| Links to HEAD: | (view) (annotate) |
| Sticky Revision: | |
| Sort logs by: |
reconstruct: -rmsd to mirrored pdb has been added in the report file Pdb: -comment for outputing missing atoms added PairwiseSequenceAlignment: -constructor with parameters openScore and extendScore for the gaps has been added
Fixed bug: the check for contact type validity was not correctly done
Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.
some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)
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.
Copied the aglappe-jung branch into trunk.
Now exiting upon distgeom error
Added option for min range and max range filtering (-m, -M) Fixed output of an exception
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)
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)
Re-branching for JUNG2 development
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
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
Fixed (yet again) the report output, now also outputting size (number of residues) of protein
Now parsing tinker's error function value, changed report file format (again!!)
Changed name of native output pdb file
Now writing also original pdb file Fixed output of rmsd: now only few decimal figures output
Now tinker.log has also baseName in file name
Writing report to file instead of standard output Catching unknown errors in runDistgeom (all other non-zero exit values)
Doing more input error checks In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used
cathing InterruptedException from TinkerRunner
Fixed the output
Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason! Throwing less exceptions in ConstraintsMaker
This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, enter a numeric revision.