 ../
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proteinstructure/
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817
(13 years ago)
by stehr:
fixed bug in runAccess : temporary file could not be created when pdb code was not known, now using '1xxx' in this case
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tests/
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813
(13 years ago)
by duarte:
Fixed runNaccess to use unique file names and documented it. Wrote also a junit test case for it.
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graphAveraging/
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811
(13 years ago)
by duarte:
New options -e and -i in reconstruct (for forcing angle constraints)
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tinker/
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809
(13 years ago)
by duarte:
Introduced some more checks for validity of contact types.
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sequence/
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806
(13 years ago)
by duarte:
New method contains().
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embed/
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804
(13 years ago)
by duarte:
Made Bound[][] bounds a member, thus changing the signature of most methods. Refactored getBoundsAllPairs(bounds) to better name computeTriangleInequality: now it uses as input the bounds member variable and updates it as output.
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ppi/
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788
(13 years ago)
by filippis:
white TO talyn
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tools/
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788
(13 years ago)
by filippis:
white TO talyn
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litNet/
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788
(13 years ago)
by filippis:
white TO talyn
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vecmath/
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524
(14 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
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sadp/
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501
(14 years ago)
by duarte:
Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
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actionTools/
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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writeSASAtoBFactor.java
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815
(13 years ago)
by stehr:
new executables for pairwise all-against-all sequence alignments (pairwiseSeqId) and for calculating surface accessibilities and writing them to the b-factor column
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pairwiseSeqId.java
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815
(13 years ago)
by stehr:
new executables for pairwise all-against-all sequence alignments (pairwiseSeqId) and for calculating surface accessibilities and writing them to the b-factor column
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reconstruct.java
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812
(13 years ago)
by duarte:
Fixed bug: in check of input of intervals wasn't checking ig intervals was null.
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genGraph.java
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794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
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genDbGraph.java
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794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
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dumppdb.java
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794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
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dumpseq.java
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794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
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testPdb.java
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793
(13 years ago)
by duarte:
Cleaned up and updated the testPdb example code.
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testMySQLConnection.java
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792
(13 years ago)
by duarte:
Cleaned up and updated the mysql connection example
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createGraphDb.sh
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790
(13 years ago)
by filippis:
white TO talyn
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doClassifySingleModels.sh
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789
(13 years ago)
by filippis:
white TO talyn
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testGetChains.java
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788
(13 years ago)
by filippis:
white TO talyn
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benchmarkGraphAlgorithm.java
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788
(13 years ago)
by filippis:
white TO talyn
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testDbRIGraph.java
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788
(13 years ago)
by filippis:
white TO talyn
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calculateGridDensity.java
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788
(13 years ago)
by filippis:
white TO talyn
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averageGraph.java
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782
(13 years ago)
by duarte:
New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf.
Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.
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make-aglappe.sh
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777
(13 years ago)
by duarte:
Added drmaa.jar to make file
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superimposeMult.java
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771
(13 years ago)
by stehr:
now taking command line parameters
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addSeq2Mcma.java
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769
(13 years ago)
by stehr:
added methods and executables to calculate 3d superimpositions using PolyposeRunner
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compareAlignments.java
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769
(13 years ago)
by stehr:
added methods and executables to calculate 3d superimpositions using PolyposeRunner
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Manifest.txt
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730
(13 years ago)
by duarte:
Updated version to 1.1.0
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runMD.java
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715
(13 years 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)
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testJUNGframework.java
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660
(14 years ago)
by duarte:
Put another test: finding edges is independent of order of indices given for UNDIRECTED.
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computeEnergies.java
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573
(14 years ago)
by duarte:
Fixed script: was exiting after computing native energy!
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testDeltaDistanceMap.java
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517
(14 years ago)
by duarte:
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this.
NOTE: graph averaging hasn't been tested after the change
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testPymolServer.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testClusterConnection.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testResidueSelectionString.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testGraph2Pml.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testPyMol.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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compareCMs.java
|
492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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