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Revision 809 - Directory Listing
Modified Mon Nov 24 11:21:01 2008 UTC (10 years, 9 months ago) by duarte
Introduced some more checks for validity of contact types.
Revision 808 - Directory Listing
Modified Fri Nov 21 15:39:19 2008 UTC (10 years, 10 months ago) by duarte
Introduced a delay between runProtein and runXyzpdb in reconstruct to make sure when we run xyzpdb the file is there: we try to find xyzFile a few times with a delay between retries.
Revision 807 - Directory Listing
Modified Fri Nov 21 13:46:35 2008 UTC (10 years, 10 months ago) by duarte
Fixed bug: wasn't checking exit value of protein, xyzpdb and pdbxyz. Now throwing exception when exit value not 0.
Revision 795 - Directory Listing
Modified Fri Nov 7 14:45:58 2008 UTC (10 years, 10 months ago) by duarte
Fixed bug (hopefully): was not closing drmaa session after every runParallelDistgeom, only in the shutdown hook. We need to close it always in case there is more than one run within the same instance of the JVM.
Revision 786 - Directory Listing
Modified Fri Oct 31 10:40:30 2008 UTC (10 years, 10 months ago) by duarte
Implemented a more robust approach to failure of jobs in parallel distgeom. Now we send 1.1*n jobs and require that only n of them finish successfully. These solves many issues: even if 0.1*n jobs fail the whole thing will be successful, if a jobs hangs forever we will not wait for it to finish.
Revision 785 - Directory Listing
Modified Thu Oct 30 16:07:54 2008 UTC (10 years, 10 months ago) by duarte
Fixed bug: now parallel distgeom works even if a relative path  specified in caller script.
Revision 781 - Directory Listing
Modified Fri Oct 24 15:23:27 2008 UTC (10 years, 10 months ago) by duarte
Implemented shutdown hook. Now all jobs killed upon CTRL-c.
Now submitting directly the distgeom binary without needing writing a shell script. That removes the dependency on java6 (needed for set execution permission on the shell script). 
Introduced (but not in use yet and not fully implemented) the submission of more jobs for failure tolerance.
Revision 780 - Directory Listing
Modified Fri Oct 24 09:37:41 2008 UTC (10 years, 10 months ago) by duarte
Some minor fixes and cleanup. Changed timeout to 2hours.
Revision 779 - Directory Listing
Modified Thu Oct 23 08:49:01 2008 UTC (10 years, 10 months ago) by duarte
Better error messages
Revision 778 - Directory Listing
Modified Wed Oct 22 16:09:19 2008 UTC (10 years, 11 months ago) by duarte
Fixed bug: now correctly capturing exit state. Correctly cleaning up (killing jobs) after a failure. Closing the drmaa session properly.
Revision 776 - Directory Listing
Modified Wed Oct 8 17:09:19 2008 UTC (10 years, 11 months ago) by duarte
Implemented first version of a parallel (using distributed distgeom jobs through sge) reconstruction. Experimental so far, not well tested.
Revision 754 - Directory Listing
Modified Mon Sep 22 10:30:06 2008 UTC (11 years ago) by duarte
New method geometrizeContactMap
Revision 727 - Directory Listing
Modified Tue Aug 26 15:56:20 2008 UTC (11 years ago) by duarte
Better implementation of getViolatedEdges
Revision 726 - Directory Listing
Modified Tue Aug 26 14:22:33 2008 UTC (11 years ago) by duarte
Added static method to report violations.
Revision 724 - Directory Listing
Modified Thu Aug 21 12:17:26 2008 UTC (11 years, 1 month ago) by duarte
Removing test commit
Revision 723 - Directory Listing
Modified Thu Aug 21 12:15:15 2008 UTC (11 years, 1 month ago) by duarte
Test commit
Revision 715 - Directory Listing
Modified Thu Aug 7 11:13:06 2008 UTC (11 years, 1 month ago) by duarte
New option -s to do split output. 
Now converting final gro file to pdb
Fixed bugs:
- now flushing correctly the gromacs.log (by closing log)
- now properly cleaning up temp files (the ones written to /tmp)

Revision 713 - Directory Listing
Modified Wed Aug 6 14:35:49 2008 UTC (11 years, 1 month ago) by duarte
Initial commit of script and classes to interface with gromacs.
Revision 680 - Directory Listing
Modified Fri May 30 12:09:42 2008 UTC (11 years, 3 months ago) by duarte
New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond.
New method in Pdb: getOmega
Revision 678 - Directory Listing
Modified Wed May 28 13:53:03 2008 UTC (11 years, 3 months ago) by duarte
Changed default force constants to tinker's defaults ones (100.0 for distances and 1.0 for torsions). Reconstruction from averaged graphs was not working well sometimes, with really bad clashes. We think the distance force constant=10 was causing this.
Revision 670 - Directory Listing
Modified Sat May 24 17:48:28 2008 UTC (11 years, 3 months ago) by duarte
Fixed bug: can't assign phi/psi torsion angle restraint to first and last residues.
Revision 663 - Directory Listing
Modified Fri May 23 13:44:38 2008 UTC (11 years, 4 months ago) by duarte
Added phi/psi angle constraints to the reconstruction pipeline. New option -F in averageGraph for using phi/psi angle constraints
Revision 621 - Directory Listing
Modified Thu May 8 17:17:07 2008 UTC (11 years, 4 months ago) by stehr
Added members and method to ProtStructGraph and Pdb to write AUTHOR and METHOD fields to Casp files. Added missing reconstructFast methods to TinkerRunner.
Revision 609 - Directory Listing
Modified Wed Apr 30 14:11:50 2008 UTC (11 years, 4 months ago) by duarte
Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph
Revision 574 - Directory Listing
Modified Fri Mar 28 17:10:55 2008 UTC (11 years, 5 months ago) by duarte
Introduced another check in runMinimize: now we check for CHKXYZ warnings, that happened when the xyz file is somehow not well formatted. In some cases that leads to strange output in minimize.
Revision 572 - Directory Listing
Modified Fri Mar 28 15:43:07 2008 UTC (11 years, 5 months ago) by duarte
New feature in TinkerRunner: now it can run "analyze" and "minimize" programs from the tinker package
Fixed some bugs and improved TinkerRunner: 
- flushing instead of closing the log PrintWriter when throwing TinkerError exception. Before it would close and nothing more would get logged after the first error.
- now writing command line to log
- now flusing at the end of each runXXX() method
New script computeEnergies for calculating energies of a set of decoys using tinker.
Revision 541 - Directory Listing
Modified Thu Feb 14 18:30:47 2008 UTC (11 years, 7 months ago) by duarte
Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.
Revision 540 - Directory Listing
Modified Thu Feb 14 16:19:04 2008 UTC (11 years, 7 months ago) by duarte
Fixed mega-nasty bug: after introducing the PRMType enum, there was still one instance of the "type" variable being compared to a String in getCorrectedPdbAtomName method
Revision 539 - Directory Listing
Modified Thu Feb 14 13:38:29 2008 UTC (11 years, 7 months ago) by stehr
some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)
Revision 538 - Directory Listing
Modified Thu Feb 14 11:56:26 2008 UTC (11 years, 7 months ago) by duarte
New option in reconstruct: -f force constant. New constructor in TinkerRunner that takes the force constant, previous constructor will work as before with the default constant.
Revision 492 - Directory Listing
Modified Wed Jan 2 13:18:57 2008 UTC (11 years, 8 months ago) by duarte
Copied from: branches/aglappe-jung/tinker revision 491
Copied the aglappe-jung branch into trunk.

Revision 488 - Directory Listing
Modified Wed Jan 2 10:23:13 2008 UTC (11 years, 8 months ago) by duarte
Original Path: branches/aglappe-jung/tinker
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Revision 474 - Directory Listing
Modified Thu Dec 13 13:45:01 2007 UTC (11 years, 9 months ago) by duarte
Original Path: branches/aglappe-jung/tinker
Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph
Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise
Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0
Revision 441 - Directory Listing
Modified Thu Nov 29 15:19:37 2007 UTC (11 years, 9 months ago) by duarte
Original Path: branches/aglappe-jung/tinker
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
Revision 420 - Directory Listing
Modified Thu Nov 22 17:27:44 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/tinker
First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there.
NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Revision 419 - Directory Listing
Modified Thu Nov 22 14:09:18 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/tinker
Re-branching for JUNG2 development
Revision 393 - Directory Listing
Modified Thu Nov 8 11:49:38 2007 UTC (11 years, 10 months ago) by duarte
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
Revision 392 - Directory Listing
Modified Thu Nov 8 11:25:06 2007 UTC (11 years, 10 months ago) by stehr
new methods getLastModelFiles and getGdtsToNative (using MaxClusterRunner)
Revision 379 - Directory Listing
Modified Fri Nov 2 14:22:54 2007 UTC (11 years, 10 months ago) by stehr
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph

Revision 368 - Directory Listing
Modified Thu Oct 25 09:38:02 2007 UTC (11 years, 10 months ago) by duarte
Now parsing tinker's error function value, changed report file format (again!!)
Revision 347 - Directory Listing
Modified Thu Oct 11 08:54:50 2007 UTC (11 years, 11 months ago) by duarte
Writing report to file instead of standard output
Catching unknown errors in runDistgeom (all other non-zero exit values)
Revision 346 - Directory Listing
Modified Thu Oct 11 08:38:36 2007 UTC (11 years, 11 months ago) by duarte
Doing more input error checks
In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used
Revision 343 - Directory Listing
Modified Wed Oct 10 16:19:18 2007 UTC (11 years, 11 months ago) by stehr
fixed bug when running distgeom, now waiting for process to exit before checking exit status
Revision 342 - Directory Listing
Modified Wed Oct 10 15:52:36 2007 UTC (11 years, 11 months ago) by stehr
added error handling for killed tinker process with error code 139 (presumably out of memory)
Revision 341 - Directory Listing
Modified Wed Oct 10 15:14:55 2007 UTC (11 years, 11 months ago) by duarte
Now capturing exit status 137 (2 instances of tinker running in same machine)
Now outputting progress per model
Revision 338 - Directory Listing
Modified Fri Oct 5 11:56:28 2007 UTC (11 years, 11 months ago) by duarte
Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason!
Throwing less exceptions in ConstraintsMaker
Revision 335 - Directory Listing
Modified Tue Oct 2 14:59:28 2007 UTC (11 years, 11 months ago) by duarte
Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"
Revision 333 - Directory Listing
Modified Mon Oct 1 17:17:42 2007 UTC (11 years, 11 months ago) by duarte
Now does correct atom mapping for any atom of any residue ONLY for amber prm files
createConstraints does not work yet with multi atom contact types
Got rid of all the commented out mapAtoms code + some refactoring
Revision 328 - Directory Listing
Modified Mon Oct 1 10:57:08 2007 UTC (11 years, 11 months ago) by duarte
First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo
Revision 323 - Directory Listing
Added Tue Sep 18 14:13:14 2007 UTC (12 years ago) by duarte
Moved tinker stuff to its own package