Revision
474 -
Directory Listing
Modified
Thu Dec 13 13:45:01 2007 UTC
(16 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
(16 years, 10 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
(16 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
393 -
Directory Listing
Modified
Thu Nov 8 11:49:38 2007 UTC
(16 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
(16 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
(16 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
(16 years, 11 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
(16 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
(16 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
(16 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
(16 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
(16 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
(16 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
(16 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
(17 years 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
(17 years 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
(17 years ago)
by
duarte
Moved tinker stuff to its own package
