 ../
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sadp/
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501
(13 years ago)
by duarte:
Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
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ppi/
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788
(12 years ago)
by filippis:
white TO talyn
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litNet/
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788
(12 years ago)
by filippis:
white TO talyn
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graphAveraging/
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811
(12 years ago)
by duarte:
New options -e and -i in reconstruct (for forcing angle constraints)
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actionTools/
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877
(11 years ago)
by stehr:
Testing package-info.java for adding javadoc comment at the package level
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features/
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879
(11 years ago)
by stehr:
moving all classes in proteinstructure.features to features
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sequence/
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883
(11 years ago)
by stehr:
some cosmetic changes
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embed/
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884
(11 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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tests/
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885
(11 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
(11 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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tools/
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889
(11 years ago)
by duarte:
New spearman method
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proteinstructure/
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892
(11 years ago)
by duarte:
Added isAllAtom to Pdb and getNumHeavyAtoms to Pdb and Residue. Fixed some docs that were still not properly clarifying about hydrogens.
Added complete main methods to AtomTypeScorer and ResTypeScorer with command line options and defaults.
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testPymolServer.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testClusterConnection.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testGraph2Pml.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testPyMol.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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compareCMs.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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computeEnergies.java
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573
(12 years ago)
by duarte:
Fixed script: was exiting after computing native energy!
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testJUNGframework.java
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660
(12 years ago)
by duarte:
Put another test: finding edges is independent of order of indices given for UNDIRECTED.
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runMD.java
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715
(12 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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addSeq2Mcma.java
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769
(12 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
(12 years ago)
by stehr:
added methods and executables to calculate 3d superimpositions using PolyposeRunner
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superimposeMult.java
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771
(12 years ago)
by stehr:
now taking command line parameters
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make-aglappe.sh
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777
(12 years ago)
by duarte:
Added drmaa.jar to make file
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averageGraph.java
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782
(12 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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benchmarkGraphAlgorithm.java
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788
(12 years ago)
by filippis:
white TO talyn
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testDbRIGraph.java
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788
(12 years ago)
by filippis:
white TO talyn
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calculateGridDensity.java
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788
(12 years ago)
by filippis:
white TO talyn
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doClassifySingleModels.sh
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789
(12 years ago)
by filippis:
white TO talyn
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createGraphDb.sh
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790
(12 years ago)
by filippis:
white TO talyn
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testMySQLConnection.java
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792
(12 years ago)
by duarte:
Cleaned up and updated the mysql connection example
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testPdb.java
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793
(12 years ago)
by duarte:
Cleaned up and updated the testPdb example code.
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genGraph.java
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794
(12 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
(12 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
(12 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
(12 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
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pairwiseSeqId.java
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815
(12 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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writeSASAtoBFactor.java
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819
(12 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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reconstruct.java
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834
(11 years ago)
by duarte:
Now using file name as id for reports when reconstructing from cm files.
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mapMutations.java
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839
(11 years ago)
by stehr:
added option to keep pymol script
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mirrorIt.java
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844
(11 years ago)
by duarte:
New script to mirror a pdb
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alignSeq.java
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847
(11 years ago)
by stehr:
new executable for pairwise (global) sequence alignment
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analyseHistone.java
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866
(11 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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Manifest.txt
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882
(11 years ago)
by stehr:
updated version to 1.2.0 (forgot to change version number in last tag)
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writePerAtomDistancesToBFactor.java
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887
(11 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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