 ../
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proteinstructure/
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890
(12 years ago)
by duarte:
Bug fixes in pdb file parser. Was throwing string out of bounds exception with some pdb files.
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tools/
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889
(12 years ago)
by duarte:
New spearman method
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tests/
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885
(12 years ago)
by duarte:
Major change: now hydrogens are read in Pdb and subclasses
New getChirality method in Residue.
Added some more unit tests.
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tinker/
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885
(12 years ago)
by duarte:
Major change: now hydrogens are read in Pdb and subclasses
New getChirality method in Residue.
Added some more unit tests.
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embed/
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884
(12 years ago)
by duarte:
Major commit:
- change of the implementation of Pdb (interface remains backwards compatible). Now data stored in a proper object-oriented way. Pdb not abstract anymore, a protein model can be created by using one of the constructors
- added many tests and test files for Pdb (and merged some already existing tests from the default package)
- removed obsolete classes related to msd
- bug fix: PdbfilePdb now properly reads files with alt codes
- all tests passed
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sequence/
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883
(12 years ago)
by stehr:
some cosmetic changes
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features/
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879
(12 years ago)
by stehr:
moving all classes in proteinstructure.features to features
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actionTools/
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877
(12 years ago)
by stehr:
Testing package-info.java for adding javadoc comment at the package level
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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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ppi/
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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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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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writePerAtomDistancesToBFactor.java
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887
(12 years ago)
by stehr:
rewrote method getPerAtomDistances such that atom serials do not need to match between the two structures (matching corresponding atoms based in resser)
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Manifest.txt
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882
(12 years ago)
by stehr:
updated version to 1.2.0 (forgot to change version number in last tag)
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analyseHistone.java
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866
(12 years ago)
by duarte:
Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
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alignSeq.java
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847
(13 years ago)
by stehr:
new executable for pairwise (global) sequence alignment
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mirrorIt.java
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844
(13 years ago)
by duarte:
New script to mirror a pdb
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mapMutations.java
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839
(13 years ago)
by stehr:
added option to keep pymol script
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reconstruct.java
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834
(13 years ago)
by duarte:
Now using file name as id for reports when reconstructing from cm files.
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writeSASAtoBFactor.java
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819
(13 years ago)
by stehr:
new command line tools for visualizing surface accessibility and for printing information about a mutated site in a protein structure
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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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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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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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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
(13 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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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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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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