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Revision 1647 - Directory Listing
Modified Thu Jul 4 08:39:06 2013 UTC (6 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 (6 years, 2 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 (6 years, 2 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 (6 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 (6 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 (6 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 (6 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 1639 - Directory Listing
Modified Tue Apr 16 12:17:08 2013 UTC (6 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 1637 - Directory Listing
Modified Wed Mar 20 09:47:07 2013 UTC (6 years, 6 months ago) by jmduarteg
Minor javadoc improvement
Revision 1636 - Directory Listing
Modified Mon Mar 18 14:06:43 2013 UTC (6 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 (6 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 (6 years, 6 months ago) by jmduarteg
Introduced a check to see if pisa server returns data or not
Revision 1632 - Directory Listing
Modified Tue Feb 26 13:37:13 2013 UTC (6 years, 6 months ago) by jmduarteg
Now sorting the mappings in the order they happen in the PDB chain
Revision 1630 - Directory Listing
Modified Fri Feb 15 11:54:22 2013 UTC (6 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 (6 years, 7 months ago) by nikhilbiyani
Removed Warnings from SiftsConnection
Revision 1628 - Directory Listing
Modified Thu Feb 14 10:28:18 2013 UTC (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 years, 7 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 (6 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 (6 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 (6 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 1599 - Directory Listing
Modified Fri Nov 16 10:02:32 2012 UTC (6 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 (6 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 (6 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 1595 - Directory Listing
Modified Sun Nov 4 19:36:53 2012 UTC (6 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 (6 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 (6 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 (6 years, 11 months ago) by jmduarteg
Another element
Revision 1591 - Directory Listing
Modified Wed Oct 3 14:57:46 2012 UTC (6 years, 11 months ago) by jmduarteg
New element added
Revision 1590 - Directory Listing
Modified Mon Oct 1 16:08:49 2012 UTC (6 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 (6 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 (6 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 (7 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 (7 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 (7 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 (7 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 (7 years, 1 month ago) by jmduarteg
Made new CrystalTransform class serializable
Revision 1582 - Directory Listing
Modified Tue Aug 21 13:13:25 2012 UTC (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 1570 - Directory Listing
Modified Thu Aug 9 16:07:22 2012 UTC (7 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 (7 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 (7 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 (7 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 (7 years, 1 month ago) by jmduarteg
Adding another atom type
Revision 1565 - Directory Listing
Modified Wed Jul 25 16:31:48 2012 UTC (7 years, 1 month 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 (7 years, 1 month ago) by jmduarteg
Minor fixes in entropy calculation
Revision 1563 - Directory Listing
Modified Fri Jun 22 08:39:56 2012 UTC (7 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 (7 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 (7 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 (7 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 (7 years, 4 months ago) by jmduarteg
Method to close the connection
Revision 1558 - Directory Listing
Modified Mon May 14 14:14:13 2012 UTC (7 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 (7 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 (7 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 years, 4 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 (7 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 1547 - Directory Listing
Modified Thu Mar 15 16:43:01 2012 UTC (7 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 (7 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 (7 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 (7 years, 6 months ago) by jmduarteg
Changed how uniprotver is read
Revision 1543 - Directory Listing
Modified Thu Mar 1 18:23:02 2012 UTC (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 years, 6 months ago) by jmduarteg
Changed naming convention of uniprot db/tables
Revision 1536 - Directory Listing
Modified Fri Feb 24 17:23:03 2012 UTC (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 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 (7 years, 6 months ago) by jmduarteg
Some refactoring
Revision 1529 - Directory Listing
Modified Wed Feb 22 17:07:14 2012 UTC (7 years, 7 months ago) by jmduarteg
A new parser for uniref xml files
Revision 1527 - Directory Listing
Modified Fri Feb 17 13:28:03 2012 UTC (7 years, 7 months ago) by jmduarteg
Added atom type
Revision 1526 - Directory Listing
Modified Fri Feb 17 09:59:08 2012 UTC (7 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 (7 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 (7 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 (7 years, 7 months ago) by jmduarteg
Implemented caching of alignment files
Revision 1522 - Directory Listing
Modified Tue Feb 7 08:58:41 2012 UTC (7 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 (7 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 (7 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 (7 years, 7 months ago) by jmduarteg
Improved the symmetry redundancy elimination test and added exclude list for a special case
Revision 1517 - Directory Listing
Modified Fri Jan 27 16:32:26 2012 UTC (7 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 (7 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 (7 years, 7 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 (7 years, 7 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 (7 years, 7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 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 (7 years, 9 months ago) by jmduarteg
New method to produce statistics of the sequence entropies variability
Revision 1501 - Directory Listing
Modified Tue Dec 6 11:02:46 2011 UTC (7 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 (7 years, 9 months ago) by jmduarteg
Switching off surface rendering
Revision 1499 - Directory Listing
Modified Mon Dec 5 15:57:36 2011 UTC (7 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 (7 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 (7 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 (7 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 (7 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 (7 years, 9 months ago) by jmduarteg
New method
Revision 1493 - Directory Listing
Modified Fri Nov 25 10:48:53 2011 UTC (7 years, 9 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 (7 years, 10 months ago) by jmduarteg
Improved the blast cache checking
Revision 1491 - Directory Listing
Modified Thu Nov 17 14:56:11 2011 UTC (7 years, 10 months ago) by jmduarteg
Now can pass option -v to blast (max number of hits reported)
Revision 1489 - Directory Listing
Modified Wed Nov 16 14:26:57 2011 UTC (7 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 (7 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 (7 years, 10 months ago) by jmduarteg
More logging
Revision 1486 - Directory Listing
Modified Wed Nov 16 08:20:28 2011 UTC (7 years, 10 months ago) by jmduarteg
Now blasting against uniref also supported in UniprotHomologList
Revision 1484 - Directory Listing
Modified Fri Nov 11 16:06:07 2011 UTC (7 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 (7 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 (7 years, 10 months ago) by jmduarteg
Now we consider pisa gray predictions as well
Revision 1480 - Directory Listing
Modified Tue Oct 18 08:43:32 2011 UTC (7 years, 11 months ago) by jmduarteg
Minor fix
Revision 1479 - Directory Listing
Modified Fri Oct 14 09:26:13 2011 UTC (7 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 (7 years, 11 months ago) by jmduarteg
New feature: pisa assembly parsing
Revision 1477 - Directory Listing
Modified Thu Oct 6 13:10:49 2011 UTC (7 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 (7 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 (7 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 (7 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 (7 years, 11 months ago) by jmduarteg
A few more atom types
Revision 1472 - Directory Listing
Modified Wed Sep 28 15:06:19 2011 UTC (7 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 (8 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 (8 years ago) by jmduarteg
Removing some fields to do with zooming and refactoring
Revision 1468 - Directory Listing
Modified Wed Sep 7 16:15:49 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 years ago) by jmduarteg
New methods for transforming vectors to orthonormal or to crystal basis
Revision 1462 - Directory Listing
Modified Tue Aug 30 16:20:36 2011 UTC (8 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 (8 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 (8 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 (8 years ago) by jmduarteg
New method to get the chain2repchain map
Revision 1458 - Directory Listing
Modified Wed Aug 24 14:43:45 2011 UTC (8 years, 1 month ago) by jmduarteg
Adapted to changes in PymolRunner
Revision 1457 - Directory Listing
Modified Wed Aug 24 13:30:58 2011 UTC (8 years, 1 month ago) by jmduarteg
Some more modified aminoacids
Revision 1456 - Directory Listing
Modified Mon Aug 22 14:52:42 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 years, 1 month ago) by jmduarteg
Another peptide-linked HET residue
Revision 1449 - Directory Listing
Modified Fri Aug 19 12:38:59 2011 UTC (8 years, 1 month ago) by jmduarteg
New method getBSA
Revision 1448 - Directory Listing
Modified Thu Aug 18 15:23:57 2011 UTC (8 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 (8 years, 1 month ago) by jmduarteg
Removing duplicate entry
Revision 1446 - Directory Listing
Modified Thu Aug 18 10:55:24 2011 UTC (8 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 (8 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 (8 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 (8 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 1435 - Directory Listing
Modified Tue Aug 16 16:03:09 2011 UTC (8 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 1432 - Directory Listing
Modified Fri Aug 5 14:44:41 2011 UTC (8 years, 1 month ago) by jmduarteg
New element
Revision 1431 - Directory Listing
Modified Mon Aug 1 15:04:21 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 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 (8 years, 3 months ago) by jmduarteg
Two more atom types
Revision 1425 - Directory Listing
Modified Tue Jun 21 10:49:33 2011 UTC (8 years, 3 months ago) by jmduarteg
Another atom type
Revision 1424 - Directory Listing
Modified Mon Jun 20 14:35:43 2011 UTC (8 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 (8 years, 3 months ago) by jmduarteg
Another atom type
Revision 1422 - Directory Listing
Modified Mon Jun 20 12:11:06 2011 UTC (8 years, 3 months ago) by jmduarteg
New atom type
Revision 1421 - Directory Listing
Modified Thu Jun 16 16:57:37 2011 UTC (8 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 (8 years, 3 months ago) by jmduarteg
Adding element
Revision 1419 - Directory Listing
Modified Thu Jun 16 13:34:25 2011 UTC (8 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 1417 - Directory Listing
Modified Fri Jun 10 08:31:42 2011 UTC (8 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 (8 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 (8 years, 3 months ago) by jmduarteg
Better doc
Revision 1414 - Directory Listing
Modified Tue Jun 7 15:19:08 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 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 (8 years, 3 months ago) by jmduarteg
Fixed minor bug: was outputting duplicate TER records when writing ChainInterface PDB files.
Revision 1407 - Directory Listing
Modified Thu Jun 2 16:34:08 2011 UTC (8 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 (8 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 (8 years, 3 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 (8 years, 3 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 years, 4 months ago) by jmduarteg
Removed obsolete classes to analyse histone. Moved some useful methods for inertia moment calculation to GeometryTools
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 years, 5 months ago) by jmduarteg
Unzip method
Revision 1387 - Directory Listing
Modified Sun Apr 10 11:10:30 2011 UTC (8 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 (8 years, 5 months ago) by jmduarteg
Changed constant name after change in kraken api
Revision 1384 - Directory Listing
Modified Wed Apr 6 07:59:43 2011 UTC (8 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 (8 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 (8 years, 5 months ago) by jmduarteg
Documented the -t option 
Revision 1381 - Directory Listing
Modified Fri Apr 1 15:48:30 2011 UTC (8 years, 5 months ago) by jmduarteg
Improved javadocs
Revision 1380 - Directory Listing
Modified Fri Apr 1 07:53:32 2011 UTC (8 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 (8 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 (8 years, 5 months ago) by jmduarteg
More debug output
Revision 1377 - Directory Listing
Modified Thu Mar 31 09:11:08 2011 UTC (8 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 (8 years, 5 months ago) by jmduarteg
Another test
Revision 1375 - Directory Listing
Modified Thu Mar 31 07:41:36 2011 UTC (8 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 (8 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 (8 years, 5 months ago) by jmduarteg
Now PdbChain also implements Iterable
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (8 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 1370 - Directory Listing
Modified Tue Mar 29 18:29:16 2011 UTC (8 years, 5 months ago) by hstehr
Updated some JavaDocs
Revision 1367 - Directory Listing
Modified Mon Mar 28 17:49:23 2011 UTC (8 years, 5 months ago) by hstehr
Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
Revision 1363 - Directory Listing
Modified Mon Mar 28 16:35:43 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 years, 5 months ago) by jmduarteg
New option -d
Revision 1358 - Directory Listing
Modified Mon Mar 28 09:32:42 2011 UTC (8 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 (8 years, 5 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 (8 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 (8 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 (8 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 (8 years, 6 months ago) by jmduarteg
Optimised and simplified the geometric hashing algorithm implementation, now runs slightly faster.
Revision 1351 - Directory Listing
Modified Tue Mar 22 16:02:05 2011 UTC (8 years, 6 months ago) by hstehr
unnecessary codes removed
Revision 1350 - Directory Listing
Modified Tue Mar 22 15:51:13 2011 UTC (8 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 (8 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 (8 years, 6 months ago) by hstehr
adding some missing documentation
Revision 1347 - Directory Listing
Modified Mon Mar 21 10:38:06 2011 UTC (8 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 (8 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 (8 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 (8 years, 6 months ago) by hstehr

Revision 1343 - Directory Listing
Modified Wed Mar 16 18:29:19 2011 UTC (8 years, 6 months ago) by hstehr

Revision 1342 - Directory Listing
Modified Wed Mar 16 17:53:02 2011 UTC (8 years, 6 months ago) by hstehr

Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (8 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 (8 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 (8 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 (8 years, 6 months ago) by jmduarteg
Fixed bug. Pymol was blocking
Revision 1337 - Directory Listing
Modified Fri Mar 11 08:47:52 2011 UTC (8 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 (8 years, 6 months ago) by jmduarteg
New runner for pymol
Revision 1335 - Directory Listing
Modified Wed Mar 9 08:38:35 2011 UTC (8 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 (8 years, 6 months ago) by jmduarteg
Refactoring xxxError to xxxException
Revision 1333 - Directory Listing
Modified Tue Mar 8 18:21:32 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 1322 - Directory Listing
Modified Thu Feb 24 10:35:11 2011 UTC (8 years, 6 months ago) by hstehr
New method hasChain(String): boolean
Revision 1321 - Directory Listing
Modified Wed Feb 23 11:16:13 2011 UTC (8 years, 6 months ago) by jmduarteg
New enum for nucleotides
Revision 1320 - Directory Listing
Modified Wed Feb 23 10:45:32 2011 UTC (8 years, 6 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 (8 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 (8 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 (8 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 (8 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 (8 years, 7 months ago) by jmduarteg
Removed a now unused method
Revision 1314 - Directory Listing
Modified Wed Feb 9 11:36:04 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 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 1308 - Directory Listing
Modified Fri Jan 28 18:44:21 2011 UTC (8 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 (8 years, 7 months ago) by jmduarteg
Methods to serialize/deserialize from file ChainInterface
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (8 years, 7 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 (8 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 (8 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 1302 - Directory Listing
Modified Fri Jan 14 18:15:38 2011 UTC (8 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 (8 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 (8 years, 8 months ago) by jmduarteg
Better docs
Revision 1298 - Directory Listing
Modified Tue Jan 11 14:35:17 2011 UTC (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 years, 9 months ago) by cvehlow
Control database access! for CGAP
Revision 1291 - Directory Listing
Modified Fri Dec 17 16:38:25 2010 UTC (8 years, 9 months ago) by cvehlow
Control database access! for CGAP
Revision 1290 - Directory Listing
Modified Fri Dec 17 14:09:48 2010 UTC (8 years, 9 months ago) by cvehlow
add setParametersDB
Revision 1287 - Directory Listing
Modified Fri Dec 10 15:17:04 2010 UTC (8 years, 9 months ago) by matt4077

Revision 1286 - Directory Listing
Modified Fri Dec 10 11:34:13 2010 UTC (8 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 (8 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 (8 years, 9 months ago) by cvehlow
Overrides removed
Revision 1283 - Directory Listing
Modified Tue Nov 23 14:29:37 2010 UTC (8 years, 10 months ago) by jmduarteg
New getName method.
Revision 1282 - Directory Listing
Modified Thu Nov 18 09:24:15 2010 UTC (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 years, 10 months ago) by jmduarteg
More methods to report on interfaces clashes. Extracted clash distance constant.
Revision 1274 - Directory Listing
Modified Fri Oct 29 10:14:41 2010 UTC (8 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 (8 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 (8 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 (8 years, 10 months ago) by jmduarteg
New method to check clashes
Revision 1270 - Directory Listing
Modified Tue Oct 26 15:28:24 2010 UTC (8 years, 10 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 (8 years, 10 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 1260 - Directory Listing
Modified Fri Oct 8 15:00:58 2010 UTC (8 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 (8 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 (8 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 1256 - Directory Listing
Modified Thu Oct 7 17:04:32 2010 UTC (8 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 (8 years, 11 months ago) by jmduarteg
Minor changes to the test.
Revision 1254 - Directory Listing
Modified Thu Oct 7 08:38:10 2010 UTC (8 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 (8 years, 11 months ago) by jmduarteg
Some minor updates
Revision 1252 - Directory Listing
Modified Wed Oct 6 14:22:03 2010 UTC (8 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 (8 years, 11 months ago) by jmduarteg
Some more complete tests.
Revision 1250 - Directory Listing
Modified Mon Oct 4 16:23:26 2010 UTC (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (8 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 (9 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 (9 years ago) by hstehr
suppressing two warnings
Revision 1239 - Directory Listing
Modified Tue Sep 21 12:01:35 2010 UTC (9 years ago) by gmueller
sparse matrix exception
Revision 1238 - Directory Listing
Modified Tue Sep 21 09:43:32 2010 UTC (9 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 (9 years ago) by cvehlow
commit latest version
Revision 1236 - Directory Listing
Modified Mon Sep 13 11:03:14 2010 UTC (9 years ago) by cvehlow
variable 2D csv-files loadable
Revision 1235 - Directory Listing
Modified Fri Sep 10 14:39:45 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 years ago) by hstehr
Adding class PhosphoSiteConnection
Revision 1230 - Directory Listing
Modified Wed Sep 8 16:30:40 2010 UTC (9 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 (9 years ago) by jmduarteg
New method for finding identical sequences (entities)
Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 years ago) by cvehlow
added methods
Revision 1223 - Directory Listing
Modified Wed Sep 1 14:26:00 2010 UTC (9 years ago) by hstehr
updated classes for evaluating our CASP predictions
Revision 1222 - Directory Listing
Modified Wed Sep 1 14:23:40 2010 UTC (9 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 (9 years ago) by hstehr
updating annotations to get rid of warnings
Revision 1220 - Directory Listing
Modified Wed Sep 1 14:20:44 2010 UTC (9 years ago) by hstehr
deleting two classes which were making problems
Revision 1219 - Directory Listing
Modified Wed Sep 1 13:35:16 2010 UTC (9 years ago) by hstehr
added some javadoc
Revision 1218 - Directory Listing
Modified Wed Sep 1 13:02:18 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 years 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 (9 years 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 (9 years 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 (9 years 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 (9 years 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 1 month ago) by hstehr
renamed class benchmarkAll to createResultWebPages
Revision 1202 - Directory Listing
Modified Thu Aug 19 10:21:08 2010 UTC (9 years, 1 month ago) by hstehr
suppress "method not used" warning
Revision 1201 - Directory Listing
Modified Thu Aug 19 10:18:59 2010 UTC (9 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 (9 years, 1 month ago) by hstehr
removed some bad characters
Revision 1199 - Directory Listing
Modified Thu Aug 19 10:14:54 2010 UTC (9 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 (9 years, 1 month ago) by cvehlow
classes moved
Revision 1197 - Directory Listing
Modified Thu Aug 19 10:08:52 2010 UTC (9 years, 1 month ago) by hstehr
Adding some javadoc
Revision 1196 - Directory Listing
Modified Thu Aug 19 10:06:15 2010 UTC (9 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 (9 years, 1 month ago) by cvehlow
classes moved
Revision 1194 - Directory Listing
Modified Thu Aug 19 09:56:40 2010 UTC (9 years, 1 month ago) by cvehlow
classes moved
Revision 1193 - Directory Listing
Modified Thu Aug 19 09:46:03 2010 UTC (9 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 (9 years, 1 month ago) by jmduarteg
Committing test class for AICGraph
Revision 1191 - Directory Listing
Modified Thu Aug 12 15:18:44 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 1 month ago) by cvehlow
bug removed nullpointer?!
Revision 1182 - Directory Listing
Modified Wed Aug 11 10:17:32 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 years, 1 month ago) by cvehlow
actual methods 
Revision 1177 - Directory Listing
Modified Mon Aug 9 07:44:15 2010 UTC (9 years, 1 month ago) by cvehlow
actual version
Revision 1176 - Directory Listing
Modified Fri Aug 6 10:03:26 2010 UTC (9 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 (9 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 (9 years, 1 month ago) by jmduarteg
New method setChainCode
Revision 1173 - Directory Listing
Modified Wed Aug 4 15:27:40 2010 UTC (9 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 (9 years, 1 month ago) by jmduarteg
Now using apache commons logging
Revision 1171 - Directory Listing
Modified Wed Aug 4 10:47:28 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 1 month ago) by cvehlow
slight changes
Revision 1159 - Directory Listing
Modified Fri Jul 23 14:56:35 2010 UTC (9 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 (9 years, 2 months ago) by cvehlow
print function
Revision 1157 - Directory Listing
Modified Wed Jul 7 15:31:14 2010 UTC (9 years, 2 months ago) by jmduarteg
Fixed bug, wasn't computing the nucleotide alignment correctly (was missing the last codon)
Revision 1155 - Directory Listing
Modified Wed Jul 7 13:15:06 2010 UTC (9 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 (9 years, 2 months ago) by jmduarteg
And all other amiguous codons
Revision 1153 - Directory Listing
Modified Wed Jul 7 08:46:37 2010 UTC (9 years, 2 months ago) by jmduarteg
Another ambiguous nucleotide letter
Revision 1151 - Directory Listing
Modified Tue Jul 6 16:58:04 2010 UTC (9 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 (9 years, 2 months ago) by cvehlow
PrintOut method ion RIGGeometry
Revision 1149 - Directory Listing
Modified Mon Jul 5 16:46:57 2010 UTC (9 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 (9 years, 2 months ago) by jmduarteg
New removeRedundancy method
Revision 1147 - Directory Listing
Modified Mon Jul 5 08:35:15 2010 UTC (9 years, 2 months ago) by jmduarteg
Implemented logging with log4j library
Revision 1146 - Directory Listing
Modified Fri Jul 2 09:54:46 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 2 months ago) by cvehlow
methods by saurabh included
Revision 1140 - Directory Listing
Modified Tue Jun 29 08:49:34 2010 UTC (9 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 (9 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 (9 years, 2 months ago) by cvehlow
Getter for Atoms-TreeMap.
Revision 1137 - Directory Listing
Modified Mon Jun 28 13:38:32 2010 UTC (9 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 (9 years, 2 months ago) by jmduarteg
New ambiguous nucleotide w.
Revision 1135 - Directory Listing
Modified Fri Jun 25 13:40:27 2010 UTC (9 years, 2 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1134 - Directory Listing
Modified Fri Jun 25 13:39:57 2010 UTC (9 years, 2 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1133 - Directory Listing
Modified Fri Jun 25 13:36:03 2010 UTC (9 years, 2 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 (9 years, 2 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 (9 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 (9 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 (9 years, 3 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1128 - Directory Listing
Modified Wed Jun 23 10:23:44 2010 UTC (9 years, 3 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (9 years, 3 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1126 - Directory Listing
Modified Tue Jun 22 12:19:07 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 years, 3 months ago) by jmduarteg
Some refactoring
Revision 1121 - Directory Listing
Modified Fri Jun 18 16:02:55 2010 UTC (9 years, 3 months ago) by jmduarteg
Now implementing HasFeatures
Revision 1120 - Directory Listing
Modified Fri Jun 18 13:29:34 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 3 months ago) by cvehlow
Changes in edge-cluster direction!
Revision 1114 - Directory Listing
Modified Wed Jun 16 10:26:22 2010 UTC (9 years, 3 months ago) by jmduarteg
New feature: code for dna to protein translation
Revision 1112 - Directory Listing
Modified Tue Jun 15 08:44:52 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 years, 3 months ago) by jmduarteg
Now parsing the symmetry operators.
Revision 1107 - Directory Listing
Modified Thu Jun 10 10:20:35 2010 UTC (9 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 (9 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 (9 years, 3 months ago) by jmduarteg
Our own copy file method! :-)
Revision 1104 - Directory Listing
Modified Wed Jun 9 17:04:36 2010 UTC (9 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 (9 years, 3 months ago) by jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision 1102 - Directory Listing
Modified Wed Jun 9 14:59:42 2010 UTC (9 years, 3 months ago) by cvehlow
Cluster-edge direction evaluated.
Revision 1101 - Directory Listing
Modified Wed Jun 9 09:26:27 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 3 months ago) by jmduarteg
Minor doc fix
Revision 1095 - Directory Listing
Modified Wed Jun 2 15:06:46 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 3 months ago) by matt4077
little contact map example done
Revision 1089 - Directory Listing
Modified Tue Jun 1 11:14:05 2010 UTC (9 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 (9 years, 3 months ago) by cvehlow
max number of traces
Revision 1087 - Directory Listing
Modified Mon May 31 15:41:25 2010 UTC (9 years, 3 months ago) by jmduarteg
Improved the getRimAndCore method
Revision 1086 - Directory Listing
Modified Mon May 31 15:41:16 2010 UTC (9 years, 3 months ago) by cvehlow
Extract maximum number of traces!
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (9 years, 3 months ago) by jmduarteg
Some new methods
Revision 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (9 years, 3 months ago) by matt4077
renamed  conflicting ContactMap class.
Revision 1083 - Directory Listing
Modified Mon May 31 13:31:23 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 3 months ago) by jmduarteg
Now parsing the seq_num residue number.
Revision 1077 - Directory Listing
Modified Thu May 27 09:51:50 2010 UTC (9 years, 3 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 1075 - Directory Listing
Modified Fri May 21 17:33:34 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 4 months ago) by cvehlow
HandOverThetaPhiRanges
Revision 1067 - Directory Listing
Modified Wed May 12 16:36:24 2010 UTC (9 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 (9 years, 4 months ago) by hstehr
new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
Revision 1064 - Directory Listing
Modified Tue May 11 14:57:20 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 4 months ago) by jmduarteg
Fixed java doc
Revision 1058 - Directory Listing
Modified Mon May 3 16:57:21 2010 UTC (9 years, 4 months ago) by cvehlow
Load from zip-file!
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (9 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 (9 years, 4 months ago) by stehr
New example implementation of ResidueContactScoringFunction
Revision 1055 - Directory Listing
Modified Wed Apr 28 15:08:53 2010 UTC (9 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 (9 years, 4 months ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (9 years, 4 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 (9 years, 4 months ago) by jmduarteg
Minor fix to java docs
Revision 1050 - Directory Listing
Modified Tue Apr 27 12:39:52 2010 UTC (9 years, 4 months ago) by cvehlow
Load precalc sphoxel data if possible.
Revision 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (9 years, 4 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 (9 years, 4 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 (9 years, 4 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 (9 years, 4 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 (9 years, 4 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 (9 years, 4 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 5 months ago) by cvehlow
Faster SQL queries
Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (9 years, 5 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1026 - Directory Listing
Modified Thu Apr 15 15:28:29 2010 UTC (9 years, 5 months ago) by cvehlow
changes
Revision 1025 - Directory Listing
Modified Thu Apr 15 09:28:23 2010 UTC (9 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 (9 years, 5 months ago) by cvehlow

Revision 1023 - Directory Listing
Modified Tue Apr 13 17:14:22 2010 UTC (9 years, 5 months ago) by cvehlow
FloatPairSet first commit
Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 5 months ago) by matt4077
resolving conflicts
Revision 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 5 months ago) by hstehr
starting refactoring: first creating packages owl and owl.core
Revision 1002 - Directory Listing
Modified Tue Mar 30 11:22:07 2010 UTC (9 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 (9 years, 5 months ago) by gmueller
latest version of gabriel
Revision 1000 - Directory Listing
Modified Mon Mar 29 10:20:38 2010 UTC (9 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 (9 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 (9 years, 5 months ago) by jmduarteg
Minor refactoring and comment fixes
Revision 997 - Directory Listing
Modified Mon Mar 29 09:41:31 2010 UTC (9 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 (9 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 (9 years, 6 months ago) by jmduarteg
Removed the executable property
Revision 994 - Directory Listing
Modified Wed Mar 24 15:09:16 2010 UTC (9 years, 6 months ago) by hstehr
new method AminoAcid.valuesInOrderOfHydrophobicity()
Revision 989 - Directory Listing
Modified Fri Mar 19 09:00:00 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 6 months ago) by hstehr
Introducing new StructuralDomainFeature for structural domains as defined by SCOP, CATH, DomainParser etc.
Revision 977 - Directory Listing
Modified Tue Feb 23 17:41:08 2010 UTC (9 years, 6 months ago) by duarte
Better error message for no tinker paths set up
Revision 973 - Directory Listing
Modified Tue Feb 23 14:32:00 2010 UTC (9 years, 6 months ago) by duarte
Moving the CASP project into OWL as the casp package.
Revision 970 - Directory Listing
Modified Tue Feb 23 11:47:05 2010 UTC (9 years, 6 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 (9 years, 6 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 (9 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 965 - Directory Listing
Modified Thu Feb 18 15:25:10 2010 UTC (9 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 (9 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 (9 years, 7 months ago) by gmueller
some new classes
Revision 962 - Directory Listing
Modified Tue Feb 16 11:51:18 2010 UTC (9 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 (9 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 (9 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 (9 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 (9 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 (9 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 (9 years, 7 months ago) by duarte
Removed some obsolete classes.
Revision 955 - Directory Listing
Modified Tue Feb 9 10:44:24 2010 UTC (9 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 (9 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 (9 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 (9 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
Added Fri Jan 29 16:12:34 2010 UTC (9 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.