Revision 419 - Directory Listing
Modified Thu Nov 22 14:09:18 2007 UTC (16 years, 10 months ago) by duarte

Re-branching for JUNG2 development

Revision 393 - Directory Listing
Modified Thu Nov 8 11:49:38 2007 UTC (16 years, 10 months ago) by duarte
Original Path: trunk/tinker

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 (16 years, 10 months ago) by stehr
Original Path: trunk/tinker

new methods getLastModelFiles and getGdtsToNative (using MaxClusterRunner)

Revision 379 - Directory Listing
Modified Fri Nov 2 14:22:54 2007 UTC (16 years, 10 months ago) by stehr
Original Path: trunk/tinker

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 (16 years, 11 months ago) by duarte
Original Path: trunk/tinker

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 (16 years, 11 months ago) by duarte
Original Path: trunk/tinker

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 (16 years, 11 months ago) by duarte
Original Path: trunk/tinker

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 (16 years, 11 months ago) by stehr
Original Path: trunk/tinker

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 (16 years, 11 months ago) by stehr
Original Path: trunk/tinker

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 (16 years, 11 months ago) by duarte
Original Path: trunk/tinker

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 (16 years, 11 months ago) by duarte
Original Path: trunk/tinker

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 (16 years, 11 months ago) by duarte
Original Path: trunk/tinker

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 (17 years ago) by duarte
Original Path: trunk/tinker

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 (17 years ago) by duarte
Original Path: trunk/tinker

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 (17 years ago) by duarte
Original Path: trunk/tinker

Moved tinker stuff to its own package