Revision
1520 -
Directory Listing
Modified
Mon Feb 6 16:21:48 2012 UTC
(9 years ago)
by
jmduarteg
More improvements and another exclude list
Revision
1519 -
Directory Listing
Modified
Mon Feb 6 11:54:21 2012 UTC
(9 years 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
(9 years, 1 month ago)
by
jmduarteg
A couple of fixes to the new test
Revision
1516 -
Directory Listing
Modified
Thu Jan 26 17:12:57 2012 UTC
(9 years, 1 month 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
(9 years, 1 month 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
(9 years, 1 month 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
(9 years, 1 month 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
(9 years, 1 month 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
(9 years, 2 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
(9 years, 2 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
(9 years, 2 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
(9 years, 2 months ago)
by
jmduarteg
Adding flag to use uniparc or not
Revision
1507 -
Directory Listing
Modified
Tue Dec 13 14:47:32 2011 UTC
(9 years, 2 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
(9 years, 2 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
(9 years, 2 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
(9 years, 2 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
(9 years, 2 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
(9 years, 3 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
(9 years, 3 months ago)
by
jmduarteg
Switching off surface rendering
Revision
1499 -
Directory Listing
Modified
Mon Dec 5 15:57:36 2011 UTC
(9 years, 3 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
(9 years, 3 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
(9 years, 3 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
(9 years, 3 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
(9 years, 3 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
(9 years, 3 months ago)
by
jmduarteg
New method
Revision
1493 -
Directory Listing
Modified
Fri Nov 25 10:48:53 2011 UTC
(9 years, 3 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
(9 years, 3 months ago)
by
jmduarteg
Improved the blast cache checking
Revision
1491 -
Directory Listing
Modified
Thu Nov 17 14:56:11 2011 UTC
(9 years, 3 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
(9 years, 3 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
(9 years, 3 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
(9 years, 3 months ago)
by
jmduarteg
More logging
Revision
1486 -
Directory Listing
Modified
Wed Nov 16 08:20:28 2011 UTC
(9 years, 3 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
(9 years, 3 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
(9 years, 3 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
(9 years, 4 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
(9 years, 4 months ago)
by
jmduarteg
Minor fix
Revision
1479 -
Directory Listing
Modified
Fri Oct 14 09:26:13 2011 UTC
(9 years, 4 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
(9 years, 4 months ago)
by
jmduarteg
New feature: pisa assembly parsing
Revision
1477 -
Directory Listing
Modified
Thu Oct 6 13:10:49 2011 UTC
(9 years, 5 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
(9 years, 5 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
(9 years, 5 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
(9 years, 5 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
(9 years, 5 months ago)
by
jmduarteg
A few more atom types
Revision
1472 -
Directory Listing
Modified
Wed Sep 28 15:06:19 2011 UTC
(9 years, 5 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
(9 years, 5 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
(9 years, 5 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
(9 years, 5 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
1467 -
Directory Listing
Modified
Mon Sep 5 16:53:40 2011 UTC
(9 years, 6 months ago)
by
jmduarteg
New method for getting URL of uniprot entry
Revision
1466 -
Directory Listing
Modified
Mon Sep 5 16:21:32 2011 UTC
(9 years, 6 months 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
(9 years, 6 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
(9 years, 6 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
(9 years, 6 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
(9 years, 6 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
(9 years, 6 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
(9 years, 6 months ago)
by
jmduarteg
New method to get the chain2repchain map
Revision
1458 -
Directory Listing
Modified
Wed Aug 24 14:43:45 2011 UTC
(9 years, 6 months ago)
by
jmduarteg
Adapted to changes in PymolRunner
Revision
1457 -
Directory Listing
Modified
Wed Aug 24 13:30:58 2011 UTC
(9 years, 6 months ago)
by
jmduarteg
Some more modified aminoacids
Revision
1456 -
Directory Listing
Modified
Mon Aug 22 14:52:42 2011 UTC
(9 years, 6 months 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
(9 years, 6 months 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
(9 years, 6 months 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
(9 years, 6 months ago)
by
jmduarteg
Got rid of -p option when executing pymol
Revision
1452 -
Directory Listing
Modified
Fri Aug 19 14:46:44 2011 UTC
(9 years, 6 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
(9 years, 6 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
(9 years, 6 months ago)
by
jmduarteg
Another peptide-linked HET residue
Revision
1449 -
Directory Listing
Modified
Fri Aug 19 12:38:59 2011 UTC
(9 years, 6 months ago)
by
jmduarteg
New method getBSA
Revision
1448 -
Directory Listing
Modified
Thu Aug 18 15:23:57 2011 UTC
(9 years, 6 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
1447 -
Directory Listing
Modified
Thu Aug 18 11:51:33 2011 UTC
(9 years, 6 months ago)
by
jmduarteg
Removing duplicate entry
Revision
1446 -
Directory Listing
Modified
Thu Aug 18 10:55:24 2011 UTC
(9 years, 6 months 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
(9 years, 6 months 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
(9 years, 6 months 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
(9 years, 6 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
1435 -
Directory Listing
Modified
Tue Aug 16 16:03:09 2011 UTC
(9 years, 6 months 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
(9 years, 7 months ago)
by
jmduarteg
New element
Revision
1431 -
Directory Listing
Modified
Mon Aug 1 15:04:21 2011 UTC
(9 years, 7 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
(9 years, 7 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
(9 years, 7 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
(9 years, 7 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
(9 years, 8 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
(9 years, 8 months ago)
by
jmduarteg
Two more atom types
Revision
1425 -
Directory Listing
Modified
Tue Jun 21 10:49:33 2011 UTC
(9 years, 8 months ago)
by
jmduarteg
Another atom type
Revision
1424 -
Directory Listing
Modified
Mon Jun 20 14:35:43 2011 UTC
(9 years, 8 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
(9 years, 8 months ago)
by
jmduarteg
Another atom type
Revision
1422 -
Directory Listing
Modified
Mon Jun 20 12:11:06 2011 UTC
(9 years, 8 months ago)
by
jmduarteg
New atom type
Revision
1421 -
Directory Listing
Modified
Thu Jun 16 16:57:37 2011 UTC
(9 years, 8 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
(9 years, 8 months ago)
by
jmduarteg
Adding element
Revision
1419 -
Directory Listing
Modified
Thu Jun 16 13:34:25 2011 UTC
(9 years, 8 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
(9 years, 8 months ago)
by
jmduarteg
Some improvements and fixes to enumerateInterfaces
Revision
1416 -
Directory Listing
Modified
Thu Jun 9 18:46:06 2011 UTC
(9 years, 8 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
(9 years, 8 months ago)
by
jmduarteg
Better doc
Revision
1414 -
Directory Listing
Modified
Tue Jun 7 15:19:08 2011 UTC
(9 years, 8 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
(9 years, 8 months ago)
by
jmduarteg
New option to output interfaces serialized file
Revision
1412 -
Directory Listing
Modified
Tue Jun 7 13:36:00 2011 UTC
(9 years, 8 months ago)
by
jmduarteg
Now outputs core sizes as well
Revision
1411 -
Directory Listing
Modified
Tue Jun 7 12:15:51 2011 UTC
(9 years, 8 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 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
(9 years, 9 months ago)
by
jmduarteg
Now throwing separate exceptions as before
Revision
1390 -
Directory Listing
Modified
Fri May 13 17:06:19 2011 UTC
(9 years, 9 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
(9 years, 10 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
(9 years, 10 months ago)
by
jmduarteg
Unzip method
Revision
1387 -
Directory Listing
Modified
Sun Apr 10 11:10:30 2011 UTC
(9 years, 10 months ago)
by
hstehr
adding package-info for owl.mutanom
Revision
1386 -
Directory Listing
Modified
Thu Apr 7 15:09:48 2011 UTC
(9 years, 10 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
(9 years, 11 months ago)
by
stehr
System.out.println(cmdline) is commented out.
Revision
1383 -
Directory Listing
Modified
Tue Apr 5 14:15:39 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
jmduarteg
Documented the -t option
Revision
1381 -
Directory Listing
Modified
Fri Apr 1 15:48:30 2011 UTC
(9 years, 11 months ago)
by
jmduarteg
Improved javadocs
Revision
1380 -
Directory Listing
Modified
Fri Apr 1 07:53:32 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
stehr
Fixed another problem with persistent temp files
Revision
1378 -
Directory Listing
Modified
Thu Mar 31 09:13:13 2011 UTC
(9 years, 11 months ago)
by
jmduarteg
More debug output
Revision
1377 -
Directory Listing
Modified
Thu Mar 31 09:11:08 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
jmduarteg
Another test
Revision
1375 -
Directory Listing
Modified
Thu Mar 31 07:41:36 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
jmduarteg
Adding Serializable interface to some classes
Revision
1373 -
Directory Listing
Modified
Wed Mar 30 10:23:48 2011 UTC
(9 years, 11 months ago)
by
jmduarteg
Now PdbChain also implements Iterable
Revision
1372 -
Directory Listing
Modified
Wed Mar 30 09:55:49 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
hstehr
Updated some JavaDocs
Revision
1367 -
Directory Listing
Modified
Mon Mar 28 17:49:23 2011 UTC
(9 years, 11 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
(9 years, 11 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
(9 years, 11 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
(9 years, 11 months ago)
by
jmduarteg
Fixed bug: now caching bounds properly.
Revision
1360 -
Directory Listing
Modified
Mon Mar 28 10:21:06 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
jmduarteg
New option -d
Revision
1358 -
Directory Listing
Modified
Mon Mar 28 09:32:42 2011 UTC
(9 years, 11 months ago)
by
jmduarteg
More optimisation on geometric hashing algorithm.
Revision
1357 -
Directory Listing
Modified
Sat Mar 26 16:29:27 2011 UTC
(9 years, 11 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
(9 years, 11 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
(9 years, 11 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
(9 years, 11 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
(9 years, 11 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
(9 years, 11 months ago)
by
hstehr
unnecessary codes removed
Revision
1350 -
Directory Listing
Modified
Tue Mar 22 15:51:13 2011 UTC
(9 years, 11 months ago)
by
hstehr
add -O to dump observed sequences
Revision
1349 -
Directory Listing
Modified
Mon Mar 21 18:28:31 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
hstehr
adding some missing documentation
Revision
1347 -
Directory Listing
Modified
Mon Mar 21 10:38:06 2011 UTC
(9 years, 11 months ago)
by
hstehr
moving project CCCP to this repository
Revision
1346 -
Directory Listing
Modified
Fri Mar 18 08:25:07 2011 UTC
(9 years, 11 months ago)
by
jmduarteg
Now detecting type of sequence: protein/nucleotide
Revision
1345 -
Directory Listing
Modified
Thu Mar 17 13:58:32 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
hstehr
Revision
1343 -
Directory Listing
Modified
Wed Mar 16 18:29:19 2011 UTC
(9 years, 11 months ago)
by
hstehr
Revision
1342 -
Directory Listing
Modified
Wed Mar 16 17:53:02 2011 UTC
(9 years, 11 months ago)
by
hstehr
Revision
1341 -
Directory Listing
Modified
Tue Mar 15 08:40:43 2011 UTC
(9 years, 11 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
(9 years, 11 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
(9 years, 11 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
(9 years, 11 months ago)
by
jmduarteg
Fixed bug. Pymol was blocking
Revision
1337 -
Directory Listing
Modified
Fri Mar 11 08:47:52 2011 UTC
(9 years, 11 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
(9 years, 11 months ago)
by
jmduarteg
New runner for pymol
Revision
1335 -
Directory Listing
Modified
Wed Mar 9 08:38:35 2011 UTC
(9 years, 11 months ago)
by
jmduarteg
Now throwing InterruptedException. Refactor BlastErro to BlastException
Revision
1334 -
Directory Listing
Modified
Wed Mar 9 08:13:04 2011 UTC
(9 years, 11 months ago)
by
jmduarteg
Refactoring xxxError to xxxException
Revision
1333 -
Directory Listing
Modified
Tue Mar 8 18:21:32 2011 UTC
(9 years, 11 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
(9 years, 11 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
(9 years, 11 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
(9 years, 11 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
(10 years 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
(10 years 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
(10 years ago)
by
jmduarteg
Some more atoms seen in pdb files
Revision
1326 -
Directory Listing
Modified
Thu Mar 3 13:21:18 2011 UTC
(10 years 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
(10 years 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
(10 years 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
(10 years ago)
by
hstehr
New method hasChain(String): boolean
Revision
1321 -
Directory Listing
Modified
Wed Feb 23 11:16:13 2011 UTC
(10 years ago)
by
jmduarteg
New enum for nucleotides
Revision
1320 -
Directory Listing
Modified
Wed Feb 23 10:45:32 2011 UTC
(10 years 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
(10 years ago)
by
jmduarteg
Removed the serialize/deserialize methods (now in Goodies)
Revision
1318 -
Directory Listing
Modified
Thu Feb 17 08:58:55 2011 UTC
(10 years ago)
by
jmduarteg
Methods to serialize/deserialize from file
Revision
1317 -
Directory Listing
Modified
Wed Feb 9 17:41:17 2011 UTC
(10 years 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
(10 years 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
(10 years ago)
by
jmduarteg
Removed a now unused method
Revision
1314 -
Directory Listing
Modified
Wed Feb 9 11:36:04 2011 UTC
(10 years 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
(10 years 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
(10 years 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
(10 years, 1 month 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
(10 years, 1 month 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
(10 years, 1 month 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
(10 years, 1 month ago)
by
jmduarteg
Methods to serialize/deserialize from file ChainInterface
Revision
1306 -
Directory Listing
Modified
Tue Jan 25 14:15:20 2011 UTC
(10 years, 1 month 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
(10 years, 1 month 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
(10 years, 1 month 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
(10 years, 1 month 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
(10 years, 1 month 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
(10 years, 1 month ago)
by
jmduarteg
Better docs
Revision
1298 -
Directory Listing
Modified
Tue Jan 11 14:35:17 2011 UTC
(10 years, 1 month ago)
by
jmduarteg
Now storing the query coverage cutoff.
Revision
1297 -
Directory Listing
Modified
Fri Jan 7 18:08:37 2011 UTC
(10 years, 1 month ago)
by
jmduarteg
New methods to get sequence identical chains
Revision
1296 -
Directory Listing
Modified
Fri Jan 7 11:16:43 2011 UTC
(10 years, 1 month 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
(10 years, 2 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
(10 years, 2 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
(10 years, 2 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
(10 years, 2 months ago)
by
cvehlow
Control database access! for CGAP
Revision
1291 -
Directory Listing
Modified
Fri Dec 17 16:38:25 2010 UTC
(10 years, 2 months ago)
by
cvehlow
Control database access! for CGAP
Revision
1290 -
Directory Listing
Modified
Fri Dec 17 14:09:48 2010 UTC
(10 years, 2 months ago)
by
cvehlow
add setParametersDB
Revision
1287 -
Directory Listing
Modified
Fri Dec 10 15:17:04 2010 UTC
(10 years, 2 months ago)
by
matt4077
Revision
1286 -
Directory Listing
Modified
Fri Dec 10 11:34:13 2010 UTC
(10 years, 2 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
(10 years, 3 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
(10 years, 3 months ago)
by
cvehlow
Overrides removed
Revision
1283 -
Directory Listing
Modified
Tue Nov 23 14:29:37 2010 UTC
(10 years, 3 months ago)
by
jmduarteg
New getName method.
Revision
1282 -
Directory Listing
Modified
Thu Nov 18 09:24:15 2010 UTC
(10 years, 3 months ago)
by
jmduarteg
Fixed formatting of the exception message
Revision
1281 -
Directory Listing
Modified
Wed Nov 17 13:45:09 2010 UTC
(10 years, 3 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
(10 years, 3 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
(10 years, 3 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
(10 years, 3 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
(10 years, 3 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
(10 years, 3 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
(10 years, 4 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
(10 years, 4 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
(10 years, 4 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
(10 years, 4 months ago)
by
jmduarteg
New method to check clashes
Revision
1270 -
Directory Listing
Modified
Tue Oct 26 15:28:24 2010 UTC
(10 years, 4 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
(10 years, 4 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
(10 years, 4 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
(10 years, 4 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
(10 years, 4 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
(10 years, 4 months ago)
by
jmduarteg
Now keeping track of ASA calc method
Revision
1264 -
Directory Listing
Modified
Tue Oct 19 16:58:00 2010 UTC
(10 years, 4 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
(10 years, 4 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
(10 years, 4 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
(10 years, 4 months ago)
by
jmduarteg
Using the new UniprotVerMismatchException instead of IOException
Revision
1259 -
Directory Listing
Modified
Fri Oct 8 13:45:56 2010 UTC
(10 years, 4 months ago)
by
jmduarteg
New exception for mismatching uniprot versions
Revision
1258 -
Directory Listing
Modified
Fri Oct 8 13:15:13 2010 UTC
(10 years, 4 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
(10 years, 4 months ago)
by
jmduarteg
Now reporting on percent burial too
Revision
1255 -
Directory Listing
Modified
Thu Oct 7 09:37:55 2010 UTC
(10 years, 4 months ago)
by
jmduarteg
Minor changes to the test.
Revision
1254 -
Directory Listing
Modified
Thu Oct 7 08:38:10 2010 UTC
(10 years, 4 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
(10 years, 5 months ago)
by
jmduarteg
Some minor updates
Revision
1252 -
Directory Listing
Modified
Wed Oct 6 14:22:03 2010 UTC
(10 years, 5 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
(10 years, 5 months ago)
by
jmduarteg
Some more complete tests.
Revision
1250 -
Directory Listing
Modified
Mon Oct 4 16:23:26 2010 UTC
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
(10 years, 5 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
1240 -
Directory Listing
Modified
Tue Sep 21 12:12:07 2010 UTC
(10 years, 5 months ago)
by
hstehr
suppressing two warnings
Revision
1239 -
Directory Listing
Modified
Tue Sep 21 12:01:35 2010 UTC
(10 years, 5 months ago)
by
gmueller
sparse matrix exception
Revision
1238 -
Directory Listing
Modified
Tue Sep 21 09:43:32 2010 UTC
(10 years, 5 months 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
(10 years, 5 months ago)
by
cvehlow
commit latest version
Revision
1236 -
Directory Listing
Modified
Mon Sep 13 11:03:14 2010 UTC
(10 years, 5 months ago)
by
cvehlow
variable 2D csv-files loadable
Revision
1235 -
Directory Listing
Modified
Fri Sep 10 14:39:45 2010 UTC
(10 years, 5 months ago)
by
cvehlow
Color scale class moved from gmbp to owl
Revision
1234 -
Directory Listing
Modified
Thu Sep 9 13:36:28 2010 UTC
(10 years, 5 months 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
(10 years, 5 months 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
(10 years, 5 months 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
(10 years, 5 months ago)
by
hstehr
Adding class PhosphoSiteConnection
Revision
1230 -
Directory Listing
Modified
Wed Sep 8 16:30:40 2010 UTC
(10 years, 5 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
(10 years, 5 months ago)
by
jmduarteg
New method for finding identical sequences (entities)
Revision
1228 -
Directory Listing
Modified
Tue Sep 7 15:41:50 2010 UTC
(10 years, 5 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
1227 -
Directory Listing
Modified
Tue Sep 7 09:47:02 2010 UTC
(10 years, 5 months 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
(10 years, 6 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
(10 years, 6 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
1224 -
Directory Listing
Modified
Wed Sep 1 14:30:52 2010 UTC
(10 years, 6 months ago)
by
cvehlow
added methods
Revision
1223 -
Directory Listing
Modified
Wed Sep 1 14:26:00 2010 UTC
(10 years, 6 months ago)
by
hstehr
updated classes for evaluating our CASP predictions
Revision
1222 -
Directory Listing
Modified
Wed Sep 1 14:23:40 2010 UTC
(10 years, 6 months ago)
by
hstehr
please don't check in Mac specific constants
Revision
1221 -
Directory Listing
Modified
Wed Sep 1 14:21:58 2010 UTC
(10 years, 6 months ago)
by
hstehr
updating annotations to get rid of warnings
Revision
1220 -
Directory Listing
Modified
Wed Sep 1 14:20:44 2010 UTC
(10 years, 6 months ago)
by
hstehr
deleting two classes which were making problems
Revision
1219 -
Directory Listing
Modified
Wed Sep 1 13:35:16 2010 UTC
(10 years, 6 months ago)
by
hstehr
added some javadoc
Revision
1218 -
Directory Listing
Modified
Wed Sep 1 13:02:18 2010 UTC
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
1210 -
Directory Listing
Modified
Wed Aug 25 11:28:14 2010 UTC
(10 years, 6 months 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
(10 years, 6 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
(10 years, 6 months ago)
by
cvehlow
Scoring:KendallsTau-method added to Statistics
Revision
1207 -
Directory Listing
Modified
Mon Aug 23 12:09:04 2010 UTC
(10 years, 6 months ago)
by
cvehlow
Scoring:KendallsTau-method added to Statistics
Revision
1206 -
Directory Listing
Modified
Fri Aug 20 13:29:09 2010 UTC
(10 years, 6 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
(10 years, 6 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
(10 years, 6 months 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
(10 years, 6 months ago)
by
hstehr
renamed class benchmarkAll to createResultWebPages
Revision
1202 -
Directory Listing
Modified
Thu Aug 19 10:21:08 2010 UTC
(10 years, 6 months ago)
by
hstehr
suppress "method not used" warning
Revision
1201 -
Directory Listing
Modified
Thu Aug 19 10:18:59 2010 UTC
(10 years, 6 months 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
(10 years, 6 months ago)
by
hstehr
removed some bad characters
Revision
1199 -
Directory Listing
Modified
Thu Aug 19 10:14:54 2010 UTC
(10 years, 6 months ago)
by
hstehr
added some debug output (commented out)
Revision
1198 -
Directory Listing
Modified
Thu Aug 19 10:11:45 2010 UTC
(10 years, 6 months ago)
by
cvehlow
classes moved
Revision
1197 -
Directory Listing
Modified
Thu Aug 19 10:08:52 2010 UTC
(10 years, 6 months ago)
by
hstehr
Adding some javadoc
Revision
1196 -
Directory Listing
Modified
Thu Aug 19 10:06:15 2010 UTC
(10 years, 6 months 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
(10 years, 6 months ago)
by
cvehlow
classes moved
Revision
1194 -
Directory Listing
Modified
Thu Aug 19 09:56:40 2010 UTC
(10 years, 6 months ago)
by
cvehlow
classes moved
Revision
1193 -
Directory Listing
Modified
Thu Aug 19 09:46:03 2010 UTC
(10 years, 6 months 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
(10 years, 6 months ago)
by
jmduarteg
Committing test class for AICGraph
Revision
1191 -
Directory Listing
Modified
Thu Aug 12 15:18:44 2010 UTC
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
1187 -
Directory Listing
Modified
Wed Aug 11 14:46:34 2010 UTC
(10 years, 6 months 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
(10 years, 6 months ago)
by
cvehlow
max Cluster Path two possibilities (Mac Unix)
Revision
1185 -
Directory Listing
Modified
Wed Aug 11 13:34:13 2010 UTC
(10 years, 6 months ago)
by
cvehlow
Method added which returns complete result in TreeMap
Revision
1184 -
Directory Listing
Modified
Wed Aug 11 13:13:50 2010 UTC
(10 years, 6 months 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
(10 years, 6 months ago)
by
cvehlow
bug removed nullpointer?!
Revision
1182 -
Directory Listing
Modified
Wed Aug 11 10:17:32 2010 UTC
(10 years, 6 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
(10 years, 6 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
(10 years, 6 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
(10 years, 6 months 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
(10 years, 6 months ago)
by
cvehlow
actual methods
Revision
1177 -
Directory Listing
Modified
Mon Aug 9 07:44:15 2010 UTC
(10 years, 6 months ago)
by
cvehlow
actual version
Revision
1176 -
Directory Listing
Modified
Fri Aug 6 10:03:26 2010 UTC
(10 years, 7 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
(10 years, 7 months ago)
by
cvehlow
Method to get translated and rotated coordinates.
Revision
1174 -
Directory Listing
Modified
Thu Aug 5 14:47:11 2010 UTC
(10 years, 7 months ago)
by
jmduarteg
New method setChainCode
Revision
1173 -
Directory Listing
Modified
Wed Aug 4 15:27:40 2010 UTC
(10 years, 7 months ago)
by
hstehr
minor modifications to casp benchmarking script
Revision
1172 -
Directory Listing
Modified
Wed Aug 4 15:26:03 2010 UTC
(10 years, 7 months ago)
by
jmduarteg
Now using apache commons logging
Revision
1171 -
Directory Listing
Modified
Wed Aug 4 10:47:28 2010 UTC
(10 years, 7 months 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
(10 years, 7 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
1169 -
Directory Listing
Modified
Mon Aug 2 17:29:07 2010 UTC
(10 years, 7 months 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
(10 years, 7 months 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
(10 years, 7 months 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
(10 years, 7 months 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
(10 years, 7 months ago)
by
cvehlow
HahpMap keytype changed to Pair instead of String
Revision
1164 -
Directory Listing
Modified
Fri Jul 30 09:56:39 2010 UTC
(10 years, 7 months 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
(10 years, 7 months 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
(10 years, 7 months 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
(10 years, 7 months ago)
by
cvehlow
slight changes
Revision
1159 -
Directory Listing
Modified
Fri Jul 23 14:56:35 2010 UTC
(10 years, 7 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
(10 years, 7 months ago)
by
cvehlow
print function
Revision
1157 -
Directory Listing
Modified
Wed Jul 7 15:31:14 2010 UTC
(10 years, 7 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
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
And all other amiguous codons
Revision
1153 -
Directory Listing
Modified
Wed Jul 7 08:46:37 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
Another ambiguous nucleotide letter
Revision
1151 -
Directory Listing
Modified
Tue Jul 6 16:58:04 2010 UTC
(10 years, 8 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
(10 years, 8 months ago)
by
cvehlow
PrintOut method ion RIGGeometry
Revision
1149 -
Directory Listing
Modified
Mon Jul 5 16:46:57 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
Changed level of some logging messages
Revision
1148 -
Directory Listing
Modified
Mon Jul 5 16:16:44 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
New removeRedundancy method
Revision
1147 -
Directory Listing
Modified
Mon Jul 5 08:35:15 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
Implemented logging with log4j library
Revision
1146 -
Directory Listing
Modified
Fri Jul 2 09:54:46 2010 UTC
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
Now can filter also on query coverage
Revision
1144 -
Directory Listing
Modified
Thu Jul 1 10:09:55 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
Changed the order of checks in isReferenceSeqPositionReliable
Revision
1143 -
Directory Listing
Modified
Thu Jul 1 10:02:53 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 8 months ago)
by
cvehlow
methods by saurabh included
Revision
1140 -
Directory Listing
Modified
Tue Jun 29 08:49:34 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 8 months ago)
by
cvehlow
Getter for Atoms-TreeMap.
Revision
1137 -
Directory Listing
Modified
Mon Jun 28 13:38:32 2010 UTC
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
New ambiguous nucleotide w.
Revision
1135 -
Directory Listing
Modified
Fri Jun 25 13:40:27 2010 UTC
(10 years, 8 months ago)
by
cvehlow
Check for consistency in translation rotation framework.
Revision
1134 -
Directory Listing
Modified
Fri Jun 25 13:39:57 2010 UTC
(10 years, 8 months ago)
by
cvehlow
Check for consistency in translation rotation framework.
Revision
1133 -
Directory Listing
Modified
Fri Jun 25 13:36:03 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 8 months ago)
by
cvehlow
Changes: use different db for traces!
Revision
1130 -
Directory Listing
Modified
Thu Jun 24 09:42:57 2010 UTC
(10 years, 8 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
(10 years, 8 months ago)
by
cvehlow
Additional method for coordinate transversion.
Revision
1128 -
Directory Listing
Modified
Wed Jun 23 10:23:44 2010 UTC
(10 years, 8 months ago)
by
cvehlow
Additional method for coordinate transversion.
Revision
1127 -
Directory Listing
Modified
Wed Jun 23 09:44:17 2010 UTC
(10 years, 8 months ago)
by
matt4077
New Residuescoringfunctionimplementation
Revision
1126 -
Directory Listing
Modified
Tue Jun 22 12:19:07 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
Improved the selection of representative CDS
Revision
1122 -
Directory Listing
Modified
Mon Jun 21 10:48:05 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
Some refactoring
Revision
1121 -
Directory Listing
Modified
Fri Jun 18 16:02:55 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
Now implementing HasFeatures
Revision
1120 -
Directory Listing
Modified
Fri Jun 18 13:29:34 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
Now checking codon length before translating
Revision
1116 -
Directory Listing
Modified
Thu Jun 17 09:48:22 2010 UTC
(10 years, 8 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
(10 years, 8 months ago)
by
cvehlow
Changes in edge-cluster direction!
Revision
1114 -
Directory Listing
Modified
Wed Jun 16 10:26:22 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 8 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
(10 years, 8 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
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
Now parsing the symmetry operators.
Revision
1107 -
Directory Listing
Modified
Thu Jun 10 10:20:35 2010 UTC
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
Implemented caching of blast in UniprotHomologList
Revision
1105 -
Directory Listing
Modified
Thu Jun 10 09:23:41 2010 UTC
(10 years, 8 months ago)
by
jmduarteg
Our own copy file method! :-)
Revision
1104 -
Directory Listing
Modified
Wed Jun 9 17:04:36 2010 UTC
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
Implemented caching for EMBWSDBfetchConnection
Revision
1102 -
Directory Listing
Modified
Wed Jun 9 14:59:42 2010 UTC
(10 years, 8 months ago)
by
cvehlow
Cluster-edge direction evaluated.
Revision
1101 -
Directory Listing
Modified
Wed Jun 9 09:26:27 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 8 months ago)
by
jmduarteg
Some fixes to the help string
Revision
1098 -
Directory Listing
Modified
Tue Jun 8 09:10:32 2010 UTC
(10 years, 8 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
(10 years, 8 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
(10 years, 9 months ago)
by
jmduarteg
Minor doc fix
Revision
1095 -
Directory Listing
Modified
Wed Jun 2 15:06:46 2010 UTC
(10 years, 9 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
(10 years, 9 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
(10 years, 9 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
(10 years, 9 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
(10 years, 9 months ago)
by
cvehlow
Class OptimalSingleEnv for scoring of different substrings.
Revision
1090 -
Directory Listing
Modified
Tue Jun 1 12:16:52 2010 UTC
(10 years, 9 months ago)
by
matt4077
little contact map example done
Revision
1089 -
Directory Listing
Modified
Tue Jun 1 11:14:05 2010 UTC
(10 years, 9 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
(10 years, 9 months ago)
by
cvehlow
max number of traces
Revision
1087 -
Directory Listing
Modified
Mon May 31 15:41:25 2010 UTC
(10 years, 9 months ago)
by
jmduarteg
Improved the getRimAndCore method
Revision
1086 -
Directory Listing
Modified
Mon May 31 15:41:16 2010 UTC
(10 years, 9 months ago)
by
cvehlow
Extract maximum number of traces!
Revision
1085 -
Directory Listing
Modified
Mon May 31 13:45:03 2010 UTC
(10 years, 9 months ago)
by
jmduarteg
Some new methods
Revision
1084 -
Directory Listing
Modified
Mon May 31 13:38:56 2010 UTC
(10 years, 9 months ago)
by
matt4077
renamed conflicting ContactMap class.
Revision
1083 -
Directory Listing
Modified
Mon May 31 13:31:23 2010 UTC
(10 years, 9 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
(10 years, 9 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
(10 years, 9 months ago)
by
jmduarteg
Fixed bug with '-' embl cds identifiers.
Revision
1080 -
Directory Listing
Modified
Fri May 28 12:55:41 2010 UTC
(10 years, 9 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
(10 years, 9 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
(10 years, 9 months ago)
by
jmduarteg
Now parsing the seq_num residue number.
Revision
1077 -
Directory Listing
Modified
Thu May 27 09:51:50 2010 UTC
(10 years, 9 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
(10 years, 9 months ago)
by
jmduarteg
PISA connection and xml interfaces description parser
Revision
1074 -
Directory Listing
Modified
Fri May 21 10:02:24 2010 UTC
(10 years, 9 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
(10 years, 9 months ago)
by
jmduarteg
Also retrieving uniprot sequence in UniprotHomolog.retrieveUniprotKBData()
Revision
1072 -
Directory Listing
Modified
Thu May 20 13:59:25 2010 UTC
(10 years, 9 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
(10 years, 9 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
(10 years, 9 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
(10 years, 9 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
(10 years, 9 months ago)
by
cvehlow
HandOverThetaPhiRanges
Revision
1067 -
Directory Listing
Modified
Wed May 12 16:36:24 2010 UTC
(10 years, 9 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
(10 years, 9 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
(10 years, 9 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
(10 years, 9 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
(10 years, 9 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 months ago)
by
jmduarteg
Fixed java doc
Revision
1058 -
Directory Listing
Modified
Mon May 3 16:57:21 2010 UTC
(10 years, 10 months ago)
by
cvehlow
Load from zip-file!
Revision
1057 -
Directory Listing
Modified
Mon May 3 15:51:54 2010 UTC
(10 years, 10 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
(10 years, 10 months ago)
by
stehr
New example implementation of ResidueContactScoringFunction
Revision
1055 -
Directory Listing
Modified
Wed Apr 28 15:08:53 2010 UTC
(10 years, 10 months ago)
by
jmduarteg
Removed code left over from debugging.
Revision
1054 -
Directory Listing
Modified
Wed Apr 28 13:37:00 2010 UTC
(10 years, 10 months ago)
by
jmduarteg
Minor changes, couple of new methods.
Revision
1052 -
Directory Listing
Modified
Tue Apr 27 16:07:48 2010 UTC
(10 years, 10 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
(10 years, 10 months ago)
by
jmduarteg
Minor fix to java docs
Revision
1050 -
Directory Listing
Modified
Tue Apr 27 12:39:52 2010 UTC
(10 years, 10 months ago)
by
cvehlow
Load precalc sphoxel data if possible.
Revision
1049 -
Directory Listing
Modified
Tue Apr 27 12:36:16 2010 UTC
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 months ago)
by
matt4077
revert. wasn't the best idea.
Revision
1037 -
Directory Listing
Modified
Tue Apr 20 09:53:00 2010 UTC
(10 years, 10 months ago)
by
matt4077
adding phi/psi constraints to edges
Revision
1036 -
Directory Listing
Modified
Mon Apr 19 14:27:11 2010 UTC
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 months ago)
by
cvehlow
Faster SQL queries
Revision
1027 -
Directory Listing
Modified
Fri Apr 16 10:03:57 2010 UTC
(10 years, 10 months ago)
by
jmduarteg
Fixed some docs and indentation
Revision
1026 -
Directory Listing
Modified
Thu Apr 15 15:28:29 2010 UTC
(10 years, 10 months ago)
by
cvehlow
changes
Revision
1025 -
Directory Listing
Modified
Thu Apr 15 09:28:23 2010 UTC
(10 years, 10 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
(10 years, 10 months ago)
by
cvehlow
Revision
1023 -
Directory Listing
Modified
Tue Apr 13 17:14:22 2010 UTC
(10 years, 10 months ago)
by
cvehlow
FloatPairSet first commit
Revision
1022 -
Directory Listing
Modified
Sun Apr 11 17:37:12 2010 UTC
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 months ago)
by
cvehlow
First version of class for sphoxel computation.
Revision
1018 -
Directory Listing
Modified
Fri Apr 9 10:40:29 2010 UTC
(10 years, 10 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
(10 years, 10 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
(10 years, 10 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
(10 years, 10 months ago)
by
jmduarteg
Fixed import (was a compile error)
Revision
1014 -
Directory Listing
Modified
Thu Apr 8 16:34:26 2010 UTC
(10 years, 10 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
(10 years, 11 months ago)
by
matt4077
resolving conflicts
Revision
1012 -
Directory Listing
Modified
Thu Apr 1 08:41:01 2010 UTC
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 months ago)
by
gmueller
latest version of gabriel (embed.contactmaps)
Revision
1001 -
Directory Listing
Modified
Tue Mar 30 11:09:04 2010 UTC
(10 years, 11 months ago)
by
gmueller
latest version of gabriel
Revision
1000 -
Directory Listing
Modified
Mon Mar 29 10:20:38 2010 UTC
(10 years, 11 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
(10 years, 11 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
(10 years, 11 months ago)
by
jmduarteg
Minor refactoring and comment fixes
Revision
997 -
Directory Listing
Modified
Mon Mar 29 09:41:31 2010 UTC
(10 years, 11 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
(10 years, 11 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
(10 years, 11 months ago)
by
jmduarteg
Removed the executable property
Revision
994 -
Directory Listing
Modified
Wed Mar 24 15:09:16 2010 UTC
(10 years, 11 months ago)
by
hstehr
new method AminoAcid.valuesInOrderOfHydrophobicity()
Revision
989 -
Directory Listing
Modified
Fri Mar 19 09:00:00 2010 UTC
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 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
(10 years, 11 months ago)
by
hstehr
adding some convenience methods to IntervalSet
Revision
982 -
Directory Listing
Modified
Tue Mar 16 13:01:01 2010 UTC
(10 years, 11 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
(10 years, 11 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
(11 years 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
(11 years 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
(11 years 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
(11 years 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
(11 years 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
(11 years 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
(11 years ago)
by
gmueller
new class for sparse double matrices
Revision
963 -
Directory Listing
Modified
Tue Feb 16 12:00:55 2010 UTC
(11 years ago)
by
gmueller
some new classes
Revision
962 -
Directory Listing
Modified
Tue Feb 16 11:51:18 2010 UTC
(11 years 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
(11 years 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
(11 years ago)
by
duarte
New executable class from my workspace.
Revision
959 -
Directory Listing
Modified
Fri Feb 12 15:25:33 2010 UTC
(11 years ago)
by
duarte
Moved IntervalTest class to test.tools package
Revision
958 -
Directory Listing
Modified
Fri Feb 12 15:22:36 2010 UTC
(11 years ago)
by
duarte
Moved Interval* and IntPair* classes to tools package
Revision
957 -
Directory Listing
Modified
Fri Feb 12 15:06:04 2010 UTC
(11 years 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
(11 years ago)
by
duarte
Removed some obsolete classes.
Revision
955 -
Directory Listing
Modified
Tue Feb 9 10:44:24 2010 UTC
(11 years 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
(11 years 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
(11 years ago)
by
duarte
Refactoring of inconsistently named methods in RIGraph
Revision
952 -
Directory Listing
Modified
Fri Feb 5 16:41:47 2010 UTC
(11 years 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
(11 years, 1 month 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.