 ../
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proteinstructure/
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798
(13 years ago)
by duarte:
New method in Pdb to set atoms for all coordinates of a given atom. Used in BoundsSmoother and Embedder mains.
Changed slightly how parameters are passed in BoundsSmoother.
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embed/
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798
(13 years ago)
by duarte:
New method in Pdb to set atoms for all coordinates of a given atom. Used in BoundsSmoother and Embedder mains.
Changed slightly how parameters are passed in BoundsSmoother.
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tinker/
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795
(13 years 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.
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sequence/
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791
(13 years ago)
by filippis:
white TO talyn
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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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graphAveraging/
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788
(13 years ago)
by filippis:
white TO talyn
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tests/
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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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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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reconstruct.java
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784
(13 years ago)
by duarte:
Minor change in help string
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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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pairwiseSeqId.java
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774
(13 years ago)
by stehr:
updated output of pairwiseSeqId
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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
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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