ago) by duarte
Got rid of the hardcoded mysql server, user, password. Now read from .my.cnf file
Revision 782 - Directory Listing
Modified Wed Oct 29 13:46:26 2008 UTC (7 years, 10 months ago) by duarte
New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf.
Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.
Revision 781 - Directory Listing
Modified Fri Oct 24 15:23:27 2008 UTC (7 years, 11 months ago) by duarte
Implemented shutdown hook. Now all jobs killed upon CTRL-c.
Now submitting directly the distgeom binary without needing writing a shell script. That removes the dependency on java6 (needed for set execution permission on the shell script). 
Introduced (but not in use yet and not fully implemented) the submission of more jobs for failure tolerance.
Revision 780 - Directory Listing
Modified Fri Oct 24 09:37:41 2008 UTC (7 years, 11 months ago) by duarte
Some minor fixes and cleanup. Changed timeout to 2hours.
Revision 779 - Directory Listing
Modified Thu Oct 23 08:49:01 2008 UTC (7 years, 11 months ago) by duarte
Better error messages
Revision 778 - Directory Listing
Modified Wed Oct 22 16:09:19 2008 UTC (7 years, 11 months ago) by duarte
Fixed bug: now correctly capturing exit state. Correctly cleaning up (killing jobs) after a failure. Closing the drmaa session properly.
Revision 777 - Directory Listing
Modified Thu Oct 9 08:29:41 2008 UTC (7 years, 11 months ago) by duarte
Added drmaa.jar to make file
Revision 776 - Directory Listing
Modified Wed Oct 8 17:09:19 2008 UTC (7 years, 11 months ago) by duarte
Implemented first version of a parallel (using distributed distgeom jobs through sge) reconstruction. Experimental so far, not well tested.
Revision 775 - Directory Listing
Modified Sat Oct 4 20:16:27 2008 UTC (7 years, 11 months ago) by stehr
better error handling in AlignmentEvaluator; calling recompiled polypose15 in PolyposeRunner
Revision 774 - Directory Listing
Modified Sat Oct 4 20:13:39 2008 UTC (7 years, 11 months ago) by stehr
updated output of pairwiseSeqId
Revision 773 - Directory Listing
Modified Sat Oct 4 15:32:25 2008 UTC (7 years, 11 months ago) by stehr
calculate the pairwise identity for a set of sequences
Revision 772 - Directory Listing
Modified Sat Oct 4 12:39:10 2008 UTC (7 years, 11 months ago) by stehr
removed output of pairwise overlaps
Revision 771 - Directory Listing
Modified Sat Oct 4 11:53:07 2008 UTC (7 years, 11 months ago) by stehr
now taking command line parameters
Revision 770 - Directory Listing
Modified Fri Oct 3 19:12:36 2008 UTC (7 years, 11 months ago) by stehr
removing debug output in moveToCenter() methods
Revision 769 - Directory Listing
Modified Fri Oct 3 19:03:07 2008 UTC (7 years, 11 months ago) by stehr
added methods and executables to calculate 3d superimpositions using PolyposeRunner
Revision 768 - Directory Listing
Modified Fri Oct 3 19:01:00 2008 UTC (7 years, 11 months ago) by stehr
added moveToOrigin() methods
Revision 767 - Directory Listing
Modified Fri Oct 3 18:58:46 2008 UTC (7 years, 11 months ago) by stehr
added getGaplessColumns(start, end)
Revision 766 - Directory Listing
Modified Tue Sep 30 17:21:02 2008 UTC (7 years, 11 months ago) by stehr
keep on evaluating common cores even if rmsd increased
Revision 765 - Directory Listing
Modified Tue Sep 30 17:01:06 2008 UTC (7 years, 11 months ago) by duarte
Minor fix in mirror(): now using getters to access data
Revision 764 - Directory Listing
Modified Tue Sep 30 16:51:53 2008 UTC (7 years, 11 months ago) by stehr
adding transform method to rotate/translate the structure
Revision 763 - Directory Listing
Modified Thu Sep 25 15:19:45 2008 UTC (8 years ago) by duarte
New method in BlastHit to transform the BlastHit local alignment into one that contains the full sequences of subject and query.
Revision 762 - Directory Listing
Modified Thu Sep 25 13:44:21 2008 UTC (8 years ago) by duarte
Added length sanity check tests
Revision 761 - Directory Listing
Modified Thu Sep 25 10:38:29 2008 UTC (8 years ago) by duarte
Fixed warnings and error handling in addSecStructAnnotation
Revision 760 - Directory Listing
Modified Wed Sep 24 18:18:53 2008 UTC (8 years ago) by duarte
Rewrote the secondary structure handling in Alignment. Also changed first parameter in writeFasta to be a PrintStream not an OutputStream
Revision 759 - Directory Listing
Modified Wed Sep 24 15:59:30 2008 UTC (8 years ago) by duarte
Added printing of pairwise alignment when checkSequnces fail for target sequence
Revision 758 - Directory Listing
Modified Wed Sep 24 15:27:48 2008 UTC (8 years ago) by duarte
GraphAverager: got rid of redundant code in countVotes. Changed signature of one of the constructors: now requires target sequence.
averageGraph: adapted accordingly
Alignment: new method removeSequence (untested), fixed some docs
Revision 757 - Directory Listing
Modified Wed Sep 24 08:31:26 2008 UTC (8 years ago) by stehr
now outputing the gapless columns; now assuming that alignment file has axtension .fa (for extracting the name)
Revision 756 - Directory Listing
Modified Tue Sep 23 18:07:25 2008 UTC (8 years ago) by duarte
New static method in BlastHit to get subjectId from templateId
New member source in TemplateList
Revision 755 - Directory Listing
Modified Tue Sep 23 15:00:46 2008 UTC (8 years ago) by duarte
New method getAlignmentWithTemplateIDtag
Revision 754 - Directory Listing
Modified Mon Sep 22 10:30:06 2008 UTC (8 years ago) by duarte
New method geometrizeContactMap
Revision 753 - Directory Listing
Modified Thu Sep 18 18:27:32 2008 UTC (8 years ago) by duarte
Fixed bug: PDB/graph/scop data loading issues were not correctly implemented. 
Revision 752 - Directory Listing
Modified Wed Sep 17 13:44:30 2008 UTC (8 years ago) by duarte
BlastHitList: new method getHit(subjectId), a new lookup HastMap member added for that.
TemplateList: new method get(i)
Sequence: new convenience method writeToFastaFile
Revision 751 - Directory Listing
Modified Tue Sep 16 16:35:34 2008 UTC (8 years ago) by duarte
Now cleaning up correctly paul temp files
Now closing tcoffee's log properly

Revision 750 - Directory Listing
Modified Tue Sep 16 13:15:25 2008 UTC (8 years ago) by duarte
Now we can run blast with multi threads option
Revision 749 - Directory Listing
Modified Tue Sep 16 09:53:42 2008 UTC (8 years ago) by stehr
set javaversion to 1.5 for compatibility with cluster
Revision 748 - Directory Listing
Modified Sun Sep 14 21:47:56 2008 UTC (8 years ago) by duarte
Initial commit, tcoffee runner for sequence to profile alignment
Revision 747 - Directory Listing
Modified Fri Sep 12 17:13:47 2008 UTC (8 years ago) by duarte
Initial commit of StructAligner interface and implementation PaulStructAligner.
New reader in Alignment: now we can read CLUSTAL alignment files, not extensively tested. Also Alignment now only throws generic FileFormatErrors instead of specific file format errors.
Revision 746 - Directory Listing
Modified Thu Sep 11 13:02:42 2008 UTC (8 years ago) by duarte
Now outputting info that omega restraints are used.
Revision 745 - Directory Listing
Modified Thu Sep 11 12:57:10 2008 UTC (8 years ago) by duarte
Now BlastHit printing works correctly for query identifier strings of any length
Revision 744 - Directory Listing
Modified Thu Sep 11 11:09:27 2008 UTC (8 years ago) by duarte
Using the new XML parser in TemplateSelection.
New method getQueryCoverage in BlastHit
Revision 743 - Directory Listing
Modified Thu Sep 11 10:06:22 2008 UTC (8 years ago) by duarte
New tests package (should be a folder and under it packages, but for now we can't do that until we move all source code to a src folder).
Moved all existing tests to appropiate tests packages.
New test PdbParsersTest: does cif against pdbase at the moment.
Adde equals method to SecStrucElement
Added some getters to Pdb

Revision 742 - Directory Listing
Modified Wed Sep 10 17:23:37 2008 UTC (8 years ago) by duarte
New BlastXMLParser together with BlastParsersTest Junit test for both xml and tabular parsers.
Added some new fields in BlastHist and BlastHitList.
Blast running methods in BlastRunner now take a new parameter: noFiltering.
Revision 741 - Directory Listing
Modified Tue Sep 9 10:47:21 2008 UTC (8 years ago) by duarte
Created getters for missing fields in BlastHit. 
New method removeAll in TemplateList.
Revision 740 - Directory Listing
Modified Thu Sep 4 17:36:41 2008 UTC (8 years ago) by duarte
Invert behaviour of -F/-O options. Now default is use phi/psi and omega constraints. If -F/-O specified then they won't be used.
New option -I to specify the angle interval for the phi/psi constraints (what used to be -F)
Revision 739 - Directory Listing
Modified Wed Sep 3 10:35:21 2008 UTC (8 years ago) by duarte
Fixed xmlrpc library dependencies (was still pointing to old ones)
Revision 738 - Directory Listing
Modified Wed Sep 3 10:30:05 2008 UTC (8 years ago) by duarte
Made active -m option. Method string not hard-coded anymore
Revision 737 - Directory Listing
Modified Wed Aug 27 14:48:57 2008 UTC (8 years ago) by stehr
Committing empty class HashGrid for later implementation
Revision 736 - Directory Listing
Modified Wed Aug 27 14:48:22 2008 UTC (8 years ago) by stehr
Committing class MachineTest as an example for a JUnit test case
Revision 735 - Directory Listing
Modified Wed Aug 27 14:46:37 2008 UTC (8 years ago) by stehr
New package litNet with classes to process our article database
Revision 734 - Directory Listing
Modified Wed Aug 27 14:10:07 2008 UTC (8 years ago) by stehr
Added a serialVersionUID and got rid of an obsolete import to avoid compiler warnings
Revision 733 - Directory Listing
Modified Wed Aug 27 14:08:07 2008 UTC (8 years ago) by stehr
New class AlignmentEvaluator to compare multiple structure alignments in terms of conserved core size and RMSD
Revision 732 - Directory Listing
Modified Wed Aug 27 13:40:11 2008 UTC (8 years ago) by duarte
Tagging ver 0.9.6 for CMView 0.9.6. Now using jung beta1 jars.
Revision 731 - Directory Listing
Modified Wed Aug 27 13:39:11 2008 UTC (8 years ago) by duarte
Tagging ver 1.1.0 for CMView 1.1.0. Now using jung beta1 jars.
Revision 730 - Directory Listing
Modified Wed Aug 27 13:25:05 2008 UTC (8 years ago) by duarte
Updated version to 1.1.0
Revision 729 - Directory Listing
Modified Wed Aug 27 13:23:56 2008 UTC (8 years ago) by duarte
Updated make-aglappe to jung beta jars.
Updated version in Manifest to 0.9.6
Revision 728 - Directory Listing
Modified Wed Aug 27 13:20:13 2008 UTC (8 years ago) by duarte
Got rid of our fix to bug in removeEdge. Now using jung-beta that fixed the bug.
Revision 727 - Directory Listing
Modified Tue Aug 26 15:56:20 2008 UTC (8 years, 1 month ago) by duarte
Better implementation of getViolatedEdges
Revision 726 - Directory Listing
Modified Tue Aug 26 14:22:33 2008 UTC (8 years, 1 month ago) by duarte
Added static method to report violations.
Revision 725 - Directory Listing
Modified Tue Aug 26 12:45:02 2008 UTC (8 years, 1 month ago) by duarte
Given a serialVersionUID to class to get rid of warning
Revision 724 - Directory Listing
Modified Thu Aug 21 12:17:26 2008 UTC (8 years, 1 month ago) by duarte
Removing test commit
Revision 723 - Directory Listing
Modified Thu Aug 21 12:15:15 2008 UTC (8 years, 1 month ago) by duarte
Test commit
Revision 722 - Directory Listing
Modified Thu Aug 21 10:35:40 2008 UTC (8 years, 1 month ago) by duarte
committed by stehr: New methods getGaplessColumns and getLongestNonGappedRegion; fixed severe bug in old getGaplessColumns
Revision 721 - Directory Listing
Modified Fri Aug 8 15:33:48 2008 UTC (8 years, 1 month ago) by duarte
Now -p accepts also pdb files as input for reconstruction.
Revision 720 - Directory Listing
Modified Fri Aug 8 14:55:29 2008 UTC (8 years, 1 month ago) by duarte
can now superimpose subsets of residues + removed canExecute() call which was incompatble with Java 5
Revision 719 - Directory Listing
Modified Fri Aug 8 13:07:02 2008 UTC (8 years, 1 month ago) by duarte
Now reconstruction from contact map files also possible. Improvements to help text and error checks.
Revision 718 - Directory Listing
Modified Fri Aug 8 10:38:21 2008 UTC (8 years, 1 month ago) by stehr
First version of PolyposeRunner (does an optiomal RMSD superimposition of multiple protein structures)
Revision 717 - Directory Listing
Modified Fri Aug 8 08:16:09 2008 UTC (8 years, 1 month ago) by stehr
adding StreamGobbler to aglappe.tools
Revision 716 - Directory Listing
Modified Thu Aug 7 14:45:25 2008 UTC (8 years, 1 month ago) by duarte
Improved help text and rationalised options.
Revision 715 - Directory Listing
Modified Thu Aug 7 11:13:06 2008 UTC (8 years, 1 month ago) by duarte
New option -s to do split output. 
Now converting final gro file to pdb
Fixed bugs:
- now flushing correctly the gromacs.log (by closing log)
- now properly cleaning up temp files (the ones written to /tmp)

Revision 714 - Directory Listing
Modified Thu Aug 7 09:09:22 2008 UTC (8 years, 1 month ago) by stehr
added comment
Revision 713 - Directory Listing
Modified Wed Aug 6 14:35:49 2008 UTC (8 years, 1 month ago) by duarte
Initial commit of script and classes to interface with gromacs.
Revision 712 - Directory Listing
Modified Mon Aug 4 15:00:57 2008 UTC (8 years, 1 month ago) by duarte
Switching to JUNG2-beta1:
- got rid of our custom fix to removeEdge
- now both addVertex and removeVertex are correctly implemented: they update properly the nodes2serials map. 
Revision 711 - Directory Listing
Modified Thu Jul 31 09:47:58 2008 UTC (8 years, 1 month ago) by stehr
added static method to print a ruler with sequence numbers
Revision 710 - Directory Listing
Modified Thu Jul 31 09:47:04 2008 UTC (8 years, 1 month ago) by stehr
added missing javadoc comment
Revision 709 - Directory Listing
Modified Thu Jul 31 09:46:14 2008 UTC (8 years, 1 month ago) by stehr
added methods to return the residue mappings for this alignment
Revision 708 - Directory Listing
Modified Thu Jul 31 09:44:35 2008 UTC (8 years, 1 month ago) by stehr
added a comment line
Revision 707 - Directory Listing
Modified Thu Jul 31 09:43:49 2008 UTC (8 years, 1 month ago) by stehr
minor update of Usage message
Revision 706 - Directory Listing
Modified Wed Jul 23 14:01:34 2008 UTC (8 years, 2 months ago) by stehr
added option to genGraph to output graph in SADP format
Revision 705 - Directory Listing
Modified Tue Jul 22 15:47:44 2008 UTC (8 years, 2 months ago) by duarte
New class RIGraphMinSpanningTree for getting the Minimum Spanning Tree of a RIGraph. This is simply a wrapper around JUNG's PrimMinimumSpanningTree.
New method setSerials2NodesMap in RIGraph.
Revision 704 - Directory Listing
Modified Tue Jul 22 15:29:23 2008 UTC (8 years, 2 months ago) by duarte
Got rid to direct references to serials2nodes Map in write graph methods, now using the getSerials() and getNodeFromSerial() methods instead.
Revision 703 - Directory Listing
Modified Mon Jul 21 16:53:28 2008 UTC (8 years, 2 months ago) by duarte
Fixed bug: was not initialising the type variable in BlastHit and GTGHit constructors
Revision 702 - Directory Listing
Modified Mon Jul 21 15:17:00 2008 UTC (8 years, 2 months ago) by duarte
Same fix as in last commit but in another part of the code (when writing CASP RR file)
Revision 701 - Directory Listing
Modified Mon Jul 21 11:09:06 2008 UTC (8 years, 2 months ago) by duarte
The change in last commit introduced a problem: we were exiting because when writing CASP TS file we try to parse out the CASP target number from the target tag. Now solved by using a regex for parsing the casp target number.
Revision 700 - Directory Listing
Modified Mon Jul 21 10:46:15 2008 UTC (8 years, 2 months ago) by duarte
Now not exiting when -c specified and target tag not in CASP format, instead we simply print a warning.
Revision 699 - Directory Listing
Modified Wed Jul 16 08:38:19 2008 UTC (8 years, 2 months ago) by duarte
Fixed bug: now Sequence class considers '.' to be part of the fasta headers (in agreement with what we do in Alignment class). The 2 FASTAHEADER_REGEXes should be always kept in sync.
Revision 698 - Directory Listing
Modified Tue Jul 15 10:11:23 2008 UTC (8 years, 2 months ago) by duarte
Fixed bug: now PhiPsiAverager behaves like GraphAverager:  consensus is on templates agreeing out of potential templates (non-gaps) instead of out of total number of templates.
Revision 697 - Directory Listing
Modified Fri Jul 11 16:34:22 2008 UTC (8 years, 2 months ago) by duarte
Made voteThreshold and angleInterval global.
Improved comments
Revision 696 - Directory Listing
Modified Fri Jul 11 14:56:08 2008 UTC (8 years, 2 months ago) by duarte
Minor change. Fixed some error output
Revision 695 - Directory Listing
Modified Fri Jul 11 14:46:53 2008 UTC (8 years, 2 months ago) by duarte
Now averageGraph can use PDB/CASP TS files as templates.
TemplateList/Template classes now can read PDB data either from pdbase database or from files.
Revision 694 - Directory Listing
Modified Fri Jul 11 13:48:55 2008 UTC (8 years, 2 months ago) by duarte
Now considering also '.' (dots) part of the  FASTA header tags.
Revision 693 - Directory Listing
Modified Mon Jun 23 09:55:22 2008 UTC (8 years, 3 months ago) by stehr
branching for CMView release 1.0 based on aglappe-0.9.5
Revision 692 - Directory Listing
Modified Mon Jun 23 09:53:23 2008 UTC (8 years, 3 months ago) by stehr
tagging version 0.9.5 matching CMView 0.9.5
Revision 691 - Directory Listing
Modified Mon Jun 23 09:52:33 2008 UTC (8 years, 3 months ago) by stehr
updated version number to 0.9.5
Revision 690 - Directory Listing
Modified Fri Jun 20 17:22:31 2008 UTC (8 years, 3 months ago) by duarte
Changed the type used for the set of template graphs/pdbs from arrays to TemplateList. Now the loading of pdb data and getting the graphs is done by TemplateList.
Revision 689 - Directory Listing
Modified Fri Jun 20 15:23:20 2008 UTC (8 years, 3 months ago) by filippis
-OligomericState class added

-Pdb
a.checkOligomeric and getOligomericState methods added
b.calcVolume, calcSurface and calcCompactnessCoefficient methods added
Revision 688 - Directory Listing
Modified Fri Jun 20 14:13:16 2008 UTC (8 years, 3 months ago) by duarte
Fixed bugs in averageGraph:
- output of benchmark statistics and pairwise comparison was overlapping
- benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes)

Improved:
- better handling of modes through mode variable that takes 1 of 3 states
- better input check
- in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph
- changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph
- now allowing alignments that contain other sequences than the target and the templates
- new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
Revision 687 - Directory Listing
Modified Fri Jun 13 16:50:02 2008 UTC (8 years, 3 months ago) by duarte
Improved dump scripts:
- new feature: dumps first chain if one not specified
- current dir now default
- better help text
Fixed bug in dumppdb: was trying to close Output stream after exception.
Revision 686 - Directory Listing
Modified Mon Jun 9 15:48:29 2008 UTC (8 years, 3 months ago) by filippis
Pdb:
-pdbCode and chainCode info added in the error messages in runDssp

Revision 685 - Directory Listing
Modified Mon Jun 9 12:39:13 2008 UTC (8 years, 3 months ago) by filippis
getNumScopRes method added in Scop class
Revision 684 - Directory Listing
Modified Thu Jun 5 19:49:43 2008 UTC (8 years, 3 months ago) by filippis
Pdb
-restrictToScopDomains methods added to restrict to multiple scop domains
-restrictToIntervalSet is public now
Revision 683 - Directory Listing
Modified Fri May 30 13:49:33 2008 UTC (8 years, 3 months ago) by duarte
Fixed bug: PhiPsiAverager was not working at all for single template case. 
Fixed bug: in ConsensusInterval changed MARGIN value to 2, for cases where max=min to make sure we pass an Interval bigger than 0 to tinker.
Revision 682 - Directory Listing
Modified Fri May 30 12:10:45 2008 UTC (8 years, 3 months ago) by stehr
now handling special cases that used to give NaN values
Revision 681 - Directory Listing
Modified Fri May 30 12:09:51 2008 UTC (8 years, 3 months ago) by stehr
added option to load only first models; added new constructor taking a map of names to protein objects
Revision 680 - Directory Listing
Modified Fri May 30 12:09:42 2008 UTC (8 years, 3 months ago) by duarte
New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond.
New method in Pdb: getOmega
Revision 679 - Directory Listing
Modified Fri May 30 09:19:09 2008 UTC (8 years, 3 months ago) by lappe
Relocated Michaels Stuff to MichaSandBox
Revision 678 - Directory Listing
Modified Wed May 28 13:53:03 2008 UTC (8 years, 3 months ago) by duarte
Changed default force constants to tinker's defaults ones (100.0 for distances and 1.0 for torsions). Reconstruction from averaged graphs was not working well sometimes, with really bad clashes. We think the distance force constant=10 was causing this.
Revision 677 - Directory Listing
Modified Wed May 28 13:29:07 2008 UTC (8 years, 3 months ago) by stehr
added boolean parameter 'showSequence' to Alignment.writeSecStructMatching()
Revision 676 - Directory Listing
Modified Tue May 27 12:38:07 2008 UTC (8 years, 4 months ago) by duarte
Tagging ver. 0.9.4 matching CMView 0.9.4
Revision 675 - Directory Listing
Modified Tue May 27 11:00:08 2008 UTC (8 years, 4 months ago) by duarte
New option -R for keeping all tinker output in outdir. Option -m now takes a file, still disabled anyway
Revision 674 - Directory Listing
Modified Tue May 27 09:02:15 2008 UTC (8 years, 4 months ago) by duarte
Added printing of alignment positions in writeSecStructMatching
Revision 673 - Directory Listing
Modified Mon May 26 18:13:29 2008 UTC (8 years, 4 months ago) by duarte
Important change: now final interval taken for restraints is not anymore of size angleInterval, but simply goes from min to max.
Revision 672 - Directory Listing
Modified Mon May 26 16:49:16 2008 UTC (8 years, 4 months ago) by filippis
chechScop now looks also for chain A in scop.cla when pdbChainCode is NULL
Revision 671 - Directory Listing
Modified Mon May 26 13:43:24 2008 UTC (8 years, 4 months ago) by duarte
Introduced some more useful debugging output in the main method: phi/psi of target (if one is avalable from a reconstruction) is also printed.
Revision 670 - Directory Listing
Modified Sat May 24 17:48:28 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: can't assign phi/psi torsion angle restraint to first and last residues.
Revision 669 - Directory Listing
Modified Fri May 23 17:19:24 2008 UTC (8 years, 4 months ago) by duarte
Hard coded the CASP method string
Revision 668 - Directory Listing
Modified Fri May 23 16:33:49 2008 UTC (8 years, 4 months ago) by duarte
Fixed small bug: was outputting a message about phi/psi when didnd't apply
Revision 667 - Directory Listing
Modified Fri May 23 16:04:48 2008 UTC (8 years, 4 months ago) by duarte
Fixed (hopefuly) the issue of wrapping angles (at -180,180). Tested minimally and seems fine.
Revision 666 - Directory Listing
Modified Fri May 23 14:47:47 2008 UTC (8 years, 4 months ago) by duarte
Added new option -m for casp method string
Revision 665 - Directory Listing
Modified Fri May 23 14:41:41 2008 UTC (8 years, 4 months ago) by duarte
Now casp method string can be several lines.
Revision 664 - Directory Listing
Modified Fri May 23 14:30:08 2008 UTC (8 years, 4 months ago) by duarte
Now can specify an angle interval with -F
Revision 663 - Directory Listing
Modified Fri May 23 13:44:38 2008 UTC (8 years, 4 months ago) by duarte
Added phi/psi angle constraints to the reconstruction pipeline. New option -F in averageGraph for using phi/psi angle constraints
Revision 662 - Directory Listing
Modified Thu May 22 16:55:39 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: algorithm to find consensus was not working correctly. We weren't taking in account the 2-dimensionality of the problem. Changed the approach completely, new algorithm.
Made the ConsensusInterval class a separate class and added new class ConsensusSquare to represent a phi/psi angle consensus region.
Revision 661 - Directory Listing
Modified Thu May 22 15:18:16 2008 UTC (8 years, 4 months ago) by stehr
Now enforcing that atom serials have to be in ascending order
Revision 660 - Directory Listing
Modified Thu May 22 14:46:18 2008 UTC (8 years, 4 months ago) by duarte
Put another test: finding edges is independent of order of indices given for UNDIRECTED.
Revision 659 - Directory Listing
Modified Thu May 22 13:00:05 2008 UTC (8 years, 4 months ago) by stehr
Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
Revision 658 - Directory Listing
Modified Thu May 22 12:21:22 2008 UTC (8 years, 4 months ago) by stehr
Changed return type of sortMapByValue from Map to LinkedHashMap
Revision 657 - Directory Listing
Modified Thu May 22 12:18:31 2008 UTC (8 years, 4 months ago) by stehr
Method sortByValue now called sortMapByValue and takes an additional argument for the sorting order (ascening/descending)
Revision 656 - Directory Listing
Modified Thu May 22 10:27:08 2008 UTC (8 years, 4 months ago) by stehr
Dummy commit (forgot comment for previous one): added field caspParents with getter and setter to Pdb. This field is filled when reading from and used when writing to from Casp TS files, therefore interface of writeToCaspTS file has changed slightly (parents now has to be set in Pdb object instead of passed to method as parameter)
Revision 655 - Directory Listing
Modified Thu May 22 10:23:21 2008 UTC (8 years, 4 months ago) by stehr

Revision 654 - Directory Listing
Modified Thu May 22 10:22:59 2008 UTC (8 years, 4 months ago) by stehr
added new mode of averaging without consensus threshold but specifiying the number of contacts to be predicted and picking starting from highest consensus down
Revision 653 - Directory Listing
Modified Thu May 22 10:02:53 2008 UTC (8 years, 4 months ago) by duarte
IntervalCandidate not Comparable anymore, finding max is now done with a specific Comparator. Additionally it now extends Interval so we can use the Interval type for the final public output.
Revision 652 - Directory Listing
Modified Thu May 22 08:26:29 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: recenterInterval was not working: was not taking min/max correctly.
New method to get the consensus mapped onto a target sequence.
Revision 651 - Directory Listing
Modified Wed May 21 18:11:02 2008 UTC (8 years, 4 months ago) by duarte
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.
Revision 650 - Directory Listing
Modified Wed May 21 16:40:05 2008 UTC (8 years, 4 months ago) by stehr
Casp 3D predictions now written with NULL chain code
Revision 649 - Directory Listing
Modified Tue May 20 07:16:23 2008 UTC (8 years, 4 months ago) by duarte
Now phi/psi angle methods using a more general getTorsionAngle. New method to get all phi/psi in a TreeMap
Revision 648 - Directory Listing
Modified Mon May 19 18:21:48 2008 UTC (8 years, 4 months ago) by duarte
Added methods to calculate phi/psi angles
Revision 647 - Directory Listing
Modified Mon May 19 14:02:46 2008 UTC (8 years, 4 months ago) by filippis

Revision 646 - Directory Listing
Modified Mon May 19 14:01:05 2008 UTC (8 years, 4 months ago) by filippis
-writeAtomLines and writePdbFileHeaders have become public
-writeAtomLines and write[CaspTS|Pdbfile]Headers take now PrintStream argument instead of PrintWriter.
Revision 645 - Directory Listing
Modified Mon May 19 13:50:52 2008 UTC (8 years, 4 months ago) by filippis
dumppdb added
Revision 644 - Directory Listing
Modified Sat May 17 17:01:04 2008 UTC (8 years, 4 months ago) by duarte
New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8.
Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.
Revision 643 - Directory Listing
Modified Fri May 16 17:26:41 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: command line option c was missing the ':'!!
Revision 642 - Directory Listing
Modified Fri May 16 17:08:04 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: writeClusterGraph shouldn't try to do anything if there's only one template.
Revision 641 - Directory Listing
Modified Fri May 16 15:48:55 2008 UTC (8 years, 4 months ago) by stehr
added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence
Revision 640 - Directory Listing
Modified Fri May 16 14:46:10 2008 UTC (8 years, 4 months ago) by duarte
Fixed problem: now -c reading AUTHOR string with underscores and converting them to hyphens (hyphens are problematic for command line parsing)
Revision 639 - Directory Listing
Modified Thu May 15 16:19:58 2008 UTC (8 years, 4 months ago) by duarte
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class. 
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
Revision 638 - Directory Listing
Modified Thu May 15 14:54:42 2008 UTC (8 years, 4 months ago) by stehr
added automatic conversion of matrix file to ps visualization (using script plot_simmatrix.sh)
Revision 637 - Directory Listing
Modified Thu May 15 14:26:22 2008 UTC (8 years, 4 months ago) by duarte
Now skipping lines with <PRE> tags.
Revision 636 - Directory Listing
Modified Thu May 15 12:03:58 2008 UTC (8 years, 4 months ago) by stehr
added 'title' member to Pdb and Template objects, currently only set when loading from Pdbase
Revision 635 - Directory Listing
Modified Thu May 15 08:44:59 2008 UTC (8 years, 4 months ago) by duarte
Changed default gravity value and default IDENTITY_SCORE for similarity graph
Revision 634 - Directory Listing
Modified Wed May 14 14:46:38 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug in BlastUtils.writeClusterGraph: was not working at all. Wrong curly brackets, was still using a GDT cutoff instead of rmsd and was never getting Pdb correctly out of the Template.
Two new members in Template: GTGHit and BlastHit, so we can reference back to the hit if needed (like if we want to get the evalue/score). Got rid on MySQLConnection as a member, not very nice design, now a parameter for the specific methods that need to query for PDB data.
Revision 633 - Directory Listing
Modified Wed May 14 12:08:52 2008 UTC (8 years, 4 months ago) by stehr
put test code for writeClusterGraph in main method of BlastUtils
Revision 632 - Directory Listing
Modified Wed May 14 09:32:41 2008 UTC (8 years, 4 months ago) by duarte
Got rid of the refined/unrefined field when writing CASP TS files. Now we should be complying correctly with the CASP 8 format.
Revision 631 - Directory Listing
Modified Tue May 13 15:30:39 2008 UTC (8 years, 4 months ago) by duarte
Now writing the PDB ids for the PARENT fields of CASP TS files correctly (with underscore between pdb code and chain code)
Revision 630 - Directory Listing
Modified Tue May 13 12:45:37 2008 UTC (8 years, 4 months ago) by duarte
Now author can be passed with the -c option so CASP TS files will be written with the AUTHOR field too.
Revision 629 - Directory Listing
Modified Tue May 13 10:55:21 2008 UTC (8 years, 4 months ago) by duarte
Now also copying caspMethodStr and caspAuthorStr in AIGraph.
Updated java docs
Revision 628 - Directory Listing
Modified Tue May 13 10:34:44 2008 UTC (8 years, 4 months ago) by duarte
Now writeClusterGraph uses rmsd for similarity measure instead of GDT (maxcluster was failing almost always with GDT)
Revision 627 - Directory Listing
Modified Fri May 9 16:02:01 2008 UTC (8 years, 4 months ago) by duarte
Yet another format check
Revision 626 - Directory Listing
Modified Fri May 9 15:29:04 2008 UTC (8 years, 4 months ago) by duarte
Added one more file format check.
Revision 625 - Directory Listing
Modified Fri May 9 14:57:37 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: wasn't catching wrong format in GTG output
Revision 624 - Directory Listing
Modified Fri May 9 14:16:54 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: now try/catch of getPdbInfo moved down to getPdb and getScopSccsString (getScopSccsString was throwing NullPointer when pdb load failed)
Revision 623 - Directory Listing
Modified Fri May 9 14:10:27 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: now catching when the mapping of observed residue sequence serials to internal residue serials is out of range, which happens in some extremely rare cases (because GTG uses pre-remediation data)
Revision 622 - Directory Listing
Modified Fri May 9 12:56:27 2008 UTC (8 years, 4 months ago) by duarte
Added code to be able to filter out template ids (pdb codes) by maximum release date.
Some improvements in Hit classes.
Revision 621 - Directory Listing
Modified Thu May 8 17:17:07 2008 UTC (8 years, 4 months ago) by stehr
Added members and method to ProtStructGraph and Pdb to write AUTHOR and METHOD fields to Casp files. Added missing reconstructFast methods to TinkerRunner.
Revision 620 - Directory Listing
Modified Thu May 8 13:17:36 2008 UTC (8 years, 4 months ago) by duarte
Added a few more methods to the Template classes: Template now behaves differently in that it doesn't load the PDB data on construction but on demand (when calling getPdb() or getScop())

Revision 619 - Directory Listing
Modified Thu May 8 10:13:10 2008 UTC (8 years, 4 months ago) by duarte
Added methods to be able to print "graphical" output for GTGHits, all equivalent to the methods in BlastHit
Added compare() and writeIdsToFile() in TemplateList.
Revision 618 - Directory Listing
Modified Wed May 7 12:06:56 2008 UTC (8 years, 4 months ago) by duarte
Initial commit of GTG parsing classes.
Added method in PdbasePdb to map observed residue sequence serials to internal (cif) residue serials
Revision 617 - Directory Listing
Modified Tue May 6 16:16:49 2008 UTC (8 years, 4 months ago) by duarte
New method getObservedSequence
Revision 616 - Directory Listing
Modified Tue May 6 13:12:33 2008 UTC (8 years, 4 months ago) by duarte
Fixed error output of PdbCodeNotFoundException
Revision 615 - Directory Listing
Modified Mon May 5 15:17:02 2008 UTC (8 years, 4 months ago) by stehr
new class tools.Statistics with currently only one method pearson(x,y) to compute the pearson correlation coefficient of two double[] vectors
Revision 614 - Directory Listing
Modified Mon May 5 14:07:16 2008 UTC (8 years, 4 months ago) by stehr
PdbfilePdb: catching previously unhandled NumberFormatException, added method setSequence() to override sequence read from file (needed for Casp prediction where 'real' sequence is known but residues may be missing in prediction)
RIGEnsemble: many changes
Revision 613 - Directory Listing
Modified Mon May 5 14:05:06 2008 UTC (8 years, 4 months ago) by stehr
Changed behaviour of graphAverager: Now evaluating consensus threshold based only on edges that could really exist (i.e. both ends map to non-gaps) rather than simple count of templates. The old behaviour can be restored (for comparison) by setting legacyMode=true in getAverageGraph() and getConsensusGraph().
Revision 612 - Directory Listing
Modified Wed Apr 30 18:20:09 2008 UTC (8 years, 4 months ago) by duarte
Now checking wheter read sequence contains spaces and throwing FastaFileFormatError
Revision 611 - Directory Listing
Modified Wed Apr 30 17:45:06 2008 UTC (8 years, 4 months ago) by duarte
Added some more error output
Revision 610 - Directory Listing
Modified Wed Apr 30 17:12:34 2008 UTC (8 years, 4 months ago) by duarte
Fixed bug: was opening different MySQLConnections for every PdbasePdb object created. Now opening just 1 global connection.
Revision 609 - Directory Listing
Modified Wed Apr 30 14:11:50 2008 UTC (8 years, 4 months ago) by duarte
Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph
Revision 608 - Directory Listing
Modified Wed Apr 30 10:37:53 2008 UTC (8 years, 4 months ago) by duarte
Introduced a new load method, so that is possible to specify cif chain codes (asym_ids) as input. Default is as before: input is pdbChainCode. NOT TESTED.
Revision 607 - Directory Listing
Modified Wed Apr 30 09:02:55 2008 UTC (8 years, 4 months ago) by duarte
Moved readTemplatesFile method to TemplateList class (as a static)
Revision 606 - Directory Listing
Modified Tue Apr 29 16:02:17 2008 UTC (8 years, 4 months ago) by duarte
Improved javadocs and comments
Revision 605 - Directory Listing
Modified Tue Apr 29 11:52:46 2008 UTC (8 years, 4 months ago) by stehr
changed regexp for Casp header to allow target tag with lower case 't'
Revision 604 - Directory Listing
Modified Tue Apr 29 10:38:24 2008 UTC (8 years, 4 months ago) by duarte
Added option -c to output final reconstructed model also in CASP TS format
Revision 603 - Directory Listing
Modified Tue Apr 29 10:29:34 2008 UTC (8 years, 4 months ago) by duarte
Added method writeToCaspTSFile. Outsourced writing the headers for PDB files and CASP TS files to other methods.
Refactored dumpseq to writeSeqToFile.
Improved a lot the java docs.
Revision 602 - Directory Listing
Modified Tue Apr 29 08:36:22 2008 UTC (8 years, 4 months ago) by duarte
Moved method to writeSeqs to Sequence class.
Tidied up the help text in averageGraph

Revision 601 - Directory Listing
Modified Mon Apr 28 18:34:11 2008 UTC (8 years, 4 months ago) by duarte
Added -N option for no FASTA header, now -s by default will have fasta headers
Revision 600 - Directory Listing
Modified Mon Apr 28 18:22:39 2008 UTC (8 years, 4 months ago) by duarte
Not reporting time anymore in genGraph
Fixed again the help text
Revision 599 - Directory Listing
Modified Mon Apr 28 18:02:17 2008 UTC (8 years, 4 months ago) by duarte
New switch -P to write file in paul format instead of aglappe format
Revision 598 - Directory Listing
Modified Mon Apr 28 18:01:54 2008 UTC (8 years, 4 months ago) by duarte
Now FASTA header in format pdbCode+pdbChainCode (no underscore) to be consistent with what we do elsewhere
Fixed the help text.
Revision 597 - Directory Listing
Modified Fri Apr 25 16:53:47 2008 UTC (8 years, 5 months ago) by duarte
Fixed the fasta header regex to take only first token of header as sequence name (same behaviour as in Alignment class)
Revision 596 - Directory Listing
Modified Thu Apr 24 10:50:35 2008 UTC (8 years, 5 months ago) by filippis
RIGraph:
-getCommonEdgesCount added
Revision 595 - Directory Listing
Modified Tue Apr 22 10:33:51 2008 UTC (8 years, 5 months ago) by stehr
changed type definitions (Class<?> and Iterator<?> instead of Class and Iterator)
Revision 594 - Directory Listing
Modified Tue Apr 22 09:06:57 2008 UTC (8 years, 5 months ago) by stehr
removed import which caused a warning
Revision 593 - Directory Listing
Modified Tue Apr 22 09:05:33 2008 UTC (8 years, 5 months ago) by stehr
merged in some changes (now writing similarity matrix in blast utils)
Revision 592 - Directory Listing
Modified Tue Apr 22 09:04:14 2008 UTC (8 years, 5 months ago) by stehr
fixed one null pointer bug and some spelling mistakes
Revision 591 - Directory Listing
Modified Fri Apr 11 14:57:25 2008 UTC (8 years, 5 months ago) by duarte
Added some missing packages to compilation
Revision 590 - Directory Listing
Modified Fri Apr 11 14:43:53 2008 UTC (8 years, 5 months ago) by duarte
Added code to run psipred.
Fixed a few minor bugs.
Revision 589 - Directory Listing
Modified Wed Apr 9 16:16:08 2008 UTC (8 years, 5 months ago) by duarte
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
Revision 588 - Directory Listing
Modified Wed Apr 9 09:40:22 2008 UTC (8 years, 5 months ago) by filippis
write_graph_to_motiffile:
-node serials are assigned now only to non-orphan nodes
Revision 587 - Directory Listing
Modified Tue Apr 8 15:56:18 2008 UTC (8 years, 5 months ago) by stehr
fixed bug in writing to gdl file (gravity 1 -> 1.0)
Revision 586 - Directory Listing
Modified Tue Apr 8 15:41:02 2008 UTC (8 years, 5 months ago) by stehr
changed some parameters for writing GDL files
Revision 585 - Directory Listing
Modified Tue Apr 8 15:40:36 2008 UTC (8 years, 5 months ago) by stehr
added method calculateSequenceIndependentMatrix()
Revision 584 - Directory Listing
Modified Tue Apr 8 15:18:22 2008 UTC (8 years, 5 months ago) by stehr
added BlastUtils.writeClusterGraph(String[] templateIds, outFile)
Revision 583 - Directory Listing
Modified Tue Apr 8 13:02:28 2008 UTC (8 years, 5 months ago) by duarte
New methods to get the template ids and write them to file
Revision 582 - Directory Listing
Modified Tue Apr 8 12:36:49 2008 UTC (8 years, 5 months ago) by filippis
RIGraph:
-bugs in write_graph_to_db methods concerning the node_id field have been fixed.
Revision 581 - Directory Listing
Modified Tue Apr 8 11:00:45 2008 UTC (8 years, 5 months ago) by stehr
Made printing hits with graphical overview the default using print() method. Print() takes no parameters, but BlastHitList.setQueryLength() has to be called once to set the length of the query. Introduced new printSome() function to output only the first n hits.
Revision 580 - Directory Listing
Modified Tue Apr 8 10:01:57 2008 UTC (8 years, 5 months ago) by filippis
createGraphDb:
-the node_id in the single_model_node table changed to AUTO_INCREMENT

doClassifySingleModels:
-the interSS for CR added

RIGraph:
-write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT
-write_graph_to_motiffile method added
Revision 579 - Directory Listing
Modified Mon Apr 7 17:57:54 2008 UTC (8 years, 5 months ago) by stehr
added class Sequence, added ascii-art output of blast hits to BlastHitList
Revision 578 - Directory Listing
Modified Mon Apr 7 15:57:24 2008 UTC (8 years, 5 months ago) by duarte
Added a main method for testing
Revision 577 - Directory Listing
Modified Fri Apr 4 16:46:23 2008 UTC (8 years, 5 months ago) by duarte
New package sequence. Initial commit of classes to run blast and parse its output.
Revision 576 - Directory Listing
Modified Tue Apr 1 15:56:06 2008 UTC (8 years, 5 months ago) by filippis
RIGraph:Now you can store unweighted graphs in db and also select the db that contains the ids for the single models.
-paramater weighted added to write_graph_to_db and write_graph_to_db_fast methods. If true, it works as before (atomWeight is written to db field weight) else the db field weight gets always value 1. Methods without this parameter still exist and work as before.
-protected field singleModelsDb and corresponding methods getSingleModelsDb and setSingleModelsDb have been added. All constructors set the singleModelsDb field to DEFAULT_SINGLEMODELS_DB which equals to "ioannis". Changes have been also made to write_graph_to_db and write_graph_to_db_fast methods to deal with the singleModelsDb field.

DbRIGraph, testDbRIGraph:Changes have been also made to address the reading of (un)weighted graphs from db.

doClassifySingleModels.sh has been added. You can create your own table with ids for the single models wherever you want.

createGraphDs.sh: mode to drop tables has been added.

Revision 575 - Directory Listing
Modified Tue Apr 1 09:37:23 2008 UTC (8 years, 5 months ago) by filippis
reconstruct:
-rmsd to mirrored pdb has been added in the report file

Pdb:
-comment for outputing missing atoms added

PairwiseSequenceAlignment:
-constructor with parameters openScore and extendScore for the gaps has been added
Revision 574 - Directory Listing
Modified Fri Mar 28 17:10:55 2008 UTC (8 years, 5 months ago) by duarte
Introduced another check in runMinimize: now we check for CHKXYZ warnings, that happened when the xyz file is somehow not well formatted. In some cases that leads to strange output in minimize.
Revision 573 - Directory Listing
Modified Fri Mar 28 15:56:24 2008 UTC (8 years, 5 months ago) by duarte
Fixed script: was exiting after computing native energy!
Revision 572 - Directory Listing
Modified Fri Mar 28 15:43:07 2008 UTC (8 years, 5 months ago) by duarte
New feature in TinkerRunner: now it can run "analyze" and "minimize" programs from the tinker package
Fixed some bugs and improved TinkerRunner: 
- flushing instead of closing the log PrintWriter when throwing TinkerError exception. Before it would close and nothing more would get logged after the first error.
- now writing command line to log
- now flusing at the end of each runXXX() method
New script computeEnergies for calculating energies of a set of decoys using tinker.
Revision 571 - Directory Listing
Modified Thu Mar 20 10:02:43 2008 UTC (8 years, 6 months ago) by duarte
Fixed bug: the check for contact type validity was not correctly done
Revision 570 - Directory Listing
Modified Thu Mar 20 10:02:08 2008 UTC (8 years, 6 months ago) by duarte
Added comments and better javadoc for the get_graph methods
Revision 569 - Directory Listing
Modified Wed Mar 12 14:32:02 2008 UTC (8 years, 6 months ago) by duarte
Change command line parameters: eliminated -c and -C. Now pdb codes and chain codes are read together as a xxxxA string that we then split to get pdb/chain codes. The list of templates is now read from file.
Revision 568 - Directory Listing
Modified Sun Mar 9 16:15:19 2008 UTC (8 years, 6 months ago) by duarte
Correction in javadoc
Revision 567 - Directory Listing
Modified Fri Mar 7 19:04:10 2008 UTC (8 years, 6 months ago) by duarte
Now takes targetDb also from command line. Some clean up
Revision 566 - Directory Listing
Modified Thu Mar 6 19:02:15 2008 UTC (8 years, 6 months ago) by duarte
Minor fix: was printing headers in non-benchmark mode
Revision 565 - Directory Listing
Modified Thu Mar 6 18:47:42 2008 UTC (8 years, 6 months ago) by duarte
New feature: now can specify more than 1 ct/cutoff. Reconstruction will be done with all of them
Fixed bug with seqFile variable. Was being used for totally different files.
Wrapped muscle call in separate method runMuscle
Changed output style: less verbose and much cleaner (table with statistics)
Revision 564 - Directory Listing
Modified Thu Mar 6 16:29:24 2008 UTC (8 years, 6 months ago) by duarte
Better comments, better handling of files, now always using the File object
Revision 563 - Directory Listing
Modified Thu Mar 6 16:05:57 2008 UTC (8 years, 6 months ago) by duarte
Added new convenience method printSummary
Revision 562 - Directory Listing
Modified Thu Mar 6 13:19:21 2008 UTC (8 years, 6 months ago) by duarte
RIGEnsemble doesn't extend ArrayList anymore, now the ensemble ArrayList is a member, so we now must use the RIGEnsemble interface exclusively
Revision 561 - Directory Listing
Modified Thu Mar 6 12:08:46 2008 UTC (8 years, 6 months ago) by duarte
Added reconstruction option (not tested). Improved help text
Revision 560 - Directory Listing
Modified Thu Mar 6 11:47:21 2008 UTC (8 years, 6 months ago) by duarte
Initial commit of averageGraph script.
Revision 559 - Directory Listing
Modified Thu Mar 6 11:35:22 2008 UTC (8 years, 6 months ago) by duarte
Fixed bug: was printing the value of accuracy for the coverage field.
Revision 558 - Directory Listing
Modified Thu Mar 6 10:52:11 2008 UTC (8 years, 6 months ago) by duarte
Changed dumpseq: now complies with FASTA format (80 characters per line) and tag is now pdbCode+pdbChainCode (with no underscore)
Revision 557 - Directory Listing
Modified Tue Mar 4 16:26:30 2008 UTC (8 years, 6 months ago) by duarte
New method writeToPaulFile
Revision 556 - Directory Listing
Modified Tue Mar 4 15:31:49 2008 UTC (8 years, 6 months ago) by filippis
Added mirror() method in Pdb class
Added getComplement() method in RIGraph class
Revision 555 - Directory Listing
Modified Thu Feb 28 14:29:15 2008 UTC (8 years, 6 months ago) by duarte
Tagging 0.9.3 for CMView release 0.9.3
Revision 554 - Directory Listing
Modified Thu Feb 28 14:28:19 2008 UTC (8 years, 6 months ago) by duarte
Deleting tag 1.0-rc1. That was too premature for a RC
Revision 553 - Directory Listing
Modified Thu Feb 28 14:27:21 2008 UTC (8 years, 6 months ago) by duarte
Changed version in Manifest to 0.9.3
Revision 552 - Directory Listing
Modified Fri Feb 22 15:26:34 2008 UTC (8 years, 7 months ago) by duarte
Now throwing exception in checkLengths().
Now fast checking of FASTA/PIR format (we check if first non-empty line starts with ">")
Revision 551 - Directory Listing
Modified Thu Feb 21 18:51:53 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
Revision 550 - Directory Listing
Modified Thu Feb 21 14:26:13 2008 UTC (8 years, 7 months ago) by stehr
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
Revision 549 - Directory Listing
Modified Thu Feb 21 09:17:24 2008 UTC (8 years, 7 months ago) by stehr
deleted testGraphAverager from aglappe/default, now in project CaspConsensusContactPrediction
Revision 548 - Directory Listing
Modified Thu Feb 21 08:42:22 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug: write_graph_to_file now writes blank instead of "null" when pdbCode, pdbChainCode or chainCode are null.
Revision 547 - Directory Listing
Modified Wed Feb 20 16:20:26 2008 UTC (8 years, 7 months ago) by stehr
Added constant NO_SEQ_SEP_VAL
Revision 546 - Directory Listing
Modified Wed Feb 20 15:53:51 2008 UTC (8 years, 7 months ago) by duarte
New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble

Revision 545 - Directory Listing
Modified Tue Feb 19 16:29:50 2008 UTC (8 years, 7 months ago) by duarte
Tagging version 1.0-rc1 for CMView-1.0-rc1
Revision 544 - Directory Listing
Modified Tue Feb 19 16:28:47 2008 UTC (8 years, 7 months ago) by duarte
Updated version to 1.0-rc1
Revision 543 - Directory Listing
Modified Mon Feb 18 18:04:27 2008 UTC (8 years, 7 months ago) by duarte
Now forcing i<j in CASP RR files (as specified by the CASP RR format)
Revision 542 - Directory Listing
Modified Mon Feb 18 18:03:49 2008 UTC (8 years, 7 months ago) by duarte
Using Ca/Cg for testing as Ca/Cb is now allowed
Revision 541 - Directory Listing
Modified Thu Feb 14 18:30:47 2008 UTC (8 years, 7 months ago) by duarte
Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.
Revision 540 - Directory Listing
Modified Thu Feb 14 16:19:04 2008 UTC (8 years, 7 months ago) by duarte
Fixed mega-nasty bug: after introducing the PRMType enum, there was still one instance of the "type" variable being compared to a String in getCorrectedPdbAtomName method
Revision 539 - Directory Listing
Modified Thu Feb 14 13:38:29 2008 UTC (8 years, 7 months ago) by stehr
some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)
Revision 538 - Directory Listing
Modified Thu Feb 14 11:56:26 2008 UTC (8 years, 7 months ago) by duarte
New option in reconstruct: -f force constant. New constructor in TinkerRunner that takes the force constant, previous constructor will work as before with the default constant.
Revision 537 - Directory Listing
Modified Wed Feb 13 18:29:05 2008 UTC (8 years, 7 months ago) by duarte
Fixed another bug in GraphAverager. Was still not working correctly: was putting edges twice in the final graph. 
Also now handling correctly graph averaging for directed or undirected graphs.
Revision 536 - Directory Listing
Modified Wed Feb 13 17:44:40 2008 UTC (8 years, 7 months ago) by duarte
Fixed GraphAverager: wasn't working since we introduced JUNG. 
Also added some better output in checkSequences() when sequence don't match between alignment/graphs. Now we take the 2 sequences calculate a pairwise alignment (using jaligner) and output it. This is useful for picking up unobserves and similars.
Revision 535 - Directory Listing
Modified Wed Feb 13 14:11:10 2008 UTC (8 years, 7 months ago) by duarte
Added option to output to standard output
Revision 534 - Directory Listing
Modified Wed Feb 13 11:33:26 2008 UTC (8 years, 7 months ago) by duarte
Now compiling also scripts in default package
Revision 533 - Directory Listing
Modified Tue Feb 12 11:50:05 2008 UTC (8 years, 7 months ago) by duarte
New constructor to read from simple graph files, i.e. list of contacts without any headers
Revision 532 - Directory Listing
Modified Fri Feb 8 12:07:10 2008 UTC (8 years, 7 months ago) by spriya
Fixed bug: addEdgeIJ was not checking for presence of contacts
Revision 531 - Directory Listing
Modified Tue Feb 5 15:48:25 2008 UTC (8 years, 7 months ago) by spriya
Added convenience methods: containsVertexI, addEdgeIJ
Revision 530 - Directory Listing
Modified Tue Feb 5 15:08:00 2008 UTC (8 years, 7 months ago) by spriya
New methods getFisrt/Last residue serial
Revision 529 - Directory Listing
Modified Tue Feb 5 14:53:57 2008 UTC (8 years, 7 months ago) by spriya
Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1
Revision 528 - Directory Listing
Modified Tue Feb 5 14:31:46 2008 UTC (8 years, 7 months ago) by duarte
Fixed bug in compare(), was not checking correctly for sequence matching
Revision 527 - Directory Listing
Modified Thu Jan 31 09:15:44 2008 UTC (8 years, 7 months ago) by duarte
Tagging ver 0.9.2 for CMView 0.9.2
Revision 526 - Directory Listing
Modified Wed Jan 30 11:04:12 2008 UTC (8 years, 7 months ago) by stehr
updated version in Manifest to 0.9.2
Revision 525 - Directory Listing
Modified Wed Jan 30 10:54:05 2008 UTC (8 years, 7 months ago) by stehr
new package ppi with classes for protein interaction networks
Revision 524 - Directory Listing
Modified Tue Jan 29 12:03:32 2008 UTC (8 years, 7 months ago) by duarte
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
Revision 523 - Directory Listing
Modified Thu Jan 24 16:18:16 2008 UTC (8 years, 8 months ago) by stehr
Added new package vecmath with classes Tuple3d, Point3d, Vector3d, Point3i to replace javax.vecmath while maintaining the same interface. The idea is that our package can be used by simply changing the import statement to remove the dependency on java3d.
Revision 522 - Directory Listing
Modified Fri Jan 18 16:51:31 2008 UTC (8 years, 8 months ago) by stehr
Minor change of some error message
Revision 521 - Directory Listing
Modified Wed Jan 16 17:58:38 2008 UTC (8 years, 8 months ago) by duarte
Fixed bug! actually it was not an abbot bug but our own, now calling AAinfo.class correctly (instead of System.getRunTime()....). With this abbot runs fine without any dirty fixes
Revision 520 - Directory Listing
Modified Wed Jan 16 15:35:36 2008 UTC (8 years, 8 months ago) by duarte
Fixed to be able to run CMView under Abbot (because of abbot getResourceAsStream bug). The ABBOT_FIX flag is turned off.
Revision 519 - Directory Listing
Modified Tue Jan 15 17:53:44 2008 UTC (8 years, 8 months ago) by stehr
updated classpath in makefile, changed permissions to execute by all
Revision 518 - Directory Listing
Modified Tue Jan 15 16:18:33 2008 UTC (8 years, 8 months ago) by filippis
checkConsurf: if the file is not found and the chain code given is "A", we check now also for results for NULL chain code 
Revision 517 - Directory Listing
Modified Tue Jan 15 13:19:36 2008 UTC (8 years, 8 months ago) by duarte
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this. 
NOTE: graph averaging hasn't been tested after the change
Revision 516 - Directory Listing
Modified Mon Jan 14 14:25:14 2008 UTC (8 years, 8 months ago) by duarte
Removed PairwiseAlignmentGraphConverter, not needed anymore by CMView + was very buggy
Improved some comments/java docs
Revision 515 - Directory Listing
Modified Mon Jan 14 10:02:28 2008 UTC (8 years, 8 months ago) by stehr
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
Revision 514 - Directory Listing
Modified Fri Jan 11 14:59:43 2008 UTC (8 years, 8 months ago) by filippis
Latest scop and csa versions updated.
Revision 513 - Directory Listing
Modified Fri Jan 11 13:33:56 2008 UTC (8 years, 8 months ago) by filippis
Fixing the fixed bug!
-if graph read is chain graph, then fullLength is set to the maximum observed residue serial
-else if graph is scop graph, then fullLength is set to the number of observed residues
NOTE:In the case of a wholechain scop graph, there might be inconsistensy between a graph I created with Pdb/RIGraph classes and stored in db and the corresponding graph i read from db. Specifically, the fullLength of graph I equals the length of the chain while the fullLength of graph i equals the number of observed residues.
Revision 512 - Directory Listing
Modified Fri Jan 11 10:57:40 2008 UTC (8 years, 8 months ago) by duarte
Added getCommanSeparatedResSerials to RIGCommonNbhood
Revision 511 - Directory Listing
Modified Fri Jan 11 09:42:35 2008 UTC (8 years, 8 months ago) by duarte
Added -f command line parameter
Revision 510 - Directory Listing
Modified Thu Jan 10 16:30:27 2008 UTC (8 years, 8 months ago) by stehr
tagging version 0.9.1 for CMView 0.9.1
Revision 509 - Directory Listing
Modified Thu Jan 10 16:22:03 2008 UTC (8 years, 8 months ago) by stehr
added some comments
Revision 508 - Directory Listing
Modified Thu Jan 10 15:39:00 2008 UTC (8 years, 8 months ago) by stehr
Fixed bug in DSSP secondary structure assignment, first element was starting at index 0
Revision 507 - Directory Listing
Modified Thu Jan 10 14:55:35 2008 UTC (8 years, 8 months ago) by stehr
changed version to 0.9.1
Revision 506 - Directory Listing
Modified Thu Jan 10 14:46:11 2008 UTC (8 years, 8 months ago) by duarte
New method to convert secondary structure
Revision 505 - Directory Listing
Modified Thu Jan 10 13:37:09 2008 UTC (8 years, 8 months ago) by duarte
Now converting also secondary structure in pairwise alignment graph conversion
Revision 504 - Directory Listing
Modified Thu Jan 10 10:30:46 2008 UTC (8 years, 8 months ago) by stehr
Fixed three compiler warnings for unused imports (DbRIGraph, Pdb) and an untyped iterator (CatalSiteSet)
Revision 503 - Directory Listing
Modified Tue Jan 8 19:51:39 2008 UTC (8 years, 8 months ago) by filippis
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned

!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added

!!!!AIGraph:
-getResidueSerial method added

RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field

DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.

testDbRIGraph added:
It reads one graph from a source db based either 
-on pdbcode, chaincode and graph properties or 
-on scop id and graph properties or 
-on a graph id 
and it writes the graph to a destination db.

Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence

CatalSiteSet:
- removeCatalSiteRes(int resser) method added

CatalyticSite:
-remRes(int resser) method added

Scop:
-remove(ScopRegion e) method added

genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.


Revision 502 - Directory Listing
Modified Tue Jan 8 11:00:15 2008 UTC (8 years, 8 months ago) by stehr
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
Revision 501 - Directory Listing
Modified Tue Jan 8 10:04:46 2008 UTC (8 years, 8 months ago) by duarte
Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
Revision 500 - Directory Listing
Modified Mon Jan 7 13:41:26 2008 UTC (8 years, 8 months ago) by duarte
New functionality: now we can get sequences and reset tags based on the order the sequences appear on the file.
Revision 499 - Directory Listing
Modified Fri Jan 4 15:00:11 2008 UTC (8 years, 8 months ago) by duarte
Got rid of check for equality of tags
Revision 498 - Directory Listing
Modified Thu Jan 3 17:16:03 2008 UTC (8 years, 8 months ago) by duarte
Now also copying the CASP RR identifier fields in RIGraph.copy() and in PairwiseAlignmentGraphConverter.converGraph().
Revision 497 - Directory Listing
Modified Thu Jan 3 14:20:03 2008 UTC (8 years, 8 months ago) by duarte
Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
Revision 496 - Directory Listing
Modified Wed Jan 2 14:11:56 2008 UTC (8 years, 8 months ago) by duarte
Rescued the make-aglappe.sh script from the old trunk
Revision 495 - Directory Listing
Modified Wed Jan 2 14:07:57 2008 UTC (8 years, 8 months ago) by stehr
added main function and loading from Multi-model PDB files
Revision 494 - Directory Listing
Modified Wed Jan 2 14:02:55 2008 UTC (8 years, 8 months ago) by stehr
Tagging version 0.9 to use with CMView 0.9 (same as aglappe-jung 0.1.2 but moved to trunk)
Revision 493 - Directory Listing
Modified Wed Jan 2 13:57:31 2008 UTC (8 years, 8 months ago) by stehr
Changed version number to 0.9
Revision 492 - Directory Listing
Modified Wed Jan 2 13:18:57 2008 UTC (8 years, 8 months ago) by duarte
Copied the aglappe-jung branch into trunk.

Revision 491 - Directory Listing
Modified Wed Jan 2 12:02:46 2008 UTC (8 years, 8 months ago) by duarte
Deleting everything in trunk to later replace with JUNG branch

Revision 490 - Directory Listing
Modified Wed Jan 2 11:13:39 2008 UTC (8 years, 8 months ago) by duarte
Tagging version 0.8.7 from trunk: last pre-JUNG before merging the JUNG branch to the trunk
Revision 489 - Directory Listing
Modified Wed Jan 2 11:09:19 2008 UTC (8 years, 8 months ago) by duarte
Updated version to 0.8.7 in Manifest
Revision 488 - Directory Listing
Modified Wed Jan 2 10:23:13 2008 UTC (8 years, 8 months ago) by duarte
T
Revision 487 - Directory Listing
Modified Thu Dec 20 11:19:54 2007 UTC (8 years, 9 months ago) by stehr
added new classes RIGEnsemble and FileTypeGuesser (used by Casp Consensus Contact prediction)
Revision 486 - Directory Listing
Modified Thu Dec 20 11:13:54 2007 UTC (8 years, 9 months ago) by lpetzo
version for CMView-jung-0.1.2
Revision 485 - Directory Listing
Modified Wed Dec 19 15:42:46 2007 UTC (8 years, 9 months ago) by duarte
Now exiting upon distgeom error
Revision 484 - Directory Listing
Modified Wed Dec 19 14:27:48 2007 UTC (8 years, 9 months ago) by stehr
changed call to graphAverager.doAveraging() into getConsensusGraph() after refactoring
Revision 483 - Directory Listing
Modified Wed Dec 19 14:25:30 2007 UTC (8 years, 9 months ago) by stehr
added methods to calculate and filter by consensus scores
Revision 482 - Directory Listing
Modified Wed Dec 19 14:23:32 2007 UTC (8 years, 9 months ago) by stehr
added missing class for RR file i/o
Revision 481 - Directory Listing
Modified Wed Dec 19 14:22:36 2007 UTC (8 years, 9 months ago) by stehr
added reading from and writing to casp contact prediction (RR) files
Revision 480 - Directory Listing
Modified Wed Dec 19 12:54:56 2007 UTC (8 years, 9 months ago) by duarte
New method calculateRadGyration
Revision 479 - Directory Listing
Modified Tue Dec 18 11:19:24 2007 UTC (8 years, 9 months ago) by duarte
Submission of commands is now async
Revision 478 - Directory Listing
Modified Mon Dec 17 17:03:24 2007 UTC (8 years, 9 months ago) by lpetzo
if the pdb file contains SEQRES records we do not allow the sequence length to be shorter than the full-length of the graph. otherwise a PdbfileFormatError is thrown in function read_data_from_file()
Revision 477 - Directory Listing
Modified Mon Dec 17 14:31:38 2007 UTC (8 years, 9 months ago) by duarte
Adapted IO methods in NodesAndEdges to JUNG framework:
added 2 classes: 
- GraphIODb: does reading and writing a Graph<V,E> from/to database
- GraphIOGDLFile: does writing of a Graph<V,E> to GDL file for aiSee exporting

Revision 476 - Directory Listing
Modified Sat Dec 15 09:51:44 2007 UTC (8 years, 9 months ago) by lpetzo
version for CMView-jung-0.1.1
Revision 475 - Directory Listing
Modified Thu Dec 13 15:37:40 2007 UTC (8 years, 9 months ago) by duarte
Now maxcluster ranking works in all cases. 
Fixed some bugs and tested for both rmsd and gdt
Revision 474 - Directory Listing
Modified Thu Dec 13 13:45:01 2007 UTC (8 years, 9 months ago) by duarte
Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph
Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise
Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0
Revision 473 - Directory Listing
Modified Thu Dec 13 10:23:03 2007 UTC (8 years, 9 months ago) by lpetzo
to be used for CMView-jung-0.1
Revision 472 - Directory Listing
Modified Thu Dec 13 10:18:10 2007 UTC (8 years, 9 months ago) by lpetzo
new function: createSelectionString(TreeSet<Integer>)
Revision 471 - Directory Listing
Modified Wed Dec 12 17:17:01 2007 UTC (8 years, 9 months ago) by duarte
Added option for min range and max range filtering (-m, -M)
Fixed output of an exception
Revision 470 - Directory Listing
Modified Wed Dec 12 12:03:49 2007 UTC (8 years, 9 months ago) by stehr
Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
Revision 469 - Directory Listing
Modified Tue Dec 11 14:23:07 2007 UTC (8 years, 9 months ago) by duarte
Fixed potentially dangerous bug: was constructing edges wrongly!: with i residue number as the weight!
Revision 468 - Directory Listing
Modified Tue Dec 11 10:11:39 2007 UTC (8 years, 9 months ago) by duarte
Fixed bug: now assigning frequency 0 to case where countTotal=0 (no observations)
Revision 467 - Directory Listing
Modified Mon Dec 10 14:37:19 2007 UTC (8 years, 9 months ago) by lpetzo
don't touch br!!!
Revision 466 - Directory Listing
Modified Mon Dec 10 13:49:51 2007 UTC (8 years, 9 months ago) by lpetzo
MAJOR CHANGES:
- merge the changes from the jung-branch: *Pdb loading scheme together with new methods getChains(), getModels()
- different exceptions
Revision 465 - Directory Listing
Modified Fri Dec 7 16:53:10 2007 UTC (8 years, 9 months ago) by duarte
New feature: now Pdb objects can be restricted to SCOP domains
New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
Revision 464 - Directory Listing
Modified Fri Dec 7 12:01:27 2007 UTC (8 years, 9 months ago) by lpetzo
added getter function for the cif-filename
Revision 463 - Directory Listing
Modified Thu Dec 6 19:26:59 2007 UTC (8 years, 9 months ago) by duarte
Minor change: comments
Revision 462 - Directory Listing
Modified Thu Dec 6 19:18:19 2007 UTC (8 years, 9 months ago) by duarte
Minor change: javadoc
Revision 461 - Directory Listing
Modified Thu Dec 6 19:15:50 2007 UTC (8 years, 9 months ago) by duarte
Fixed bug: in removeVertex we were calling getResidueSerial instead of getAtomSerial
Revision 460 - Directory Listing
Modified Thu Dec 6 18:14:59 2007 UTC (8 years, 9 months ago) by duarte
Now overriding removeEdge(E) to fix a bug in SparseGraph JUNG2 alpha2
Not implementing anymore SimpleGraph (was useless and it will be removed in coming JUNG2 releases)

Revision 459 - Directory Listing
Modified Thu Dec 6 15:05:43 2007 UTC (8 years, 9 months ago) by stehr
moved GraphAverager to subpackage, added removeVertex function to RIGraph and AIGraph, added getEdgeFromSerials and containsEdgeIJ functions to ProtStructGraph
Revision 458 - Directory Listing
Modified Thu Dec 6 11:40:51 2007 UTC (8 years, 9 months ago) by stehr
moved GraphAverager and testGraphAverager to repository CaspConsensusContactPrediction
Revision 457 - Directory Listing
Modified Thu Dec 6 11:04:49 2007 UTC (8 years, 9 months ago) by duarte
Initial commit: script to dump sequences of pdb entries
Revision 456 - Directory Listing
Modified Tue Dec 4 19:03:54 2007 UTC (8 years, 9 months ago) by duarte
Now also reads secondary structure
Revision 455 - Directory Listing
Modified Tue Dec 4 19:01:47 2007 UTC (8 years, 9 months ago) by duarte
Minor change : fixed comments
Revision 454 - Directory Listing
Modified Tue Dec 4 18:58:14 2007 UTC (8 years, 9 months ago) by duarte
Fixed bug: getCommaSeparatedResSerials was failing when there was 0 neighbors
Revision 453 - Directory Listing
Modified Tue Dec 4 18:46:00 2007 UTC (8 years, 9 months ago) by duarte
Fixed bug: -r option was not being set by default
Revision 452 - Directory Listing
Modified Tue Dec 4 15:40:17 2007 UTC (8 years, 9 months ago) by duarte
New class NbhoodBackgrnd representing a set of neighbourhoods loaded from a set of graphs of a non redundant pdb structures set.
Rewrote RIGNbhood so that the TreeMap now contains also the central residue. Added methods equals() and match().
Adapted RIGraph.getNbhood to the new constructor in RIGNbhood
Revision 451 - Directory Listing
Modified Tue Dec 4 15:37:08 2007 UTC (8 years, 9 months ago) by duarte
Fixed for new exceptions thrown by Pdb.load()
Revision 450 - Directory Listing
Modified Tue Dec 4 15:21:35 2007 UTC (8 years, 9 months ago) by lpetzo
... some more comments
Revision 449 - Directory Listing
Modified Tue Dec 4 15:20:15 2007 UTC (8 years, 9 months ago) by lpetzo
Johannes provided us we the debugged version of noncrossing(), kept the old version for sentimental reason as noncrossing_()
Revision 448 - Directory Listing
Modified Tue Dec 4 15:19:15 2007 UTC (8 years, 9 months ago) by lpetzo
class *Pdb:
- implemented new exception handling scheme for function Getter.get() -> getChains() and getModels() throw all possible exceptions encapsulated in GetterError exceptions
Revision 447 - Directory Listing
Modified Tue Dec 4 15:11:22 2007 UTC (8 years, 9 months ago) by lpetzo
class Getter:
- function get() is now throwing GetterError exception

class GetterError:
- wrapper exception for all type of exceptions thrown in the get() function of class Getter
Revision 446 - Directory Listing
Modified Tue Dec 4 14:51:54 2007 UTC (8 years, 9 months ago) by lpetzo
Johannes provided us we the debugged version of noncrossing(), kept the old version for sentimental reason as noncrossing_()
Revision 445 - Directory Listing
Modified Tue Dec 4 10:18:44 2007 UTC (8 years, 9 months ago) by filippis
Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance
Revision 444 - Directory Listing
Modified Tue Dec 4 10:18:21 2007 UTC (8 years, 9 months ago) by filippis
Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance
Revision 443 - Directory Listing
Modified Fri Nov 30 13:38:35 2007 UTC (8 years, 9 months ago) by duarte
Now not using ORDER BY in nodes and edges queries, was useless and slowing down queries
Now reading correctly empty graphs, just keeping it empty without throwing exception
Revision 442 - Directory Listing
Modified Fri Nov 30 10:36:09 2007 UTC (8 years, 9 months ago) by duarte
Memory leak problem is gone with rewrite in jung! Now genDbGraph/genGraph work without needing an external shell script to do the loop. Thus removing runGenDbGraph.sh
Revision 441 - Directory Listing
Modified Thu Nov 29 15:19:37 2007 UTC (8 years, 9 months ago) by duarte
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
Revision 440 - Directory Listing
Modified Wed Nov 28 16:42:41 2007 UTC (8 years, 9 months ago) by duarte
Tagging ver. 0.8.6. This will be the last pre-JUNG tag
Revision 439 - Directory Listing
Modified Wed Nov 28 16:39:22 2007 UTC (8 years, 9 months ago) by duarte
Updated version in Manifest for tagging
Revision 438 - Directory Listing
Modified Wed Nov 28 15:44:57 2007 UTC (8 years, 9 months ago) by filippis
AAInfo
-isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+"
-isOverlapping method has been added

AIGEdge
-copy method added

AIGNode
-equals and copy methods has been added

AIGraph
-getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed
-distances are now set for RIGNodes in getRIGraph
-for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph
-we set now the secondaryStructure object of RIGraph in getRIGraph
-addGraph has been added

Box
-we throw away wrong check in getDistancesWithinBox - read the comment

DbRIGraph
-constructors now take argument directed and directionality doesn't depend anymore on isCrossed
-distances are read also from db and set for RIGEdges

Pdb
-get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed
-there is check for forbidden cts in get_graph
-cts with + are taken into account in get_graph

RIGEdge
-setAtomWeight and setDistance methods have been added

RIGNode
-equals method has been added

RIGraph
-getObsLength has been deleted
-we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast

genDbGraph
-argument for directionality is now added


Revision 437 - Directory Listing
Modified Wed Nov 28 15:43:52 2007 UTC (8 years, 9 months ago) by lpetzo
an abstract getter
Revision 436 - Directory Listing
Modified Wed Nov 28 13:29:55 2007 UTC (8 years, 9 months ago) by filippis
-expBB is treated correctly now as int field in db in DBGraph and Graph classes
-null secondary structure case fixed in write_graph_to_db in Graph class
Revision 435 - Directory Listing
Modified Wed Nov 28 12:11:11 2007 UTC (8 years, 9 months ago) by duarte
Reverted to unobserved RIGNodes not present in the RIGraph
Revision 434 - Directory Listing
Modified Wed Nov 28 09:34:44 2007 UTC (8 years, 9 months ago) by duarte
Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false.
Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes.
New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
Revision 433 - Directory Listing
Modified Tue Nov 27 17:58:26 2007 UTC (8 years, 9 months ago) by duarte
Added more comments

Revision 432 - Directory Listing
Modified Tue Nov 27 11:43:03 2007 UTC (8 years, 10 months ago) by duarte
Initial commit: script to make aglappe project into one compiled jar
Revision 431 - Directory Listing
Modified Tue Nov 27 08:48:28 2007 UTC (8 years, 10 months ago) by duarte
Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :
Revision 430 - Directory Listing
Modified Mon Nov 26 18:20:04 2007 UTC (8 years, 10 months ago) by duarte
Fixed tester after changes in getAllCommonNnhSizes
Revision 429 - Directory Listing
Modified Mon Nov 26 17:27:29 2007 UTC (8 years, 10 months ago) by filippis
DbGraph-fix bug
Revision 428 - Directory Listing
Modified Mon Nov 26 16:01:11 2007 UTC (8 years, 10 months ago) by duarte
Fixed bug: was missing last sequence element when adding gap nodes
Revision 427 - Directory Listing
Modified Mon Nov 26 15:57:37 2007 UTC (8 years, 10 months ago) by duarte
Fixed bug in PairwiseAlignmentGraphConverter: was not adding the nodes for gaps, also some other minor bugs fixed in copying of objects
Fixed bug in getAllCommonNbhSizes, 1) now returning a HashMap on 
Pair<Integer>, not Pair<RIGNode> 2) was filling cells when size=0
Added method getIncidentNodes to IntPairSet as a temporary fix

Revision 426 - Directory Listing
Modified Fri Nov 23 18:04:15 2007 UTC (8 years, 10 months ago) by duarte
Now PairWiseAlignmentConverter and PairwiseAlignmentGraphConverter work in the new JUNG framework.
New class IntPairComparator
Now sorting output in RIGraph.write_graph_to_file
Revision 425 - Directory Listing
Modified Fri Nov 23 17:55:51 2007 UTC (8 years, 10 months ago) by duarte
Fixed bug in Graph constructor from sadp's ContactMap
Revision 424 - Directory Listing
Modified Fri Nov 23 14:21:33 2007 UTC (8 years, 10 months ago) by duarte
Added last i/o method from old Graph (write to file in Ioannis network format)
Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods
Fixed the write_graph_to_file method name in executables in default package

Revision 423 - Directory Listing
Modified Fri Nov 23 13:37:17 2007 UTC (8 years, 10 months ago) by duarte
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
Revision 422 - Directory Listing
Modified Fri Nov 23 10:08:40 2007 UTC (8 years, 10 months ago) by duarte
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
Revision 421 - Directory Listing
Modified Thu Nov 22 19:42:11 2007 UTC (8 years, 10 months ago) by duarte
Now graph generation in Pdb also works when we pass a crossed contact type with overlapping atom sets, e.g. ALL/BB (changes were: added a couple of new conditions in Box and in Pdb's AIGraph getGraph(ct,cutoff))
Loads of better comments
Revision 420 - Directory Listing
Modified Thu Nov 22 17:27:44 2007 UTC (8 years, 10 months ago) by duarte
First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there.
NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Revision 419 - Directory Listing
Modified Thu Nov 22 14:09:18 2007 UTC (8 years, 10 months ago) by duarte
Re-branching for JUNG2 development
Revision 418 - Directory Listing
Modified Thu Nov 22 13:59:33 2007 UTC (8 years, 10 months ago) by duarte
Deleted the branch, we are going to branch from a newer revision
Revision 417 - Directory Listing
Modified Thu Nov 22 11:23:49 2007 UTC (8 years, 10 months ago) by lpetzo
abstract class implementing the Runnable interface
Revision 416 - Directory Listing
Modified Thu Nov 22 11:18:28 2007 UTC (8 years, 10 months ago) by lpetzo
- changed the identation mode
- added some comments
Revision 415 - Directory Listing
Modified Thu Nov 22 10:19:16 2007 UTC (8 years, 10 months ago) by duarte
Branching for development of new graph framework using JUNG2
Revision 414 - Directory Listing
Modified Thu Nov 22 10:09:50 2007 UTC (8 years, 10 months ago) by duarte
Minor changes. Got rid of some warnings
Revision 413 - Directory Listing
Modified Wed Nov 21 21:23:19 2007 UTC (8 years, 10 months ago) by filippis
createGraphDb.sh
-pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code
-index for pdb_residue_info table added
Revision 412 - Directory Listing
Modified Wed Nov 21 16:12:26 2007 UTC (8 years, 10 months ago) by filippis
Changes in Pdb
-checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores

-writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file.
-another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false
-dump2pdbfile has also been changed in similar way
-runDssp and runNaccess now call the above methods with true pdbCompatible

Changes in genDbGraph
-1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ...
-DSSP is run with 3state
Revision 411 - Directory Listing
Modified Tue Nov 20 19:41:16 2007 UTC (8 years, 10 months ago) by filippis
minor changes
Revision 410 - Directory Listing
Modified Tue Nov 20 19:40:36 2007 UTC (8 years, 10 months ago) by filippis
minor change
Revision 409 - Directory Listing
Modified Tue Nov 20 19:09:21 2007 UTC (8 years, 10 months ago) by filippis
createGraphDb.sh added
Revision 408 - Directory Listing
Modified Tue Nov 20 18:44:03 2007 UTC (8 years, 10 months ago) by filippis
minor change
Revision 407 - Directory Listing
Modified Tue Nov 20 18:41:56 2007 UTC (8 years, 10 months ago) by filippis
contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Revision 406 - Directory Listing
Modified Tue Nov 20 16:50:32 2007 UTC (8 years, 10 months ago) by duarte
Reverting to last revision, changes made in 405 were wrong
Revision 405 - Directory Listing
Modified Tue Nov 20 16:37:54 2007 UTC (8 years, 10 months ago) by duarte
Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet
Revision 404 - Directory Listing
Modified Fri Nov 16 17:22:33 2007 UTC (8 years, 10 months ago) by duarte
Not asserting anymore pdbChainCode to be uppercase. pdb chain codes are case sensitive!
Revision 403 - Directory Listing
Modified Fri Nov 16 16:52:03 2007 UTC (8 years, 10 months ago) by filippis
OXT is taken into account now also for BB contact type
Revision 402 - Directory Listing
Modified Thu Nov 15 16:15:32 2007 UTC (8 years, 10 months ago) by duarte
Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
Revision 401 - Directory Listing
Modified Thu Nov 15 15:58:30 2007 UTC (8 years, 10 months ago) by duarte
Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
Revision 400 - Directory Listing
Modified Tue Nov 13 15:55:30 2007 UTC (8 years, 10 months ago) by filippis
-pdb_seq_num is used instead of auth_seq_num in get_ressers_mappings. Now resser2pdbresser contains all residues even the unobserved ones. This has been changed in PdbasePdb and CiffilePdb classes.

-pdb_strand_id not needed in the query in read_seq in PdbasePdb class. Asym_id and pdb_strand_id have 1-1 mapping in case sensitive mode.

-comments have been added about the entity_id-asym_id-pdb_strand_id 1-1-1 mapping and some filters in queries that are no longer necessary.
Revision 399 - Directory Listing
Modified Mon Nov 12 15:56:00 2007 UTC (8 years, 10 months ago) by stehr
added class PairwiseSequenceAlignment
Revision 398 - Directory Listing
Modified Fri Nov 9 15:12:33 2007 UTC (8 years, 10 months ago) by filippis
Minor changes
Revision 397 - Directory Listing
Modified Thu Nov 8 16:04:21 2007 UTC (8 years, 10 months ago) by filippis
Pdb code forced to lowercase in CiffilePdb
Revision 396 - Directory Listing
Modified Thu Nov 8 15:01:04 2007 UTC (8 years, 10 months ago) by filippis
Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)
Revision 395 - Directory Listing
Modified Thu Nov 8 12:53:09 2007 UTC (8 years, 10 months ago) by duarte
Initial commit. Provisional script to use the genDbGraph program when iterating through loads of structures, because of the "memory leak" problem is not possible to use directly genDbGraph to iterate over many structures (~1000)
Revision 394 - Directory Listing
Modified Thu Nov 8 12:40:01 2007 UTC (8 years, 10 months ago) by duarte
New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)
Revision 393 - Directory Listing
Modified Thu Nov 8 11:49:38 2007 UTC (8 years, 10 months ago) by duarte
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
Revision 392 - Directory Listing
Modified Thu Nov 8 11:25:06 2007 UTC (8 years, 10 months ago) by stehr
new methods getLastModelFiles and getGdtsToNative (using MaxClusterRunner)
Revision 391 - Directory Listing
Modified Thu Nov 8 11:22:40 2007 UTC (8 years, 10 months ago) by stehr
started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)
Revision 390 - Directory Listing
Modified Thu Nov 8 11:21:28 2007 UTC (8 years, 10 months ago) by duarte
Not creating anymore the score table
Revision 389 - Directory Listing
Modified Thu Nov 8 11:20:59 2007 UTC (8 years, 10 months ago) by stehr
implemented tinker reconstruction of consensus graphs created with GraphAverager
Revision 388 - Directory Listing
Modified Thu Nov 8 11:14:01 2007 UTC (8 years, 10 months ago) by duarte
New method setSequence
Revision 387 - Directory Listing
Modified Wed Nov 7 21:37:20 2007 UTC (8 years, 10 months ago) by filippis
deleted the print part in the checkCSA method in pdb class
Revision 386 - Directory Listing
Modified Wed Nov 7 17:35:26 2007 UTC (8 years, 10 months ago) by lpetzo
MODIFICATIONS
-------------

class SADP:
- added exception handling stuff for exceptions thrown by class Alignment
Revision 385 - Directory Listing
Modified Wed Nov 7 17:32:43 2007 UTC (8 years, 10 months ago) by lpetzo
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError

MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
 * writeFasta
 
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class

class GraphFileFormatError:
- s. class CiffileFormatError

class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment

class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter

class PdbFileFormatError:
- s. class CifffileFormatError
Revision 384 - Directory Listing
Modified Tue Nov 6 18:53:11 2007 UTC (8 years, 10 months ago) by filippis
hasCSA and getCSA methods added in Pdb.java
Revision 383 - Directory Listing
Modified Tue Nov 6 18:35:17 2007 UTC (8 years, 10 months ago) by filippis
inSameSheet, isOther and getSheetSerial methods added in SecStrucElement
Revision 382 - Directory Listing
Modified Tue Nov 6 15:42:05 2007 UTC (8 years, 10 months ago) by filippis
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table

Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
Revision 381 - Directory Listing
Modified Fri Nov 2 17:27:56 2007 UTC (8 years, 10 months ago) by lpetzo
a generic pair class
Revision 380 - Directory Listing
Modified Fri Nov 2 17:26:43 2007 UTC (8 years, 10 months ago) by lpetzo
added a new version of getDiffDistMap(...) that take a sequence alignment as an input to allow for residue mappings between two pdb-models of different size
Revision 379 - Directory Listing
Modified Fri Nov 2 14:22:54 2007 UTC (8 years, 10 months ago) by stehr
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph

Revision 378 - Directory Listing
Modified Thu Nov 1 15:46:58 2007 UTC (8 years, 10 months ago) by stehr
finally implemented the setCutoff method ;)
Revision 377 - Directory Listing
Modified Thu Nov 1 15:02:56 2007 UTC (8 years, 10 months ago) by stehr
fixed nasty bug in constructor Graph(sequence) (residue indexing was wrong)
Revision 376 - Directory Listing
Modified Thu Nov 1 14:14:24 2007 UTC (8 years, 10 months ago) by stehr
added method setCutoff() and some javadocs
Revision 375 - Directory Listing
Modified Thu Nov 1 11:43:13 2007 UTC (8 years, 10 months ago) by duarte
Cleaned up. More command line parameters
Revision 374 - Directory Listing
Modified Wed Oct 31 16:40:29 2007 UTC (8 years, 10 months ago) by duarte
Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters
Revision 373 - Directory Listing
Modified Wed Oct 31 15:25:46 2007 UTC (8 years, 10 months ago) by duarte
Fixed (yet again) the report output, now also outputting size (number of residues) of protein
Revision 372 - Directory Listing
Modified Wed Oct 31 10:20:22 2007 UTC (8 years, 10 months ago) by lpetzo

Revision 371 - Directory Listing
Modified Thu Oct 25 15:33:49 2007 UTC (8 years, 11 months ago) by lpetzo
Class ContactMap:
- Exception ContactMapConstructionError is thrown if the construction of a contact map from a Graph object fails.
- changed method to determine the number of nodes of a graph object.
- changed method to iterate through the set of edges of the graph (though the previous version seemed to be much more efficient ...)

Class SADP:
- added some new members controlling to input order of the contact maps (preservedInputOrder)
- the progress status of the run() method is send to a Retriever object
- added getters and setter for all data member.
- implemented methods to compute the sequence alignment and the node matching
- a couple of changes in method main
Revision 370 - Directory Listing
Modified Thu Oct 25 15:19:22 2007 UTC (8 years, 11 months ago) by lpetzo
to be thrown if the construction of a contact map from a proteinstructure.Graph instance fails
Revision 369 - Directory Listing
Modified Thu Oct 25 13:51:00 2007 UTC (8 years, 11 months ago) by lpetzo
This package provides a set of very basic abstract classes serving as interfaces to very basic tasks such as:

1. condition checkings (class Checker),
2. data retrieval (class Retriever) and 
3. pure workers that perform any kind of actions that do not depend on any kind of input data (class Doer).

Each of these classes is a subclass of class Action which only purpose is to store the object affected by the subclasses action method.
Revision 368 - Directory Listing
Modified Thu Oct 25 09:38:02 2007 UTC (8 years, 11 months ago) by duarte
Now parsing tinker's error function value, changed report file format (again!!)
Revision 367 - Directory Listing
Modified Wed Oct 24 13:29:15 2007 UTC (8 years, 11 months ago) by duarte
Changed name of native output pdb file
Revision 366 - Directory Listing
Modified Tue Oct 23 10:54:29 2007 UTC (8 years, 11 months ago) by duarte
Now throwing all exceptions
Revision 365 - Directory Listing
Modified Tue Oct 23 08:36:58 2007 UTC (8 years, 11 months ago) by duarte
New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object
Revision 364 - Directory Listing
Modified Mon Oct 22 08:47:44 2007 UTC (8 years, 11 months ago) by stehr
tagging version 0.8.5 in sync with CMView-0.8.5
Revision 363 - Directory Listing
Modified Fri Oct 19 15:45:49 2007 UTC (8 years, 11 months ago) by filippis
Method writeUndirUnweightGraphToNetworkFiles added in Graph class
Revision 362 - Directory Listing
Modified Thu Oct 18 15:08:09 2007 UTC (8 years, 11 months ago) by stehr
renamed precision to accuracy (in accordance with Casp)
Revision 361 - Directory Listing
Modified Wed Oct 17 17:40:18 2007 UTC (8 years, 11 months ago) by duarte
Now weights are kept in the Edge objects rather than separately in a member variable in Graph
Revision 360 - Directory Listing
Modified Wed Oct 17 16:10:28 2007 UTC (8 years, 11 months ago) by stehr
Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files
Revision 359 - Directory Listing
Modified Wed Oct 17 15:45:30 2007 UTC (8 years, 11 months ago) by duarte
Now can do multiple contact types/cutoffs per pdb structure
Revision 358 - Directory Listing
Modified Wed Oct 17 13:22:01 2007 UTC (8 years, 11 months ago) by duarte
Now closing db connection. Better help string.
Revision 357 - Directory Listing
Modified Wed Oct 17 08:01:13 2007 UTC (8 years, 11 months ago) by duarte
Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)
Revision 356 - Directory Listing
Modified Sat Oct 13 15:55:41 2007 UTC (8 years, 11 months ago) by duarte
Fixed bug: wasn't tokenising well when first field in line was quoted
Revision 355 - Directory Listing
Modified Fri Oct 12 18:42:37 2007 UTC (8 years, 11 months ago) by duarte
FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n
Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format
Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal
Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor
Revision 354 - Directory Listing
Modified Thu Oct 11 15:32:08 2007 UTC (8 years, 11 months ago) by duarte
Fixed bug: was outputing an empty column before the 'total' column
Revision 353 - Directory Listing
Modified Thu Oct 11 13:00:12 2007 UTC (8 years, 11 months ago) by duarte
Changed constructor with all parameters to protected, now shouldn't be used at all outside of package
Revision 352 - Directory Listing
Modified Thu Oct 11 12:49:08 2007 UTC (8 years, 11 months ago) by stehr
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
Revision 351 - Directory Listing
Modified Thu Oct 11 12:43:54 2007 UTC (8 years, 11 months ago) by stehr
added some test programs to default package
Revision 350 - Directory Listing
Modified Thu Oct 11 12:38:07 2007 UTC (8 years, 11 months ago) by stehr
Machine: added main and some other methods; MySQLConnection: added explicit handling of some exceptions
Revision 349 - Directory Listing
Modified Thu Oct 11 12:29:42 2007 UTC (8 years, 11 months ago) by duarte
Now writing also original pdb file
Fixed output of rmsd: now only few decimal figures output
Revision 348 - Directory Listing
Modified Thu Oct 11 12:09:57 2007 UTC (8 years, 11 months ago) by duarte
Now tinker.log has also baseName in file name
Revision 347 - Directory Listing
Modified Thu Oct 11 08:54:50 2007 UTC (8 years, 11 months ago) by duarte
Writing report to file instead of standard output
Catching unknown errors in runDistgeom (all other non-zero exit values)
Revision 346 - Directory Listing
Modified Thu Oct 11 08:38:36 2007 UTC (8 years, 11 months ago) by duarte
Doing more input error checks
In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used
Revision 345 - Directory Listing
Modified Wed Oct 10 16:27:12 2007 UTC (8 years, 11 months ago) by duarte
Fixed documentation
Revision 344 - Directory Listing
Modified Wed Oct 10 16:24:50 2007 UTC (8 years, 11 months ago) by stehr
cathing InterruptedException from TinkerRunner
Revision 343 - Directory Listing
Modified Wed Oct 10 16:19:18 2007 UTC (8 years, 11 months ago) by stehr
fixed bug when running distgeom, now waiting for process to exit before checking exit status
Revision 342 - Directory Listing
Modified Wed Oct 10 15:52:36 2007 UTC (8 years, 11 months ago) by stehr
added error handling for killed tinker process with error code 139 (presumably out of memory)
Revision 341 - Directory Listing
Modified Wed Oct 10 15:14:55 2007 UTC (8 years, 11 months ago) by duarte
Now capturing exit status 137 (2 instances of tinker running in same machine)
Now outputting progress per model
Revision 340 - Directory Listing
Modified Wed Oct 10 15:13:45 2007 UTC (8 years, 11 months ago) by duarte
Fixed the output
Revision 339 - Directory Listing
Modified Wed Oct 10 14:18:11 2007 UTC (8 years, 11 months ago) by duarte
Now much faster thanks to hashing on pairs (separate script create the hash tables)
Revision 338 - Directory Listing
Modified Fri Oct 5 11:56:28 2007 UTC (8 years, 11 months ago) by duarte
Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason!
Throwing less exceptions in ConstraintsMaker
Revision 337 - Directory Listing
Modified Thu Oct 4 10:12:49 2007 UTC (8 years, 11 months ago) by stehr
Added two new constructors for Graph (sequence only and no parameters), changed interface of GraphAverager (pass target sequence instead of target graph), extracted constant DEFAULT_WEIGHT in Edge.
Revision 336 - Directory Listing
Modified Tue Oct 2 16:14:20 2007 UTC (8 years, 11 months ago) by stehr
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
Revision 335 - Directory Listing
Modified Tue Oct 2 14:59:28 2007 UTC (8 years, 11 months ago) by duarte
Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"
Revision 334 - Directory Listing
Modified Tue Oct 2 07:35:26 2007 UTC (8 years, 11 months ago) by stehr
New class NodesAndEdges (simple graph class), some added javadocs
Revision 333 - Directory Listing
Modified Mon Oct 1 17:17:42 2007 UTC (8 years, 11 months ago) by duarte
Now does correct atom mapping for any atom of any residue ONLY for amber prm files
createConstraints does not work yet with multi atom contact types
Got rid of all the commented out mapAtoms code + some refactoring
Revision 332 - Directory Listing
Modified Mon Oct 1 16:20:06 2007 UTC (8 years, 11 months ago) by stehr
added constructor for trivial alignment, renamed getSequence to getAlignedSequence
Revision 331 - Directory Listing
Modified Mon Oct 1 16:12:48 2007 UTC (8 years, 11 months ago) by duarte
Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference
Revision 330 - Directory Listing
Modified Mon Oct 1 15:57:22 2007 UTC (8 years, 11 months ago) by stehr
added a weight field to Edge class (set using alternative constructor, maintaining backwards compatibility)
Revision 329 - Directory Listing
Modified Mon Oct 1 15:41:28 2007 UTC (8 years, 11 months ago) by duarte
Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs
Revision 328 - Directory Listing
Modified Mon Oct 1 10:57:08 2007 UTC (8 years, 11 months ago) by duarte
First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo
Revision 327 - Directory Listing
Modified Mon Oct 1 08:23:57 2007 UTC (8 years, 11 months ago) by stehr
fixed missing references to constants in class AA
Revision 326 - Directory Listing
Modified Thu Sep 20 14:49:55 2007 UTC (9 years ago) by duarte
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly
Revision 325 - Directory Listing
Modified Thu Sep 20 10:48:55 2007 UTC (9 years ago) by stehr
added parsing of residue selection strings
Revision 324 - Directory Listing
Modified Tue Sep 18 16:28:58 2007 UTC (9 years ago) by duarte
2 new methods: getAllAtomSerials, getAtomCoord
Revision 323 - Directory Listing
Modified Tue Sep 18 14:13:14 2007 UTC (9 years ago) by duarte
Moved tinker stuff to its own package
Revision 322 - Directory Listing
Modified Tue Sep 18 13:59:33 2007 UTC (9 years ago) by duarte
Initial commit of TinkerRunner and exception class to go with it TinkerError
Revision 321 - Directory Listing
Modified Tue Sep 18 08:44:30 2007 UTC (9 years ago) by stehr
added test program for difference distance maps, updated Manifest to v0.8.5
Revision 320 - Directory Listing
Modified Tue Sep 18 08:38:33 2007 UTC (9 years ago) by stehr
added calculation of difference distance map
Revision 319 - Directory Listing
Modified Mon Sep 17 16:10:32 2007 UTC (9 years ago) by stehr
added constructors for loading from online pdb
Revision 318 - Directory Listing
Modified Mon Sep 17 10:37:31 2007 UTC (9 years ago) by stehr
added some javadoc comments
Revision 317 - Directory Listing
Modified Thu Sep 13 16:09:10 2007 UTC (9 years ago) by duarte
Fixed some comments
Revision 316 - Directory Listing
Modified Thu Sep 13 08:47:55 2007 UTC (9 years ago) by lpetzo
initial version of sadp
Revision 315 - Directory Listing
Modified Thu Sep 13 08:13:40 2007 UTC (9 years ago) by duarte
Now parsing each element in different methods (re-opening the file). Parsing first pdbx_poly_seq_scheme so we get the chainCode that we can use for reading the rest
Now taking care of cases where struct_sheet_range is not a loop element
In tokeniseFields now also unquoting double-quoted strings
Tested on a set of 12000 entries
Revision 314 - Directory Listing
Modified Wed Sep 12 14:50:48 2007 UTC (9 years ago) by duarte
Checking number of fields per line in loop elements and throwing exception if count is not correect
Doing tokenisation of lines through new function that takes care of possible quoted string with spaces
New exception CiffileFormatError
Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception

Revision 313 - Directory Listing
Modified Mon Sep 10 08:22:40 2007 UTC (9 years ago) by lappe
short form to compress nbstrings = condense multiple occurence of a symbol in the nbhstring to 1. Still a bitz buggy. sometimes 2 symbols are left in ? 
Revision 312 - Directory Listing
Modified Mon Sep 10 07:43:00 2007 UTC (9 years ago) by lappe

Revision 311 - Directory Listing
Modified Thu Aug 30 17:31:38 2007 UTC (9 years ago) by duarte
Fixed buf: sometimes struct_conf can be non-loop elements, now also taking care of that particular case
Revision 310 - Directory Listing
Modified Thu Aug 30 16:00:08 2007 UTC (9 years ago) by duarte
Bug with '?' in auth_seq_num was not really fixed. Now should be fine: behaviour is the same as PdbasePdb
Revision 309 - Directory Listing
Modified Thu Aug 30 15:55:53 2007 UTC (9 years ago) by duarte
Fixed bug: needed to read alt locs in advance in another scan of the file because the order of the elements in the cif file is not guaranteed. As read of atom_site needs of alt locs, we need to do first the parsing of atom_sites_alt
Revision 308 - Directory Listing
Modified Thu Aug 30 14:54:38 2007 UTC (9 years ago) by duarte
Fixed bugs:
- was reading HETATM lines as well as ATOM in atom_site
- auth_seq_num with '?' not taken now when populating the pdbresser2resser map (same behaviour as in PdbasePdb)
- now using chainCodeStr and auth_asym_id to identify chains in pdbx_poly_seq_scheme, struct_conf and struct_sheet_range. atom_site is not guaranteed to appear in file before all the others so we can't rely on having read a chainCode (asym_id) when parsing the other elements
Revision 307 - Directory Listing
Modified Thu Aug 30 10:41:55 2007 UTC (9 years ago) by duarte
Now taking indices for fields from parsed field names. Still only minimal testing
Revision 306 - Directory Listing
Modified Thu Aug 30 09:09:24 2007 UTC (9 years ago) by duarte
First implementation of mmCIF file parser. Tested minimally.
Revision 305 - Directory Listing
Modified Wed Aug 29 09:46:32 2007 UTC (9 years ago) by duarte
Got rid of useless (and potential bug) chainCode=getChainCode (self reference!)
Revision 304 - Directory Listing
Modified Mon Aug 27 14:42:40 2007 UTC (9 years, 1 month ago) by stehr
tagging version 0.8.3 corresponding to CMView 0.8.3
Revision 303 - Directory Listing
Modified Mon Aug 27 14:29:18 2007 UTC (9 years, 1 month ago) by stehr
added writeResultsToFile()
Revision 302 - Directory Listing
Modified Mon Aug 27 14:28:23 2007 UTC (9 years, 1 month ago) by stehr
changes to calcGridDensity, now also counts number of neighbouring non-empty grid cells
Revision 301 - Directory Listing
Modified Mon Aug 27 14:26:48 2007 UTC (9 years, 1 month ago) by stehr
changed constant for unknown pdb code from "Unknown" to XXXX
Revision 300 - Directory Listing
Modified Wed Aug 22 14:59:10 2007 UTC (9 years, 1 month ago) by lappe
Faster version that writes to stdoutput, minor changes 
Revision 299 - Directory Listing
Modified Wed Aug 22 14:55:21 2007 UTC (9 years, 1 month ago) by lappe
only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell
Revision 298 - Directory Listing
Modified Wed Aug 22 14:55:01 2007 UTC (9 years, 1 month ago) by lappe
only one out of both BB/SC insertion per moves based
on sc/bb domin. out of temp shell 
Revision 297 - Directory Listing
Modified Tue Aug 21 14:06:53 2007 UTC (9 years, 1 month ago) by lappe
Faster version that writes to stdoutput
Revision 296 - Directory Listing
Modified Tue Aug 21 09:11:57 2007 UTC (9 years, 1 month ago) by lappe
Lame version that directly updates a table ...
have to change to stdoutput 
Revision 295 - Directory Listing
Modified Tue Aug 21 08:45:59 2007 UTC (9 years, 1 month ago) by lappe
Cleaned up and debugged version (sc/bb were xchanged)   
Revision 294 - Directory Listing
Modified Mon Aug 20 15:19:54 2007 UTC (9 years, 1 month ago) by lappe
2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other)
Revision 293 - Directory Listing
Modified Mon Aug 20 12:10:13 2007 UTC (9 years, 1 month ago) by lappe
1st version for the pdb_reps25_graph_4_2
Revision 292 - Directory Listing
Modified Mon Aug 20 12:09:13 2007 UTC (9 years, 1 month ago) by lappe
2nd version using  cull_pdb and denoting BB domin. contacts in nbhoodstring as z(helix), b(strand) and o(other) 
Revision 291 - Directory Listing
Modified Mon Aug 20 09:22:36 2007 UTC (9 years, 1 month ago) by lappe
1st version scoring with pdb_reps_graph_4_2 and full nbhood string
Revision 290 - Directory Listing
Modified Mon Aug 20 09:21:59 2007 UTC (9 years, 1 month ago) by lappe
1st version scoring with pdb_reps_graph_4_2 and full nbhood string
Revision 289 - Directory Listing
Modified Mon Aug 20 09:21:22 2007 UTC (9 years, 1 month ago) by lappe
1st version scoring with pdb_reps_graph_4_2 and full nbhood string 
Revision 288 - Directory Listing
Modified Fri Aug 17 15:03:22 2007 UTC (9 years, 1 month ago) by spriya
Better checks for sequence equality in compare
Revision 287 - Directory Listing
Modified Fri Aug 17 14:32:14 2007 UTC (9 years, 1 month ago) by duarte
Now also filling chain_pdb_code in write_graph_to_db
Revision 286 - Directory Listing
Modified Fri Aug 17 12:40:00 2007 UTC (9 years, 1 month ago) by spriya
Fixed bug in  compare, wasn't assigning new weights
Revision 285 - Directory Listing
Modified Thu Aug 16 15:10:11 2007 UTC (9 years, 1 month ago) by duarte
Fixed a few bugs in reading of list file
Better output and error messages
Revision 284 - Directory Listing
Modified Thu Aug 16 14:57:31 2007 UTC (9 years, 1 month ago) by duarte
Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
Revision 283 - Directory Listing
Modified Wed Aug 15 10:22:36 2007 UTC (9 years, 1 month ago) by duarte
Wasn't deep copying secondary structure when passing it to Graph
Revision 282 - Directory Listing
Modified Tue Aug 14 16:15:59 2007 UTC (9 years, 1 month ago) by duarte
Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore
Revision 281 - Directory Listing
Modified Tue Aug 14 13:49:52 2007 UTC (9 years, 1 month ago) by stehr
fixed little bug in NodeNbh
Revision 280 - Directory Listing
Modified Tue Aug 14 12:38:51 2007 UTC (9 years, 1 month ago) by stehr
changed internal implementation of runDssp method (not using getFullLength anymore)
Revision 279 - Directory Listing
Modified Tue Aug 14 12:26:28 2007 UTC (9 years, 1 month ago) by duarte
Fixed bug in Graph constructor: was not getting correct fullLength (related to last bug fix)
Revision 278 - Directory Listing
Modified Tue Aug 14 12:14:04 2007 UTC (9 years, 1 month ago) by duarte
Fixed bug with getFullLength when reading from pdb file
Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers
New member variables obsLength and fullLength
Revision 277 - Directory Listing
Modified Tue Aug 14 10:54:24 2007 UTC (9 years, 1 month ago) by duarte
New script genGraph (generates graph to files)
Better error messages in both
Revision 276 - Directory Listing
Modified Tue Aug 14 10:53:27 2007 UTC (9 years, 1 month ago) by duarte
Added secondary structure to write_graph_to_db
New method getNumSecStructureElements in SecondaryStructure
Revision 275 - Directory Listing
Modified Tue Aug 14 10:28:01 2007 UTC (9 years, 1 month ago) by duarte
Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph
Revision 274 - Directory Listing
Modified Tue Aug 14 10:26:32 2007 UTC (9 years, 1 month ago) by stehr
Added new SecondaryStructure object to Pdb and Graph
Revision 273 - Directory Listing
Modified Tue Aug 14 09:13:07 2007 UTC (9 years, 1 month ago) by lappe

Revision 272 - Directory Listing
Modified Tue Aug 14 09:12:41 2007 UTC (9 years, 1 month ago) by lappe

Revision 271 - Directory Listing
Modified Tue Aug 14 09:12:21 2007 UTC (9 years, 1 month ago) by lappe

Revision 270 - Directory Listing
Modified Tue Aug 14 09:11:59 2007 UTC (9 years, 1 month ago) by lappe

Revision 269 - Directory Listing
Modified Tue Aug 14 09:11:18 2007 UTC (9 years, 1 month ago) by lappe

Revision 268 - Directory Listing
Modified Tue Aug 14 09:11:07 2007 UTC (9 years, 1 month ago) by lappe

Revision 267 - Directory Listing
Modified Tue Aug 14 09:10:58 2007 UTC (9 years, 1 month ago) by lappe

Revision 266 - Directory Listing
Modified Tue Aug 14 09:10:47 2007 UTC (9 years, 1 month ago) by lappe

Revision 265 - Directory Listing
Modified Tue Aug 14 09:10:29 2007 UTC (9 years, 1 month ago) by lappe
final version 
incl. pessimistic tie-break
Revision 264 - Directory Listing
Modified Mon Aug 13 13:53:13 2007 UTC (9 years, 1 month ago) by duarte
Initial commit of genDbGraph script
Revision 263 - Directory Listing
Modified Mon Aug 13 11:48:23 2007 UTC (9 years, 1 month ago) by duarte
Fixed potential bug in regex for ATOM lines
Revision 262 - Directory Listing
Modified Mon Aug 13 08:55:05 2007 UTC (9 years, 1 month ago) by duarte
Was still not fixed!, forgot to insert X for non standard aa
Revision 261 - Directory Listing
Modified Mon Aug 13 08:53:11 2007 UTC (9 years, 1 month ago) by duarte
Fixed reading of SEQRES, was putting nulls for non-standard aas
Revision 260 - Directory Listing
Modified Fri Aug 10 18:30:47 2007 UTC (9 years, 1 month ago) by duarte
Implemented write_graph_to_db
New member variable model in Graph, thus changed constructor
New methods to get degree of a node in Graph
New methos in NodeNbh to write other kinds of neighbourhood strings
Revision 259 - Directory Listing
Modified Fri Aug 10 16:40:44 2007 UTC (9 years, 1 month ago) by stehr
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Revision 258 - Directory Listing
Modified Fri Aug 10 16:06:53 2007 UTC (9 years, 1 month ago) by duarte
Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size
Revision 257 - Directory Listing
Modified Thu Aug 9 16:43:32 2007 UTC (9 years, 1 month ago) by stehr
fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)
Revision 256 - Directory Listing
Modified Thu Aug 9 14:21:39 2007 UTC (9 years, 1 month ago) by duarte
Added getNumAtoms
Revision 255 - Directory Listing
Modified Thu Aug 9 13:45:10 2007 UTC (9 years, 1 month ago) by stehr
PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')
Revision 254 - Directory Listing
Modified Thu Aug 9 13:28:02 2007 UTC (9 years, 1 month ago) by duarte
Also writing graph to file
Revision 253 - Directory Listing
Modified Thu Aug 9 13:24:12 2007 UTC (9 years, 1 month ago) by duarte
Initial commit. Script to benchmark the graph generation algorithm 
Revision 252 - Directory Listing
Modified Thu Aug 9 10:37:14 2007 UTC (9 years, 1 month ago) by duarte
Made constructor public
Revision 251 - Directory Listing
Modified Mon Aug 6 15:55:26 2007 UTC (9 years, 1 month ago) by stehr
tagging version 0.8.2 to be used with CM2PyMol 0.8.2
Revision 250 - Directory Listing
Modified Mon Aug 6 14:48:37 2007 UTC (9 years, 1 month ago) by stehr
added application to count grid density, suppressed warning for secondary structure reassignment
Revision 249 - Directory Listing
Modified Sat Aug 4 17:53:11 2007 UTC (9 years, 1 month ago) by duarte
New methods containsContact and resetContacts
Revision 248 - Directory Listing
Modified Sat Aug 4 17:50:00 2007 UTC (9 years, 1 month ago) by duarte
Added method hasTag
Revision 247 - Directory Listing
Modified Sat Aug 4 17:07:23 2007 UTC (9 years, 1 month ago) by duarte
Made regex a constant and added | and \\-
Revision 246 - Directory Listing
Modified Sat Aug 4 17:00:58 2007 UTC (9 years, 1 month ago) by duarte
Doing now everythin with maps (using seqTags) rather than arrays. Cleaned up, refactored, using more consistent naming
Revision 245 - Directory Listing
Modified Sat Aug 4 15:40:20 2007 UTC (9 years, 1 month ago) by duarte
Added reverse map (from sequences serials to alignment serials) and did a bit of refactoring
Revision 244 - Directory Listing
Modified Wed Aug 1 14:34:36 2007 UTC (9 years, 1 month ago) by duarte
Initial commit of Alignmnent, a class representing a multiple sequence alignment
Revision 243 - Directory Listing
Modified Wed Aug 1 14:21:09 2007 UTC (9 years, 1 month ago) by lappe
Added correction by matrix size (yields avgdeltaRank)
plus correction jcnsize-1 for direct nbs 
and pessimistic tie-break 
Revision 242 - Directory Listing
Modified Wed Aug 1 07:47:18 2007 UTC (9 years, 1 month ago) by duarte
Got rid of doneRes ArrayList in getRanks, was redundant
Revision 241 - Directory Listing
Modified Tue Jul 31 16:38:13 2007 UTC (9 years, 1 month ago) by duarte
Now dealing correctly with ties.
Implemented getResiduesSortedByRank
Changed dist to be a TreeMap
Revision 240 - Directory Listing
Modified Tue Jul 31 13:51:59 2007 UTC (9 years, 1 month ago) by duarte
Fixed bug in delEdge. Wasn't taking care of if contact was given as i>j in undirected case. Also recount of contacts and set of modified to true was wrong
Revision 239 - Directory Listing
Modified Mon Jul 30 10:57:28 2007 UTC (9 years, 1 month ago) by duarte
Fixed bug in addEdge method. In case of undirected we need to check that the contact is inserted in the right order j>i
Revision 238 - Directory Listing
Modified Fri Jul 20 10:02:03 2007 UTC (9 years, 2 months ago) by duarte
Optimised slightly the compareTo method in Edge
Revision 237 - Directory Listing
Modified Thu Jul 19 14:23:35 2007 UTC (9 years, 2 months ago) by duarte
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
Revision 236 - Directory Listing
Modified Thu Jul 19 12:57:29 2007 UTC (9 years, 2 months ago) by duarte
Fixed bug. Was not doing correctly reflection along smallest principal axis in is_reflection case
Revision 235 - Directory Listing
Modified Thu Jul 19 12:43:12 2007 UTC (9 years, 2 months ago) by duarte
Implemented rmsd calculation (based on Jama matrix package)
rmsd method still not taking care of unobserved or missing atoms. Also not returning individual distances between optimally superimposed structures (although it can calculate them in commented out code)

Revision 234 - Directory Listing
Modified Tue Jul 10 14:14:58 2007 UTC (9 years, 2 months ago) by duarte
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge
Revision 233 - Directory Listing
Modified Tue Jul 10 13:01:50 2007 UTC (9 years, 2 months ago) by duarte
Added method getCopy
Revision 232 - Directory Listing
Modified Tue Jul 10 13:00:23 2007 UTC (9 years, 2 months ago) by duarte
Now checking in addEdge that we don't duplicate edges
New methods: get2ndshell, copyKeepingNodes
Revision 231 - Directory Listing
Modified Tue Jul 10 09:57:20 2007 UTC (9 years, 2 months ago) by lappe
production - stable
Revision 230 - Directory Listing
Modified Mon Jul 9 15:35:01 2007 UTC (9 years, 2 months ago) by stehr
added class NodeSet
Revision 229 - Directory Listing
Modified Mon Jul 9 15:02:24 2007 UTC (9 years, 2 months ago) by duarte
Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases
Revision 228 - Directory Listing
Modified Mon Jul 9 14:32:47 2007 UTC (9 years, 2 months ago) by duarte
Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)
Revision 227 - Directory Listing
Modified Fri Jul 6 14:23:51 2007 UTC (9 years, 2 months ago) by lappe
single residue target Evaluation in target* tables 
added verbosity level VL to shrink output 
Revision 226 - Directory Listing
Modified Fri Jul 6 13:43:30 2007 UTC (9 years, 2 months ago) by duarte
First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct
Revision 225 - Directory Listing
Modified Fri Jul 6 12:41:48 2007 UTC (9 years, 2 months ago) by lappe
Only cosmetic changes to polish the output 
Revision 224 - Directory Listing
Modified Thu Jul 5 13:42:37 2007 UTC (9 years, 2 months ago) by duarte
Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster
Revision 223 - Directory Listing
Modified Thu Jul 5 10:17:30 2007 UTC (9 years, 2 months ago) by duarte
Added cross contacts to isValidCT
Revision 222 - Directory Listing
Modified Wed Jul 4 15:39:01 2007 UTC (9 years, 2 months ago) by duarte
New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval
Revision 221 - Directory Listing
Modified Wed Jul 4 14:50:25 2007 UTC (9 years, 2 months ago) by lappe
minor bugfix in reportResults( cnsize*deltarank) call
Revision 220 - Directory Listing
Modified Wed Jul 4 10:02:52 2007 UTC (9 years, 2 months ago) by stehr
tagging aglappe 0.8.1 to use with cmview 0.8.1
Revision 219 - Directory Listing
Modified Tue Jul 3 15:38:21 2007 UTC (9 years, 2 months ago) by duarte
Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)
Revision 218 - Directory Listing
Modified Fri Jun 29 09:13:52 2007 UTC (9 years, 2 months ago) by lappe

Revision 217 - Directory Listing
Modified Fri Jun 29 09:04:00 2007 UTC (9 years, 2 months ago) by stehr
now casting pdb codes to lower and pdb chain codes to upper in all constructors
Revision 216 - Directory Listing
Modified Fri Jun 29 08:30:55 2007 UTC (9 years, 2 months ago) by duarte
Fixed bug: ATOM lines printing was locale dependant, thus was printing ',' for decimal separators in some locales
Revision 215 - Directory Listing
Modified Thu Jun 28 15:43:04 2007 UTC (9 years, 2 months ago) by stehr
some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
Revision 214 - Directory Listing
Modified Thu Jun 28 14:09:16 2007 UTC (9 years, 3 months ago) by lappe
debugged version of the iteration/validation of nbhoodstrings 
with added temp_table hashing for speedup (factor ca. 10x) 
needs additional (empty) database <nbhashtables> for storage
 
Revision 213 - Directory Listing
Modified Thu Jun 28 09:38:49 2007 UTC (9 years, 3 months ago) by lappe
Buggy version : 2nd to n2th row have same values 
as the first row - ? temp_nbhood stays the same?  
Revision 212 - Directory Listing
Modified Thu Jun 28 09:26:34 2007 UTC (9 years, 3 months ago) by duarte
Fixed bug in regex introduced in last revision
Revision 211 - Directory Listing
Modified Thu Jun 28 09:22:26 2007 UTC (9 years, 3 months ago) by duarte
Fixed graph file format checking, was not working properly
Revision 210 - Directory Listing
Modified Wed Jun 27 15:57:39 2007 UTC (9 years, 3 months ago) by duarte
Now throwing also SQLExceptions for individual queries, not just for connections
Revision 209 - Directory Listing
Modified Wed Jun 27 15:14:31 2007 UTC (9 years, 3 months ago) by duarte
Throwing exception also in case graph file not in right format at all (no #AGLAPPE in 1st line)
Fixed bug: was not reading correctly #PDB CHAIN CODE
Revision 208 - Directory Listing
Modified Wed Jun 27 14:42:12 2007 UTC (9 years, 3 months ago) by duarte
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
Revision 207 - Directory Listing
Modified Wed Jun 27 11:06:34 2007 UTC (9 years, 3 months ago) by duarte
Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs

Revision 206 - Directory Listing
Modified Tue Jun 26 17:01:48 2007 UTC (9 years, 3 months ago) by duarte
Major refactoring:
 accode -> pdbCode
 chaincode -> pdbChainCode
 chain -> chainCode
Major change of signatures (publics to privates)
Implemented getters for needed member variables
Major clean up
Revision 205 - Directory Listing
Modified Tue Jun 26 16:58:50 2007 UTC (9 years, 3 months ago) by stehr

Revision 204 - Directory Listing
Modified Tue Jun 26 16:57:26 2007 UTC (9 years, 3 months ago) by stehr
tagging version 0.8 to use with CM2PyMol 0.8
major change: using xmlrpc 3.0 in PyMolServerOutputStream
Revision 203 - Directory Listing
Modified Tue Jun 26 14:25:58 2007 UTC (9 years, 3 months ago) by duarte
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
Revision 202 - Directory Listing
Modified Thu Jun 21 17:18:11 2007 UTC (9 years, 3 months ago) by duarte
MySQLConnection now throwing SQLException on connect
Many files changed following this: all calling classes now re-throwing or catching the SQLException
Revision 201 - Directory Listing
Modified Tue Jun 19 09:27:11 2007 UTC (9 years, 3 months ago) by stehr
tagging version 0.7 matching CM2PyMol 0.7
Revision 200 - Directory Listing
Modified Mon Jun 18 17:43:43 2007 UTC (9 years, 3 months ago) by duarte
New isValidCT methods in AA
New method get_resser_from_atomser in Pdb
Revision 199 - Directory Listing
Modified Mon Jun 18 09:03:39 2007 UTC (9 years, 3 months ago) by duarte
Implemented getRanks()
Revision 198 - Directory Listing
Modified Mon Jun 18 08:47:26 2007 UTC (9 years, 3 months ago) by duarte
AA class is now db independent:
Hard coded getaas2atoms, not getting it anymore from db.
Revision 197 - Directory Listing
Modified Thu Jun 14 14:44:44 2007 UTC (9 years, 3 months ago) by duarte
Tagging version 0.6 for release of cmview 0.6
Revision 196 - Directory Listing
Modified Wed Jun 13 15:05:31 2007 UTC (9 years, 3 months ago) by duarte
Added toString and getMotifFullGaps missing in EdgeNbh
Revision 195 - Directory Listing
Modified Wed Jun 13 14:24:43 2007 UTC (9 years, 3 months ago) by duarte
Made contactTypes a String[]
Revision 194 - Directory Listing
Modified Wed Jun 13 10:57:00 2007 UTC (9 years, 3 months ago) by duarte
Added contactTypes method and made private methods private
Revision 193 - Directory Listing
Modified Wed Jun 13 07:57:31 2007 UTC (9 years, 3 months ago) by duarte
Moved motif static methods to Background class. They didn't belong here
Revision 192 - Directory Listing
Modified Tue Jun 12 18:27:20 2007 UTC (9 years, 3 months ago) by duarte
Made contacts public
Revision 191 - Directory Listing
Modified Tue Jun 12 17:15:17 2007 UTC (9 years, 3 months ago) by duarte
New method getAllEdgeNbhSizes
Revision 190 - Directory Listing
Modified Tue Jun 12 13:38:46 2007 UTC (9 years, 3 months ago) by duarte
NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object

Revision 189 - Directory Listing
Modified Tue Jun 12 10:38:29 2007 UTC (9 years, 3 months ago) by duarte
Added basic compare method to the Graph class and test class compareCMs
Revision 188 - Directory Listing
Modified Mon Jun 11 14:05:50 2007 UTC (9 years, 3 months ago) by duarte
Tagging version 0.5 for release of CM2PyMol version 0.5
Revision 187 - Directory Listing
Modified Mon Jun 11 14:04:54 2007 UTC (9 years, 3 months ago) by duarte
Changed to version 0.5
Revision 186 - Directory Listing
Modified Thu Jun 7 10:42:13 2007 UTC (9 years, 3 months ago) by duarte
FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning
Revision 185 - Directory Listing
Modified Thu Jun 7 09:14:46 2007 UTC (9 years, 3 months ago) by duarte
Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString
Revision 184 - Directory Listing
Modified Wed Jun 6 10:02:24 2007 UTC (9 years, 3 months ago) by duarte
New class GenericContact. To store a generic contact, i.e. a pair of residue types
Revision 183 - Directory Listing
Modified Tue Jun 5 14:32:04 2007 UTC (9 years, 3 months ago) by duarte
Fixed bug: calculateEntropy was wrong when a pi was 0
Revision 182 - Directory Listing
Modified Tue Jun 5 13:41:05 2007 UTC (9 years, 3 months ago) by duarte
FIXED BUG: the switch statement was missing the breaks
This was causing strange behaviour in counts NodeBackground getSize methods and also was making them being too slow
Revision 181 - Directory Listing
Modified Tue Jun 5 12:27:49 2007 UTC (9 years, 3 months ago) by duarte
New class NbhProbDistribution
In NodeNbh implemented a few static classes to convert between different motifs and to match motifs using differing criteria

Revision 180 - Directory Listing
Modified Fri Jun 1 15:17:40 2007 UTC (9 years, 3 months ago) by lappe

Revision 179 - Directory Listing
Modified Thu May 31 09:41:41 2007 UTC (9 years, 3 months ago) by duarte
FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them
NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh
New method getResidueType
Revision 178 - Directory Listing
Modified Tue May 29 08:01:46 2007 UTC (9 years, 3 months ago) by duarte
Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact
Revision 177 - Directory Listing
Modified Mon May 28 09:55:06 2007 UTC (9 years, 4 months ago) by duarte
Made public getUserName
Revision 176 - Directory Listing
Modified Mon May 28 09:53:00 2007 UTC (9 years, 4 months ago) by duarte
New static method getUserName and new constructor with only server and db
Revision 175 - Directory Listing
Modified Fri May 25 17:31:58 2007 UTC (9 years, 4 months ago) by duarte
FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList
New class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
New method getRange in Contact
Revision 174 - Directory Listing
Modified Fri May 25 15:07:55 2007 UTC (9 years, 4 months ago) by lappe
original version to be saved ... 
Revision 173 - Directory Listing
Modified Fri May 25 15:07:32 2007 UTC (9 years, 4 months ago) by lappe
running version summing delta Rank
still to implement sum(deltza) for entropy etc. 
Revision 172 - Directory Listing
Modified Fri May 25 13:41:19 2007 UTC (9 years, 4 months ago) by duarte
Got rid of some unnecessary warnings
Revision 171 - Directory Listing
Modified Fri May 25 13:15:19 2007 UTC (9 years, 4 months ago) by lappe
version of iterateNBHood for the uppercase background info 
pdb_reps_graph_4_2 for briefer output & calculation 
Revision 170 - Directory Listing
Modified Fri May 25 10:01:44 2007 UTC (9 years, 4 months ago) by lappe
Running version, takes graph_id and resnr as input 
Revision 169 - Directory Listing
Modified Thu May 24 16:20:12 2007 UTC (9 years, 4 months ago) by lappe

Revision 168 - Directory Listing
Modified Thu May 24 16:19:48 2007 UTC (9 years, 4 months ago) by lappe

Revision 167 - Directory Listing
Modified Thu May 24 16:19:21 2007 UTC (9 years, 4 months ago) by lappe

Revision 166 - Directory Listing
Modified Thu May 24 16:19:00 2007 UTC (9 years, 4 months ago) by lappe
First version of exchange routine contact vs. CN - non functional 
Revision 165 - Directory Listing
Modified Thu May 24 15:43:13 2007 UTC (9 years, 4 months ago) by duarte
New functionality: added methods to get node/edge neighbours
Revision 164 - Directory Listing
Modified Thu May 24 10:53:48 2007 UTC (9 years, 4 months ago) by duarte

Revision 163 - Directory Listing
Modified Thu May 24 10:52:24 2007 UTC (9 years, 4 months ago) by stehr
added Manifest
Revision 162 - Directory Listing
Modified Thu May 24 10:46:39 2007 UTC (9 years, 4 months ago) by duarte
Updated test class for Pdb/Graph objects
Revision 161 - Directory Listing
Modified Thu May 24 10:12:41 2007 UTC (9 years, 4 months ago) by stehr
made Graph.directed public
Revision 160 - Directory Listing
Modified Thu May 24 09:52:22 2007 UTC (9 years, 4 months ago) by lappe
tab-Formatted output added
Revision 159 - Directory Listing
Modified Thu May 24 09:37:25 2007 UTC (9 years, 4 months ago) by duarte
Moved ContactMap and EdgeState out of this repository. 
Extra functionality of ContactMap now in Graph:
- new member variables fullLength, obsLength, numContacts. New method getIntMatrix
- removed getCM method
Revision 158 - Directory Listing
Modified Tue May 22 15:37:15 2007 UTC (9 years, 4 months ago) by duarte
FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database
Revision 157 - Directory Listing
Modified Tue May 22 12:04:43 2007 UTC (9 years, 4 months ago) by duarte
FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!
Revision 156 - Directory Listing
Modified Tue May 22 10:40:04 2007 UTC (9 years, 4 months ago) by duarte
Now passing also chaincode from Pdb object to Graph object in get_graph
Revision 155 - Directory Listing
Modified Tue May 22 10:13:03 2007 UTC (9 years, 4 months ago) by duarte
Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file
Revision 154 - Directory Listing
Modified Fri May 18 09:32:28 2007 UTC (9 years, 4 months ago) by duarte
Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality
Revision 153 - Directory Listing
Modified Wed May 16 17:22:08 2007 UTC (9 years, 4 months ago) by duarte
NEW FUNCTIONALITY: Reading from pdb file given chain code or model serial fully implemented
Changed the chain that is dumped in dump2pdbfile directly to the Pdb.chain field i.e. internal chain identifier
Loads of new comments, including java doc for all constructors
Revision 152 - Directory Listing
Modified Wed May 16 14:12:50 2007 UTC (9 years, 4 months ago) by duarte
FIXED 2 BUGS. NEW FEATURE reading graph from db given graph_id
Bugs:
- nodes TreeMap in read_graph_from_file contained one letter res codes, now three letter codes
- in getCM was passing residues as a TreeMap of nums to three letter residue types, now passing one letter residue types
New constructor for getting graph from db given graph_id, new method to go with that get_db_graph_info

Revision 151 - Directory Listing
Modified Wed May 16 14:05:48 2007 UTC (9 years, 4 months ago) by lappe
working version for each single nbring residue 
Revision 150 - Directory Listing
Modified Wed May 16 14:05:08 2007 UTC (9 years, 4 months ago) by lappe
- functional
Revision 149 - Directory Listing
Modified Wed May 16 14:04:54 2007 UTC (9 years, 4 months ago) by lappe
min-info - functional
Revision 148 - Directory Listing
Modified Wed May 16 13:59:25 2007 UTC (9 years, 4 months ago) by lappe
list of infogain per neighbouring residue 
- still buggy w.r.t. x elimination 
Revision 147 - Directory Listing
Modified Wed May 16 12:34:49 2007 UTC (9 years, 4 months ago) by lappe
Max.Info Gain still with problems if only negative (loss) of info 
Revision 146 - Directory Listing
Modified Tue May 15 13:51:17 2007 UTC (9 years, 4 months ago) by duarte
Made cutoff and ct public
Revision 145 - Directory Listing
Modified Tue May 15 13:28:24 2007 UTC (9 years, 4 months ago) by duarte
Made some fields public: sequence, accode, chaincode, model
Revision 144 - Directory Listing
Modified Tue May 15 12:13:31 2007 UTC (9 years, 4 months ago) by duarte
NEW FEATURE: Read and write graphs from file fully implemented.

Refactored read_contacts_from_file to read_graph_from_file. Now can read other fields as well as contacts. Also gets nodes if sequence present
New method write_graph_to_file

Revision 143 - Directory Listing
Modified Tue May 15 10:06:47 2007 UTC (9 years, 4 months ago) by duarte
FIXED BUG: last commit didn't fix bug correctly:
Changed the ContactMap constructor to put into residueNums and residueTypes nums from 1 to maximum of residues.keySet()

Made public accode and chain fields in Graph
Revision 142 - Directory Listing
Modified Tue May 15 08:33:44 2007 UTC (9 years, 4 months ago) by duarte
FIXED BUG: getCM wasn't working well when reading from db and there were unobserved residues

Now setting the sequence to blank when reading from db. Also when reading from file (still nodes reading is not implemented)
In ContactMap constructor different handling when sequence is blank
Revision 141 - Directory Listing
Modified Mon May 14 15:51:54 2007 UTC (9 years, 4 months ago) by duarte
Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)
Revision 140 - Directory Listing
Modified Mon May 14 15:34:21 2007 UTC (9 years, 4 months ago) by stehr
Made Pdb.acccode public
Revision 139 - Directory Listing
Modified Mon May 14 15:29:08 2007 UTC (9 years, 4 months ago) by duarte
Changed default accode and chaincode to "Unknown" when reading from pdb file
Revision 138 - Directory Listing
Modified Mon May 14 14:58:29 2007 UTC (9 years, 4 months ago) by duarte
FIXED BUG: wasn't setting the chain field when reading from msdsd
Revision 137 - Directory Listing
Modified Mon May 14 14:53:09 2007 UTC (9 years, 4 months ago) by stehr
Made chain field in PDB class public
Revision 136 - Directory Listing
Modified Mon May 14 14:50:44 2007 UTC (9 years, 4 months ago) by duarte
FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
Revision 135 - Directory Listing
Modified Mon May 14 09:49:04 2007 UTC (9 years, 4 months ago) by duarte
NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases

New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd)
Reading chain also in Pdb in read_pdb_data_from_file
Not reading chain anymore in read_atomData of PdbaseInfo
Added oneletter2threeletter and getoneletter2threeletter to AA class
Changes in Graph:
- added db static vars and getUserName method
- new member variables graphid and sm_id
- new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db
- new method getgraphid
New Exception class GraphIdNotFoundError
Revision 134 - Directory Listing
Modified Mon May 14 07:52:10 2007 UTC (9 years, 4 months ago) by duarte
Implemented basic reading contacts from file
Revision 133 - Directory Listing
Modified Fri May 11 09:37:38 2007 UTC (9 years, 4 months ago) by duarte
New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!
Revision 132 - Directory Listing
Modified Thu May 10 16:04:06 2007 UTC (9 years, 4 months ago) by duarte
Added more tests for all cases
Revision 131 - Directory Listing
Modified Thu May 10 15:53:14 2007 UTC (9 years, 4 months ago) by duarte
2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless
Revision 130 - Directory Listing
Modified Thu May 10 15:52:24 2007 UTC (9 years, 4 months ago) by duarte
NEW FEATURE: reading pdb data from msdsd
New classes MsdsdInfo and its exception classes
FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines
Revision 129 - Directory Listing
Modified Thu May 10 13:12:32 2007 UTC (9 years, 4 months ago) by duarte
NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object
New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed
Passing more data from Pdb to Graph in get_graph
New constructor in ContactMap
Revision 128 - Directory Listing
Modified Wed May 9 16:29:39 2007 UTC (9 years, 4 months ago) by duarte
ContactMap and EdgeState classes moved here from CMPredict repository
Revision 127 - Directory Listing
Modified Wed May 9 14:54:02 2007 UTC (9 years, 4 months ago) by duarte
Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

Revision 126 - Directory Listing
Modified Wed May 9 12:04:35 2007 UTC (9 years, 4 months ago) by duarte
MYSQLUSER now taken from unix name with new getUserName method
Revision 125 - Directory Listing
Modified Wed May 9 11:58:59 2007 UTC (9 years, 4 months ago) by duarte
Initial commit of testPdb, to test the proteinstructure package
Revision 124 - Directory Listing
Modified Wed May 9 11:57:24 2007 UTC (9 years, 4 months ago) by duarte
Added error handling for PdbaseInfo: 2 new exception classes
Revision 123 - Directory Listing
Modified Wed May 9 10:45:53 2007 UTC (9 years, 4 months ago) by duarte
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures
Revision 122 - Directory Listing
Modified Thu May 3 08:32:27 2007 UTC (9 years, 4 months ago) by stehr
tagged version 0.3.4

Revision 121 - Directory Listing
Modified Thu May 3 07:40:23 2007 UTC (9 years, 4 months ago) by stehr
Updated TableSorter to compile in Java 1.5 and some trivial changes in comments
Revision 120 - Directory Listing
Modified Mon Apr 30 14:02:56 2007 UTC (9 years, 4 months ago) by stehr
added overloaded method setDistance for use in CM2Pymol for chains without chain code
Revision 119 - Directory Listing
Modified Fri Mar 30 13:28:50 2007 UTC (9 years, 5 months ago) by dinse

Revision 118 - Directory Listing
Modified Wed Mar 28 13:41:03 2007 UTC (9 years, 6 months ago) by dinse

Revision 117 - Directory Listing
Modified Wed Mar 14 09:24:24 2007 UTC (9 years, 6 months ago) by dinse
Fixed space missing in one of the queries
Revision 116 - Directory Listing
Modified Fri Mar 2 17:38:30 2007 UTC (9 years, 6 months ago) by filippis
testGraph2Pml.java fixed according to changes made in Msdsd2Pdb.java
Revision 115 - Directory Listing
Modified Fri Mar 2 13:53:04 2007 UTC (9 years, 6 months ago) by duarte
Adapted to msdsd_00_07_a
Now uses MySQLConnection and PrintWriters and not mysql client through shell (got rid of that method)
Thus all methos taking new arguments user and pdbFile
New methods:
 export2file taking accession_code, chain_pdb_code 
 export2file taking chain_id, model_id

Revision 114 - Directory Listing
Modified Tue Feb 27 08:49:10 2007 UTC (9 years, 6 months ago) by duarte
Initial commit. PyMol API script example, also using our PymolServerOutputStream to send commands directly to server
Revision 113 - Directory Listing
Modified Thu Oct 19 13:22:32 2006 UTC (9 years, 11 months ago) by duarte
Modified method getIdFromMaster to create keyTable if it didn't exist
Revision 112 - Directory Listing
Modified Mon Oct 16 15:57:50 2006 UTC (9 years, 11 months ago) by duarte
New static method getIdFromMaster. Inserts an id in a table in key_master database and gets the last_insert_id. To be used in graph generation
Revision 111 - Directory Listing
Modified Tue Sep 19 13:10:03 2006 UTC (10 years ago) by duarte
Tagging version 0.3.3. at rev110 after adding some renaming getNodes method to getMySQLNodes in DataDistribution and adding some functionality
Revision 110 - Directory Listing
Modified Tue Sep 19 13:04:55 2006 UTC (10 years ago) by duarte
New class MySQLConnectionCheck, to check whether MySQL servers are alive, uses threads
Changes in DataDistribution:
- new field: String[] nodes, initialised in constructor
- changed constructor to check for nodes that are alive, using new method nodesAlive
- renamed getNodes to getMySQLNodes. New method getNodes just returns the new field String[] nodes
DataDistributer: renamed calls to DataDistribution's getNodes to getMySQLNodes
Revision 109 - Directory Listing
Modified Tue Sep 19 09:27:12 2006 UTC (10 years ago) by duarte
Made loadMySQLDriver method public (needed to call it from other class) and static (makes more sense)
Revision 108 - Directory Listing
Modified Tue Sep 19 09:18:04 2006 UTC (10 years ago) by duarte
Added functionality to run commands in different threads
Revision 107 - Directory Listing
Modified Wed Sep 13 08:53:03 2006 UTC (10 years ago) by duarte
Initial commit, Hello World MySQLConnection program for newcomers
Revision 106 - Directory Listing
Modified Thu Sep 7 13:45:36 2006 UTC (10 years ago) by duarte
HOSTSFILE changed to new /project/StruPPi/Cluster/admin/hosts_mysql_server.txt
Revision 105 - Directory Listing
Modified Tue Aug 8 11:52:56 2006 UTC (10 years, 1 month ago) by duarte
Tagging at rev104, slight modifications in DataDistributer. To be used with a slightly improved dumpnload.java
Revision 104 - Directory Listing
Modified Tue Aug 8 11:10:01 2006 UTC (10 years, 1 month ago) by duarte
Modified finalizeDirs() to be tri-state: prompt, force or noremove. By default force. (using new field rmvtmp)
Getting rid of temp dir created in constructor when calling setDumpDir, otherwise an empty tmp dir was left lying around

Revision 103 - Directory Listing
Modified Fri Aug 4 14:50:57 2006 UTC (10 years, 1 month ago) by duarte
Tag 0.3.1 at rev 102. Introduced slight modifications in DataDistributer class to use with dumpnload.java

Revision 102 - Directory Listing
Modified Fri Aug 4 14:34:00 2006 UTC (10 years, 1 month ago) by duarte
Method finalizeDirs now prompts by default whether to delete temp dirs, unless new boolean field "force" is true.
Revision 101 - Directory Listing
Modified Tue Jul 25 10:30:02 2006 UTC (10 years, 2 months ago) by duarte
tools version 0.3 from rev98. To use with jed (includes new TableSorter)
Revision 100 - Directory Listing
Modified Tue Jul 25 10:29:27 2006 UTC (10 years, 2 months ago) by duarte
Sorry that was wrong!!
Revision 99 - Directory Listing
Modified Tue Jul 25 10:28:31 2006 UTC (10 years, 2 months ago) by duarte
tools version 0.3 from rev98. To use with jed (includes new TableSorter)
Revision 98 - Directory Listing
Modified Mon Jul 24 14:37:40 2006 UTC (10 years, 2 months ago) by stehr
Added class TableSorter to tools package
Revision 97 - Directory Listing
Modified Fri Jun 2 09:49:54 2006 UTC (10 years, 3 months ago) by duarte
Added getters/setters to host,db,user and password in MySQLConnection
Added another constructor to QueryThread to take just the MySQLConnection as argument
Revision 96 - Directory Listing
Modified Wed May 31 11:02:12 2006 UTC (10 years, 3 months ago) by duarte
Slight improve in insertIdsToKeyMaster method. Instead of querying in each insert for the nodeid, we get the node names to node id mapping in a HashMap through another query.
Revision 95 - Directory Listing
Modified Wed May 31 09:44:05 2006 UTC (10 years, 3 months ago) by duarte
Adapted also ClusterConnection and checking methods in DataDistribution to text/numeric keys.
Some methods in ClusterConnection have not changed at all even though they deal with keys. I haven't changed them because they are applicable only to numeric keys:
insertIdxInMaster, getLastInsertId and getIdxSet
Revision 94 - Directory Listing
Modified Mon May 29 15:22:13 2006 UTC (10 years, 3 months ago) by duarte
Simplified the code for dealing with text/numerical keys.
Now there's no more double methods Integer/String, rather the methos use a generic Object[] that stores either String[] or Integer[] depending on the case.
Thus modified a few methods in DataDistributer, DataDistribution and MySQLConnection.
Revision 93 - Directory Listing
Modified Wed May 24 15:44:25 2006 UTC (10 years, 4 months ago) by duarte
Now split of data also working with text-based keys as well as numerical
MySQLConnection:
- method getAllIds4KeyAndTable now splitted into two methods one for numerical ids and another for text ids
- new methods getColumnType and isKeyNumerical
DataDistribution:
- method getIdSetsFromNodes splitted into two one for numerical ids one for text ids
DataDistributer:
- new methods: splitIdsIntoSets now splitted into two methods one numerical, one text
- change methods: splitTableToCluster, splitTable, insertIdsToKeyMaster, removePK, addPK, createNewKeyMasterTbl, removeZeros, loadSplitData, dumpSplitData to make them work for both text and numeric keys. Introduced generic type T in some of them
- some bugs corrected:
-- an important one in createNewKeyMasterTbl, was introducing record in dbs_keys with srcDb instead of destDb as it should have been
-- some bugs in loadSplitData and dumpSplitData to account for cases in which there are less ids than number of nodes and thus some nodes don't get any data. Wasn't counting with this before.
Revision 92 - Directory Listing
Modified Fri May 5 14:39:20 2006 UTC (10 years, 4 months ago) by duarte
Made KEYMASTERDB in DataDistribution public. Now using in all other classes/programs that need KEYMASTERDB.
Revision 91 - Directory Listing
Modified Fri May 5 12:16:35 2006 UTC (10 years, 4 months ago) by duarte
Creating of tools version 0.2:
Freeze of tools package at rev89.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)
Revision 90 - Directory Listing
Modified Fri May 5 12:15:03 2006 UTC (10 years, 4 months ago) by duarte
This tag was wrongly created, should have contained a tools directory as a subdir. Deleting it
Revision 89 - Directory Listing
Modified Fri May 5 10:46:35 2006 UTC (10 years, 4 months ago) by duarte
Added method to setDumpDir method
Revision 88 - Directory Listing
Modified Wed May 3 11:57:23 2006 UTC (10 years, 4 months ago) by duarte
Creating of tools version 0.2:
Freeze of tools package at rev87.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)
Revision 87 - Directory Listing
Modified Wed May 3 08:50:26 2006 UTC (10 years, 4 months ago) by duarte
Improved considerably the splitTableToCluster method:
- got rid of the unnecessary step of creating partial tables before dumping.
- now directly dumping with new method dumpSplitData, a modified dumpData that dumps using a WHERE condition
- added variable NUM_CONCURRENT_SAMEHOST_WRITE_QUERIES used in dumpSplitData method. It sets the concurrency when dumping locally only from the master
Revision 86 - Directory Listing
Modified Fri Apr 28 10:31:35 2006 UTC (10 years, 5 months ago) by duarte
Added PARALLELISM in load/dump of tables using new class QueryThread (extends Thread)
Modified methods loadData, dumpData and loadSplitData to dump/load parallely in cases that is useful by using the QueryThread class.
New method initializeDirs(String[]) to do some of the dir initialization that was in dumpData
Got rid of one of the getConnectionToNode method, not needed anymore
New important 2 final static variables: NUM_CONCURRENT_READ_QUERIES and NUM_CONCURRENT_WRITE_QUERIES. They define how much concurrency we want in reads/writes to nfs for loads/dumps
Revision 85 - Directory Listing
Modified Mon Apr 24 12:41:27 2006 UTC (10 years, 5 months ago) by duarte
MAJOR change.
Split DataDistribution into 2 classes: DataDistributer and DataDistribution.
I haven't actually changed or added functionality
DataDistributer deals with the distribution of the data, while DataDistribution deals with things to do when data is already distributed, right now is only a few data checks
Note that DataDistributer now has two db fields: srcDb and destDb. This is different to before, when destDb was rather a parameter passed as arguments to the methods
Methods in DataDistributer have been tidied up a little (specially load and dump ones)
Revision 84 - Directory Listing
Modified Thu Apr 20 10:42:38 2006 UTC (10 years, 5 months ago) by duarte
Fixed bug in getTables4Db. Was closing the connection. Shouldn't do this!
Add method getAllIds4KeyAndTables, moved from DataDistribution. It makes more sense to have it here.

Revision 83 - Directory Listing
Modified Wed Apr 19 14:02:35 2006 UTC (10 years, 5 months ago) by duarte
Got rid of getTables4Db in DataDistribution
Add method getTables4Db to MySQLConnection. Makes a lot more sense.
Changed accordingly the only call to the method in DataDistribution's method chkCounts
Revision 82 - Directory Listing
Modified Thu Apr 13 10:54:05 2006 UTC (10 years, 5 months ago) by duarte
Creation of tools version 0.1:
Freezing tools rev81 to tag tools-0.1
I am planning to change completely some of the classes: DataDistribution and ClusterConnection. Will continue developing on trunk while we have this freeze so others can use programs as they are now.
Revision 81 - Directory Listing
Modified Wed Apr 12 15:27:05 2006 UTC (10 years, 5 months ago) by duarte
Changed the Connection fields to be MySQLConnection.
Thanks to this, simplify considerably a lot of the methods by using the MySQLConnection methods.
Got rid of method loadSQLDriver and URL final field
Revision 80 - Directory Listing
Modified Wed Apr 12 14:59:37 2006 UTC (10 years, 5 months ago) by duarte
Introduced better javadoc comments in constructors.
Revision 79 - Directory Listing
Modified Wed Apr 12 11:03:01 2006 UTC (10 years, 5 months ago) by duarte
Modified insertIdsToKeyMaster method. Now removing pk in table before inserting, then removing zeros and adding finally the pk back. At that point mysql should complain if there are duplicates
New methods to deal with key_master database actions. They belong in another class, but for the moment here.
- createNewKeyMasterTbl
- removePK
- addPK
- removeZeros
Revision 78 - Directory Listing
Modified Wed Apr 12 08:52:25 2006 UTC (10 years, 5 months ago) by duarte
Got rid of method createNewKeyMasterTbl
Didn't belong here but in DataDistribution (at least for now)

Revision 77 - Directory Listing
Modified Wed Apr 12 08:26:36 2006 UTC (10 years, 5 months ago) by duarte
Bug in new method createNewKeyMasterTbl
The query for inserting the new record in dbs_keys was totally wrong
Wrote something more correct and simpler!
Revision 76 - Directory Listing
Modified Tue Apr 11 16:00:26 2006 UTC (10 years, 5 months ago) by duarte
Minor change, in getHostId4Ifx one of the error messages was being written to out, now to err
Revision 75 - Directory Listing
Modified Tue Apr 11 14:33:39 2006 UTC (10 years, 5 months ago) by duarte
In latest commit method insertIdsToKeyMaster wasn't yet complying with the new way of dealing with key
Now modified insertIdsToKeyMaster accordingly. Now we create a ClusterConnection object to call the createNewKeyMasterTable method.
Revision 74 - Directory Listing
Modified Tue Apr 11 14:27:17 2006 UTC (10 years, 5 months ago) by duarte
New method createNewKeyMasterTbl
To create a new keyMaster table in the key_master database for a certain table
Will also insert a new record in dbs_keys for the new table.
If a record for it already existed it will print an error and continue as the error is harmless.
Revision 73 - Directory Listing
Modified Tue Apr 11 10:42:54 2006 UTC (10 years, 5 months ago) by duarte
Got rid of keyColumn
Now key is directly the keyColumn name, e.g. key is asu_id not asu
This makes things less confusing and simpler.
We've done this following last commit of DataDistribution to also change the ways we deal with key/keyColumn.
Note that now the checkKeyCounts and checkDifferingKeys are using to get the keyTable name a ClusterConnection object and the new ClusterConnection method getTableOnNode
Revision 72 - Directory Listing
Modified Tue Apr 11 10:29:39 2006 UTC (10 years, 5 months ago) by duarte
2 important changes:
Fixed important bug on the constructor that gets the key passed (the bug was there since a lot of revisions ago and always passed since that constructor was not used in other classes)
Got rid of keyColumn, was useless. Now key is directly the keyColumn name which is more logical and makes everything simpler
- changed all calls to keyColumn to key
- got rid of keyColumn field and setKeyColumn
- changed completely the methods setKeyTable to get the table name from the dbs_keys on key_master db
- introduced new method getTableOnNode. Gets the name of the table where splitted data is stored for this db and key
Revision 71 - Directory Listing
Modified Mon Apr 10 16:01:01 2006 UTC (10 years, 5 months ago) by duarte
New method getIdSetsFromNodes, equivalent to splitIdsIntoSets but rather a posteriori, when tables are already distributed in cluster's nodes
Modified method getAllIds4KeyAndTable, now taking host as parameter too, more general
Changed the comments a lot for all those 3 methods. There are many catches to be taken in account, the comments explain them quite well
Revision 70 - Directory Listing
Modified Fri Apr 7 14:49:02 2006 UTC (10 years, 5 months ago) by duarte
KEYMASTERDB had value for testing, change that back.
Revision 69 - Directory Listing
Modified Fri Apr 7 14:44:08 2006 UTC (10 years, 5 months ago) by duarte
Added method insertIdsToKeyMaster
Added call to the new insertIdsToKeyMaster in splitTableToCluster method
Revision 68 - Directory Listing
Modified Fri Apr 7 13:26:05 2006 UTC (10 years, 5 months ago) by duarte
Added another clusterExecuteQuery method to take a HashMap of queries rather than only one.
To be used in cases where the queries to be sent to nodes are different for each node (like in load/dump methods of this class)
Right now strictly serial must paralelize it as with the other clusterExecuteQuery
Revision 67 - Directory Listing
Modified Fri Apr 7 12:59:18 2006 UTC (10 years, 5 months ago) by duarte
Modified methods getAllIdxAndClients and getAllIdxFromMaster.
They return now:
- getAllIdxAndClients: an int[]
- getAllIdxFromMaster: a HashMap<Integer,String>
Got rid of having ResultSets returned which is very messy and dangerous.
Revision 66 - Directory Listing
Modified Fri Apr 7 09:31:08 2006 UTC (10 years, 5 months ago) by duarte
Made MASTER final static variable also public. It is in use by other classes.
Revision 65 - Directory Listing
Modified Fri Apr 7 09:26:03 2006 UTC (10 years, 5 months ago) by duarte
Initial commit of DataDistribution.java into aglappe repository
Copied from repository scripts-jose rev 69
If want to have a look at previous history must do it from repository scripts-jose, there was no way of copying with history between different repositories
Revision 64 - Directory Listing
Modified Thu Apr 6 14:47:09 2006 UTC (10 years, 5 months ago) by duarte
Added method getCreateIndex4Table
Revision 63 - Directory Listing
Modified Thu Apr 6 12:18:18 2006 UTC (10 years, 5 months ago) by duarte
Fixed bug in getAllIndexes4Table, the SELECT needed a DISTINCT
Revision 62 - Directory Listing
Modified Thu Apr 6 12:15:37 2006 UTC (10 years, 5 months ago) by duarte
Got rid of method dbExists. Was useless and not working.
Revision 61 - Directory Listing
Modified Thu Apr 6 10:07:22 2006 UTC (10 years, 5 months ago) by duarte
Added method setSqlMode, to set sql_mode server variable
Revision 60 - Directory Listing
Modified Thu Apr 6 09:24:28 2006 UTC (10 years, 5 months ago) by duarte
Added method dbExists to check whether database exists in server, used in constructor that passes a dbName
Moved all the private methods to the beginning of methods section
Revision 59 - Directory Listing
Modified Thu Apr 6 08:24:15 2006 UTC (10 years, 5 months ago) by duarte
Changed comments in constructors
Changed in method readConnectionFile:
- variable to count mandatory parameters to paramCount
- number of mandatory parameters now 4, dbname is also mandatory
Revision 58 - Directory Listing
Modified Wed Apr 5 08:45:23 2006 UTC (10 years, 5 months ago) by duarte
Now executeSQL method throws exception instead of catching it. Thought it was better than the calling class deals with these exceptions.
Revision 57 - Directory Listing
Modified Wed Apr 5 07:38:32 2006 UTC (10 years, 5 months ago) by duarte
Added getConnectionObject
Added printDbSizeInfo and 2 getRange methods from utils4DB
Made private the loadMySQLDriver and readConnectionFile methods

Revision 56 - Directory Listing
Modified Tue Apr 4 17:27:58 2006 UTC (10 years, 5 months ago) by filippis
execUpdateQuery method added and code in comments was removed
Revision 55 - Directory Listing
Modified Tue Apr 4 15:27:49 2006 UTC (10 years, 5 months ago) by duarte
Initial commit.
Class to create a connection to mysql db with basic functionality.
Cann take parameters for connection as argument in constructor or from connection file (passing the filename to the constructor)
Using code from both DBConnection (henning) and mySQLConnect (ioannis)
Revision 54 - Directory Listing
Modified Wed Mar 29 14:26:03 2006 UTC (10 years, 5 months ago) by stehr
initial import
Revision 53 - Directory Listing
Modified Wed Mar 29 13:01:40 2006 UTC (10 years, 5 months ago) by duarte
Fixed a bug with setKeyDb method, was not actually working:
 as well as setting the MASTERDB string needed to change connection to master database to point to new db!
From now on take care if setKeyDb is used in another class. It will open another master connection, thus master connection won't be always the same during the run of the program
Revision 52 - Directory Listing
Modified Wed Mar 29 12:49:13 2006 UTC (10 years, 5 months ago) by duarte
Changed error message printed in getHostId4Idx
Revision 51 - Directory Listing
Modified Wed Mar 29 12:29:56 2006 UTC (10 years, 5 months ago) by duarte
Added setKeyDb method, to be used in testing, i.e. with this method we can change from another class the default MASTERDB database.
Revision 50 - Directory Listing
Modified Tue Mar 28 15:05:31 2006 UTC (10 years, 6 months ago) by filippis
More examples added and the current ones modified according to Graph2Pml changes
Revision 49 - Directory Listing
Modified Tue Mar 28 15:04:24 2006 UTC (10 years, 6 months ago) by filippis
More flexibility in coloring, popDefaults/setDefaults methods plus comments
Revision 48 - Directory Listing
Modified Tue Mar 28 15:03:32 2006 UTC (10 years, 6 months ago) by filippis
Refresh method added plus refresh added before saving image
Revision 47 - Directory Listing
Modified Mon Mar 27 21:01:06 2006 UTC (10 years, 6 months ago) by filippis
Added cgo functionality/examples in Graph2Pml and testGraph2Pml
Revision 46 - Directory Listing
Modified Mon Mar 27 20:59:42 2006 UTC (10 years, 6 months ago) by filippis
PyMol class: adding refresh in saveImage methods
Revision 45 - Directory Listing
Modified Mon Mar 27 16:32:22 2006 UTC (10 years, 6 months ago) by filippis
Graph2Pymol class now functional
testGraph2Pymol class now functional with comments also
PyMol class:python strings methods and removeList, concatList, refresh methods added
Machine class: indentation
Revision 44 - Directory Listing
Modified Wed Mar 22 17:14:01 2006 UTC (10 years, 6 months ago) by filippis
In PyMol class, objectNameQuotes class variable is replaced by the method parameter called variable. Graph2Pml is modified accrodingly.
Revision 43 - Directory Listing
Modified Wed Mar 22 09:30:40 2006 UTC (10 years, 6 months ago) by duarte
Added executeSql method
Revision 42 - Directory Listing
Modified Tue Mar 21 19:13:20 2006 UTC (10 years, 6 months ago) by filippis
Adding Graph2Pml and testGraph2Pml classes (non functional code!)
Revision 41 - Directory Listing
Modified Tue Mar 21 18:41:48 2006 UTC (10 years, 6 months ago) by filippis
getRange methods now return double array instead of Float array. Previous code is into comments.
Revision 40 - Directory Listing
Modified Tue Mar 21 18:21:00 2006 UTC (10 years, 6 months ago) by filippis
Adding Msdsd2Pdb and PyMol classes
Revision 39 - Directory Listing
Modified Tue Mar 21 17:21:54 2006 UTC (10 years, 6 months ago) by filippis
Adding comments
Revision 38 - Directory Listing
Modified Mon Mar 20 11:37:12 2006 UTC (10 years, 6 months ago) by duarte
Added getAllIdxAndClients method:
gets all ids and client_names for a certain key
Revision 37 - Directory Listing
Modified Fri Mar 17 11:22:19 2006 UTC (10 years, 6 months ago) by duarte
Some changes in error messages to be more clear.
Revision 36 - Directory Listing
Modified Fri Mar 17 11:03:15 2006 UTC (10 years, 6 months ago) by duarte
Now using constructor without key and createStatement with key, since createStatement without key is not allowed anymore (is now private)
Revision 35 - Directory Listing
Modified Fri Mar 17 11:00:33 2006 UTC (10 years, 6 months ago) by duarte
Clean up a bit and added some more comments
Revision 34 - Directory Listing
Modified Fri Mar 17 10:48:03 2006 UTC (10 years, 6 months ago) by duarte
Refactor some method names to be more consistent.
Changed some fields to be final (and uppercase them)
Added comments for the most importat methods
Made the createStatment(idx) method private, this should only be used internally. Would be dangerous to use it from anothe class.
Revision 33 - Directory Listing
Modified Wed Mar 15 11:58:24 2006 UTC (10 years, 6 months ago) by duarte
Changed all error printing in catches to STDERR instead of STDOUT
Revision 32 - Directory Listing
Modified Tue Mar 14 09:45:57 2006 UTC (10 years, 6 months ago) by duarte
New exec method taking only a String argument wasn't working. Fixed the bug.
Revision 31 - Directory Listing
Modified Tue Mar 14 07:40:32 2006 UTC (10 years, 6 months ago) by duarte
Added exec method to take only a string as argument.
Revision 30 - Directory Listing
Modified Fri Mar 10 15:19:32 2006 UTC (10 years, 6 months ago) by stehr
introduced generics, so class will compile in Java 5, not sure though whether the functionality is the same as before, will need more testing
Revision 29 - Directory Listing
Modified Fri Mar 10 10:57:12 2006 UTC (10 years, 6 months ago) by stehr
changed server port to standard
Revision 28 - Directory Listing
Modified Fri Mar 10 10:56:22 2006 UTC (10 years, 6 months ago) by stehr
prevent overlong commands from being sent to the server
Revision 27 - Directory Listing
Modified Thu Mar 9 17:12:43 2006 UTC (10 years, 6 months ago) by stehr
initial import
Revision 26 - Directory Listing
Modified Thu Mar 9 15:55:56 2006 UTC (10 years, 6 months ago) by stehr
fixed bug for very long command strings (> 255 characters)
Revision 25 - Directory Listing
Modified Thu Mar 9 10:11:16 2006 UTC (10 years, 6 months ago) by stehr

Revision 24 - Directory Listing
Modified Thu Mar 9 10:08:44 2006 UTC (10 years, 6 months ago) by stehr
moved executables (classes with main function) to root directory
Revision 23 - Directory Listing
Modified Wed Mar 8 15:25:45 2006 UTC (10 years, 6 months ago) by duarte
Fixed important bug:
- now closing nCon connection before opening a new one in the setHost method.
- this is important. Before lots of connection were left opened after having used the ClusterConnection object
Revision 22 - Directory Listing
Modified Tue Mar 7 13:22:37 2006 UTC (10 years, 6 months ago) by duarte
Fixed bug in getIdxSet method. Wasn't reading properly the index_matrix table into the array. Was starting from columnn 1 which actually is the serial column. Now starting from column 2.
Revision 21 - Directory Listing
Modified Tue Mar 7 11:50:37 2006 UTC (10 years, 6 months ago) by duarte
New method int[][] getIdxSet. 
- Returns a 2-dimensional array with all indices for a certain key.
- Each column j corresponds to client_id j+1
- Each row i is a set of idx values for each of the client_ids. If there is no idx for a certain client_id then the value is 0.

Revision 20 - Directory Listing
Modified Mon Mar 6 15:19:40 2006 UTC (10 years, 6 months ago) by stehr
updated commentary
Revision 19 - Directory Listing
Modified Mon Mar 6 15:15:57 2006 UTC (10 years, 6 months ago) by stehr
deleted, file was a copy of makenbhtable.java, original file was lost
Revision 18 - Directory Listing
Modified Mon Mar 6 15:03:46 2006 UTC (10 years, 6 months ago) by stehr
initial import

Revision 17 - Directory Listing
Modified Mon Mar 6 09:20:16 2006 UTC (10 years, 6 months ago) by duarte
Grouped all the setIdxColumn and setMasterTable into setKey.
Also rationalised a bit the constructors by calling one from the other.
Revision 16 - Directory Listing
Modified Mon Mar 6 08:32:55 2006 UTC (10 years, 6 months ago) by duarte
Added package tools.
Revision 15 - Directory Listing
Modified Mon Mar 6 08:25:22 2006 UTC (10 years, 6 months ago) by duarte
Initial commit of the ClusterConnection class + small test class to test it out.

Revision 14 - Directory Listing
Modified Mon Mar 6 08:05:31 2006 UTC (10 years, 6 months ago) by stehr
removed ununsed imports and variables
Revision 13 - Directory Listing
Modified Fri Mar 3 15:15:31 2006 UTC (10 years, 6 months ago) by filippis
Adding SystemCmd class
Revision 12 - Directory Listing
Modified Thu Mar 2 17:21:28 2006 UTC (10 years, 6 months ago) by stehr
removed some debug code

Revision 11 - Directory Listing
Modified Thu Mar 2 15:42:09 2006 UTC (10 years, 6 months ago) by stehr
Corrected some bad mistake

Revision 10 - Directory Listing
Modified Thu Mar 2 11:42:06 2006 UTC (10 years, 6 months ago) by stehr
Initial commit of the remote-pymol-from-java stuff

Revision 9 - Directory Listing
Modified Tue Feb 14 11:00:40 2006 UTC (10 years, 7 months ago) by filippis
Adding R class
Revision 8 - Directory Listing
Modified Mon Jan 23 09:20:44 2006 UTC (10 years, 8 months ago) by duarte
Deleted old tools.trunk files
Revision 7 - Directory Listing
Modified Mon Jan 23 09:19:47 2006 UTC (10 years, 8 months ago) by duarte
Moved everything to subdir tools, so that we keep the tools name for the package. Also changed the package name in the files to tools. To work with it please check out only file:///.../svn/tools/trunk/tools
Revision 6 - Directory Listing
Modified Wed Jan 18 19:07:41 2006 UTC (10 years, 8 months ago) by filippis
Adding getDbSizeInfo method into utils4DB program
Revision 5 - Directory Listing
Modified Wed Jan 18 18:52:48 2006 UTC (10 years, 8 months ago) by filippis
Adding files utils*
Revision 4 - Directory Listing
Modified Wed Jan 18 18:49:01 2006 UTC (10 years, 8 months ago) by filippis
Package tools changed to tools.trunk because code could not compile!
Revision 3 - Directory Listing
Modified Wed Jan 18 18:23:39 2006 UTC (10 years, 8 months ago) by filippis
The name of the report table can be passed as argument now (default value is report as previous)
Revision 2 - Directory Listing
Modified Wed Jan 18 18:10:10 2006 UTC (10 years, 8 months ago) by filippis
Comments in system.out.println & Dealing with no password cases
Revision 1 - Directory Listing
Added Wed Jan 18 17:48:52 2006 UTC (10 years, 8 months ago) by filippis
Initial import of tools