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Revision 1643 - Directory Listing
Modified Mon Jun 17 12:46:07 2013 UTC (8 years, 11 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 1641 - Directory Listing
Modified Thu Jun 13 09:21:02 2013 UTC (8 years, 11 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 (9 years, 1 month 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 1627 - Directory Listing
Modified Thu Feb 14 09:54:54 2013 UTC (9 years, 3 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 (9 years, 3 months ago) by jmduarteg
Another small fix related to last commit
Revision 1625 - Directory Listing
Modified Wed Feb 13 15:57:04 2013 UTC (9 years, 3 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 (9 years, 3 months ago) by nikhilbiyani
Added AtomTypes till atomic number 110
Revision 1623 - Directory Listing
Modified Wed Feb 13 11:54:40 2013 UTC (9 years, 3 months ago) by nikhilbiyani
Bugfix: Check for nulls while reading QParams.
Revision 1622 - Directory Listing
Modified Mon Feb 11 10:57:00 2013 UTC (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 months ago) by nikhilbiyani
BugFix: Included the possibility of cell parameters being non double values.
Revision 1615 - Directory Listing
Modified Wed Jan 30 16:09:43 2013 UTC (9 years, 3 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 1613 - Directory Listing
Modified Wed Jan 30 09:25:07 2013 UTC (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 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 (9 years, 3 months ago) by jmduarteg
Adding new elements found after a sample of 10000 random pdb entries
Revision 1592 - Directory Listing
Modified Thu Oct 4 13:47:37 2012 UTC (9 years, 7 months ago) by jmduarteg
Another element
Revision 1591 - Directory Listing
Modified Wed Oct 3 14:57:46 2012 UTC (9 years, 7 months ago) by jmduarteg
New element added
Revision 1590 - Directory Listing
Modified Mon Oct 1 16:08:49 2012 UTC (9 years, 7 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 1588 - Directory Listing
Modified Thu Sep 27 13:26:00 2012 UTC (9 years, 7 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 (9 years, 8 months ago) by jmduarteg
Now using a minimum threshold value for considering a residue at surface (instead of 0 before)
Revision 1583 - Directory Listing
Modified Tue Aug 21 15:29:27 2012 UTC (9 years, 8 months ago) by jmduarteg
Made new CrystalTransform class serializable
Revision 1582 - Directory Listing
Modified Tue Aug 21 13:13:25 2012 UTC (9 years, 8 months 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 (9 years, 8 months 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 (9 years, 8 months 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 (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months 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 1569 - Directory Listing
Modified Thu Aug 9 15:47:45 2012 UTC (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months 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 (9 years, 9 months ago) by jmduarteg
Adding another atom type
Revision 1563 - Directory Listing
Modified Fri Jun 22 08:39:56 2012 UTC (9 years, 10 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 (9 years, 11 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 (9 years, 11 months ago) by jmduarteg
New method to calculate contact order
Revision 1550 - Directory Listing
Modified Mon Apr 16 15:52:28 2012 UTC (10 years, 1 month 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 1545 - Directory Listing
Modified Wed Mar 14 13:41:58 2012 UTC (10 years, 2 months ago) by jmduarteg
Better docs and clean up of core/rim calculation code
Revision 1527 - Directory Listing
Modified Fri Feb 17 13:28:03 2012 UTC (10 years, 3 months ago) by jmduarteg
Added atom type
Revision 1526 - Directory Listing
Modified Fri Feb 17 09:59:08 2012 UTC (10 years, 3 months ago) by jmduarteg
Now printing warnings if Hydrogens present when calculating interfaces
Revision 1521 - Directory Listing
Modified Mon Feb 6 17:00:30 2012 UTC (10 years, 3 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 1515 - Directory Listing
Modified Thu Jan 26 09:41:51 2012 UTC (10 years, 3 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 (10 years, 3 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 (10 years, 3 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 (10 years, 3 months ago) by jmduarteg
Fixed bug: was not setting the transl member of ChainInterface
Revision 1510 - Directory Listing
Modified Mon Dec 19 16:03:42 2011 UTC (10 years, 5 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 (10 years, 5 months ago) by jmduarteg
Now producing space group algebraic strings with fractions
Revision 1501 - Directory Listing
Modified Tue Dec 6 11:02:46 2011 UTC (10 years, 5 months ago) by jmduarteg
Fixed minor issue: now specifying what we print in tabular info
Revision 1496 - Directory Listing
Modified Wed Nov 30 13:39:15 2011 UTC (10 years, 5 months ago) by jmduarteg
New method for getting sequence with MSEs as METs
Revision 1494 - Directory Listing
Modified Tue Nov 29 18:00:50 2011 UTC (10 years, 5 months ago) by jmduarteg
New method
Revision 1483 - Directory Listing
Modified Wed Nov 9 07:01:47 2011 UTC (10 years, 6 months ago) by jmduarteg
Fixed bug CRK-29: wasn't calculating interfaces for electron crystallography or neutron diffraction entries
Revision 1477 - Directory Listing
Modified Thu Oct 6 13:10:49 2011 UTC (10 years, 7 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 (10 years, 7 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 (10 years, 7 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 (10 years, 7 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 (10 years, 7 months ago) by jmduarteg
A few more atom types
Revision 1472 - Directory Listing
Modified Wed Sep 28 15:06:19 2011 UTC (10 years, 7 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 (10 years, 8 months 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 (10 years, 8 months 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 (10 years, 8 months 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 1465 - Directory Listing
Modified Fri Sep 2 08:27:59 2011 UTC (10 years, 8 months 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 (10 years, 8 months 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 (10 years, 8 months 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 (10 years, 8 months 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 (10 years, 8 months 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 (10 years, 8 months ago) by jmduarteg
New method to get the chain2repchain map
Revision 1457 - Directory Listing
Modified Wed Aug 24 13:30:58 2011 UTC (10 years, 8 months ago) by jmduarteg
Some more modified aminoacids
Revision 1454 - Directory Listing
Modified Mon Aug 22 13:05:34 2011 UTC (10 years, 8 months ago) by jmduarteg
More features for PymolRunner to display fancy pymol interface representations
Revision 1452 - Directory Listing
Modified Fri Aug 19 14:46:44 2011 UTC (10 years, 9 months 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 (10 years, 9 months ago) by jmduarteg
Methods for asa and bsa of rim/core
Revision 1450 - Directory Listing
Modified Fri Aug 19 12:50:00 2011 UTC (10 years, 9 months ago) by jmduarteg
Another peptide-linked HET residue
Revision 1449 - Directory Listing
Modified Fri Aug 19 12:38:59 2011 UTC (10 years, 9 months ago) by jmduarteg
New method getBSA
Revision 1448 - Directory Listing
Modified Thu Aug 18 15:23:57 2011 UTC (10 years, 9 months 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 1443 - Directory Listing
Modified Thu Aug 18 08:50:54 2011 UTC (10 years, 9 months 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 1432 - Directory Listing
Modified Fri Aug 5 14:44:41 2011 UTC (10 years, 9 months ago) by jmduarteg
New element
Revision 1431 - Directory Listing
Modified Mon Aug 1 15:04:21 2011 UTC (10 years, 9 months 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 (10 years, 9 months 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 (10 years, 10 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 (10 years, 10 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 (10 years, 10 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 (10 years, 10 months ago) by jmduarteg
Two more atom types
Revision 1425 - Directory Listing
Modified Tue Jun 21 10:49:33 2011 UTC (10 years, 10 months ago) by jmduarteg
Another atom type
Revision 1424 - Directory Listing
Modified Mon Jun 20 14:35:43 2011 UTC (10 years, 10 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 (10 years, 10 months ago) by jmduarteg
Another atom type
Revision 1422 - Directory Listing
Modified Mon Jun 20 12:11:06 2011 UTC (10 years, 11 months ago) by jmduarteg
New atom type
Revision 1421 - Directory Listing
Modified Thu Jun 16 16:57:37 2011 UTC (10 years, 11 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 (10 years, 11 months ago) by jmduarteg
Adding element
Revision 1419 - Directory Listing
Modified Thu Jun 16 13:34:25 2011 UTC (10 years, 11 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 (10 years, 11 months ago) by jmduarteg
Some improvements and fixes to enumerateInterfaces
Revision 1416 - Directory Listing
Modified Thu Jun 9 18:46:06 2011 UTC (10 years, 11 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 (10 years, 11 months ago) by jmduarteg
Better doc
Revision 1410 - Directory Listing
Modified Mon Jun 6 08:52:03 2011 UTC (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 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 (10 years, 11 months ago) by jmduarteg
Minor fix: was not printing het residues in ChainInterface print methods.
Revision 1396 - Directory Listing
Modified Mon May 23 15:03:02 2011 UTC (10 years, 11 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 (11 years 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 (11 years 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 (11 years 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 1389 - Directory Listing
Modified Fri May 6 12:56:04 2011 UTC (11 years 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 1381 - Directory Listing
Modified Fri Apr 1 15:48:30 2011 UTC (11 years, 1 month ago) by jmduarteg
Improved javadocs
Revision 1378 - Directory Listing
Modified Thu Mar 31 09:13:13 2011 UTC (11 years, 1 month ago) by jmduarteg
More debug output
Revision 1375 - Directory Listing
Modified Thu Mar 31 07:41:36 2011 UTC (11 years, 1 month ago) by jmduarteg
Fixed bug in finding unique and rep chains.
Revision 1374 - Directory Listing
Modified Wed Mar 30 16:30:42 2011 UTC (11 years, 1 month ago) by jmduarteg
Adding Serializable interface to some classes
Revision 1373 - Directory Listing
Modified Wed Mar 30 10:23:48 2011 UTC (11 years, 1 month ago) by jmduarteg
Now PdbChain also implements Iterable
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (11 years, 1 month 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 (11 years, 1 month ago) by hstehr
Updated some JavaDocs
Revision 1367 - Directory Listing
Modified Mon Mar 28 17:49:23 2011 UTC (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month 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 (11 years, 1 month ago) by jmduarteg
Fixed bug: now caching bounds properly.
Revision 1360 - Directory Listing
Modified Mon Mar 28 10:21:06 2011 UTC (11 years, 1 month 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 1358 - Directory Listing
Modified Mon Mar 28 09:32:42 2011 UTC (11 years, 1 month ago) by jmduarteg
More optimisation on geometric hashing algorithm.
Revision 1356 - Directory Listing
Modified Fri Mar 25 14:59:41 2011 UTC (11 years, 1 month ago) by jmduarteg
More optimisation and simplification of geometric hashing algorithm. Runs very slightly faster.
Revision 1353 - Directory Listing
Modified Thu Mar 24 19:37:52 2011 UTC (11 years, 1 month ago) by jmduarteg
Optimised and simplified the geometric hashing algorithm implementation, now runs slightly faster.
Revision 1349 - Directory Listing
Modified Mon Mar 21 18:28:31 2011 UTC (11 years, 1 month 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 (11 years, 1 month ago) by hstehr
adding some missing documentation
Revision 1347 - Directory Listing
Modified Mon Mar 21 10:38:06 2011 UTC (11 years, 1 month ago) by hstehr
moving project CCCP to this repository
Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (11 years, 2 months ago) by jmduarteg
Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit
Revision 1333 - Directory Listing
Modified Tue Mar 8 18:21:32 2011 UTC (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 months ago) by jmduarteg
Some more atoms seen in pdb files
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (11 years, 2 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 (11 years, 2 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 (11 years, 2 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 (11 years, 2 months ago) by hstehr
New method hasChain(String): boolean
Revision 1321 - Directory Listing
Modified Wed Feb 23 11:16:13 2011 UTC (11 years, 2 months ago) by jmduarteg
New enum for nucleotides
Revision 1320 - Directory Listing
Modified Wed Feb 23 10:45:32 2011 UTC (11 years, 2 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 (11 years, 3 months ago) by jmduarteg
Removed the serialize/deserialize methods (now in Goodies)
Revision 1316 - Directory Listing
Modified Wed Feb 9 15:55:49 2011 UTC (11 years, 3 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 (11 years, 3 months ago) by jmduarteg
Removed a now unused method
Revision 1314 - Directory Listing
Modified Wed Feb 9 11:36:04 2011 UTC (11 years, 3 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1308 - Directory Listing
Modified Fri Jan 28 18:44:21 2011 UTC (11 years, 3 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 (11 years, 3 months ago) by jmduarteg
Methods to serialize/deserialize from file ChainInterface
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (11 years, 3 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 (11 years, 3 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 1302 - Directory Listing
Modified Fri Jan 14 18:15:38 2011 UTC (11 years, 4 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 (11 years, 4 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 1297 - Directory Listing
Modified Fri Jan 7 18:08:37 2011 UTC (11 years, 4 months ago) by jmduarteg
New methods to get sequence identical chains
Revision 1296 - Directory Listing
Modified Fri Jan 7 11:16:43 2011 UTC (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 4 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 (11 years, 5 months ago) by cvehlow
Control database access! for CGAP
Revision 1287 - Directory Listing
Modified Fri Dec 10 15:17:04 2010 UTC (11 years, 5 months ago) by matt4077

Revision 1286 - Directory Listing
Modified Fri Dec 10 11:34:13 2010 UTC (11 years, 5 months ago) by hstehr
calling readStructureOrNull was exiting rather than returning null
Revision 1284 - Directory Listing
Modified Mon Nov 29 10:06:28 2010 UTC (11 years, 5 months ago) by cvehlow
Overrides removed
Revision 1283 - Directory Listing
Modified Tue Nov 23 14:29:37 2010 UTC (11 years, 5 months ago) by jmduarteg
New getName method.
Revision 1282 - Directory Listing
Modified Thu Nov 18 09:24:15 2010 UTC (11 years, 6 months ago) by jmduarteg
Fixed formatting of the exception message
Revision 1281 - Directory Listing
Modified Wed Nov 17 13:45:09 2010 UTC (11 years, 6 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 (11 years, 6 months ago) by jmduarteg
Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.
Revision 1278 - Directory Listing
Modified Wed Nov 10 09:59:37 2010 UTC (11 years, 6 months ago) by jmduarteg
Fixed the rim/core zooming which wasn't working after redesign of things
Revision 1276 - Directory Listing
Modified Tue Nov 9 13:58:05 2010 UTC (11 years, 6 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 (11 years, 6 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 1272 - Directory Listing
Modified Thu Oct 28 09:54:32 2010 UTC (11 years, 6 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 (11 years, 6 months ago) by jmduarteg
New method to check clashes
Revision 1270 - Directory Listing
Modified Tue Oct 26 15:28:24 2010 UTC (11 years, 6 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 (11 years, 6 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 (11 years, 6 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 1265 - Directory Listing
Modified Wed Oct 20 08:01:41 2010 UTC (11 years, 6 months ago) by jmduarteg
Now keeping track of ASA calc method
Revision 1264 - Directory Listing
Modified Tue Oct 19 16:58:00 2010 UTC (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 1258 - Directory Listing
Modified Fri Oct 8 13:15:13 2010 UTC (11 years, 7 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 (11 years, 7 months ago) by jmduarteg
Now reporting on percent burial too
Revision 1255 - Directory Listing
Modified Thu Oct 7 09:37:55 2010 UTC (11 years, 7 months ago) by jmduarteg
Minor changes to the test.
Revision 1253 - Directory Listing
Modified Wed Oct 6 17:01:19 2010 UTC (11 years, 7 months ago) by jmduarteg
Some minor updates
Revision 1252 - Directory Listing
Modified Wed Oct 6 14:22:03 2010 UTC (11 years, 7 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 (11 years, 7 months ago) by jmduarteg
Some more complete tests.
Revision 1250 - Directory Listing
Modified Mon Oct 4 16:23:26 2010 UTC (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 (11 years, 7 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 1242 - Directory Listing
Modified Wed Sep 29 15:22:49 2010 UTC (11 years, 7 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 (11 years, 7 months 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 1230 - Directory Listing
Modified Wed Sep 8 16:30:40 2010 UTC (11 years, 8 months 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 (11 years, 8 months ago) by jmduarteg
New method for finding identical sequences (entities)
Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (11 years, 8 months 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 1226 - Directory Listing
Modified Mon Sep 6 10:15:25 2010 UTC (11 years, 8 months ago) by hstehr
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
Revision 1225 - Directory Listing
Modified Wed Sep 1 15:57:23 2010 UTC (11 years, 8 months 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 1219 - Directory Listing
Modified Wed Sep 1 13:35:16 2010 UTC (11 years, 8 months ago) by hstehr
added some javadoc
Revision 1218 - Directory Listing
Modified Wed Sep 1 13:02:18 2010 UTC (11 years, 8 months 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 (11 years, 8 months 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 (11 years, 8 months 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 (11 years, 8 months 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 (11 years, 8 months 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 (11 years, 8 months 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 (11 years, 8 months 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 (11 years, 8 months 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 1209 - Directory Listing
Modified Mon Aug 23 12:25:36 2010 UTC (11 years, 8 months ago) by jmduarteg
Fixed bug: was missing one operator in getTransformations
Revision 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (11 years, 8 months ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1206 - Directory Listing
Modified Fri Aug 20 13:29:09 2010 UTC (11 years, 8 months 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 (11 years, 8 months 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 (11 years, 9 months ago) by jmduarteg
Implemented some methods to do translations properly along crystal axes.
Revision 1191 - Directory Listing
Modified Thu Aug 12 15:18:44 2010 UTC (11 years, 9 months 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 (11 years, 9 months 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 (11 years, 9 months 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 (11 years, 9 months 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 1182 - Directory Listing
Modified Wed Aug 11 10:17:32 2010 UTC (11 years, 9 months 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 (11 years, 9 months 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 (11 years, 9 months ago) by jmduarteg
Now correctly parsing the right short name field
Revision 1179 - Directory Listing
Modified Tue Aug 10 09:26:16 2010 UTC (11 years, 9 months ago) by jmduarteg
New classes to parse and store crystallographic space groups info.
Revision 1177 - Directory Listing
Modified Mon Aug 9 07:44:15 2010 UTC (11 years, 9 months ago) by cvehlow
actual version
Revision 1176 - Directory Listing
Modified Fri Aug 6 10:03:26 2010 UTC (11 years, 9 months 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 (11 years, 9 months ago) by cvehlow
Method to get translated and rotated coordinates.
Revision 1174 - Directory Listing
Modified Thu Aug 5 14:47:11 2010 UTC (11 years, 9 months ago) by jmduarteg
New method setChainCode
Revision 1170 - Directory Listing
Modified Wed Aug 4 10:43:52 2010 UTC (11 years, 9 months 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 1165 - Directory Listing
Modified Fri Jul 30 11:03:57 2010 UTC (11 years, 9 months ago) by cvehlow
HahpMap keytype changed to Pair instead of String
Revision 1158 - Directory Listing
Modified Wed Jul 21 11:00:08 2010 UTC (11 years, 9 months ago) by cvehlow
print function
Revision 1150 - Directory Listing
Modified Tue Jul 6 10:46:50 2010 UTC (11 years, 10 months ago) by cvehlow
PrintOut method ion RIGGeometry
Revision 1138 - Directory Listing
Modified Mon Jun 28 14:51:24 2010 UTC (11 years, 10 months ago) by cvehlow
Getter for Atoms-TreeMap.
Revision 1135 - Directory Listing
Modified Fri Jun 25 13:40:27 2010 UTC (11 years, 10 months ago) by cvehlow
Check for consistency in translation rotation framework.
Revision 1129 - Directory Listing
Modified Wed Jun 23 10:24:30 2010 UTC (11 years, 10 months ago) by cvehlow
Additional method for coordinate transversion.
Revision 1127 - Directory Listing
Modified Wed Jun 23 09:44:17 2010 UTC (11 years, 10 months ago) by matt4077
New Residuescoringfunctionimplementation
Revision 1125 - Directory Listing
Modified Mon Jun 21 15:39:04 2010 UTC (11 years, 10 months ago) by cvehlow
Rotation and translation procedure transfered into extra class GmbpGeometry
Revision 1118 - Directory Listing
Modified Fri Jun 18 10:34:00 2010 UTC (11 years, 11 months ago) by cvehlow
RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.
Revision 1111 - Directory Listing
Modified Mon Jun 14 15:50:46 2010 UTC (11 years, 11 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 1109 - Directory Listing
Modified Thu Jun 10 16:29:42 2010 UTC (11 years, 11 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 1094 - Directory Listing
Modified Wed Jun 2 13:19:21 2010 UTC (11 years, 11 months ago) by jmduarteg
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Revision 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (11 years, 11 months ago) by matt4077
renamed  conflicting ContactMap class.
Revision 1067 - Directory Listing
Modified Wed May 12 16:36:24 2010 UTC (12 years 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 (12 years ago) by hstehr
new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (12 years ago) by stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision 1057 - Directory Listing
Modified Mon May 3 15:51:54 2010 UTC (12 years 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 (12 years ago) by stehr
New example implementation of ResidueContactScoringFunction
Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (12 years 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 1049 - Directory Listing
Modified Tue Apr 27 12:36:16 2010 UTC (12 years ago) by hstehr
removing @Override annotations which were causing compilation errors for me
Revision 1047 - Directory Listing
Modified Mon Apr 26 16:13:36 2010 UTC (12 years ago) by jmduarteg
SecondaryStructure now implements Iterable after refactoring of getIterator
Revision 1046 - Directory Listing
Modified Mon Apr 26 15:26:59 2010 UTC (12 years ago) by hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision 1044 - Directory Listing
Modified Mon Apr 26 10:37:14 2010 UTC (12 years ago) by hstehr
New interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.
Revision 1042 - Directory Listing
Modified Wed Apr 21 16:11:08 2010 UTC (12 years 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 (12 years 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 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (12 years, 1 month ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (12 years, 1 month ago) by matt4077
adding phi/psi constraints to edges
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (12 years, 1 month 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 (12 years, 1 month ago) by hstehr
adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()
Revision 1017 - Directory Listing
Modified Fri Apr 9 09:42:32 2010 UTC (12 years, 1 month 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 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (12 years, 1 month 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 (12 years, 1 month ago) by jmduarteg
Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (12 years, 1 month 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 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (12 years, 1 month 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 (12 years, 1 month 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
Added Wed Mar 31 12:29:26 2010 UTC (12 years, 1 month ago) by hstehr
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core