 ../
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deltaRank/
|
946
(12 years ago)
by duarte:
Now passing db explicitely instead of using the db from the connection.
|
|
proteinstructure/
|
945
(12 years ago)
by duarte:
Added new scoring method: atom distance based scoring (scoring based on multiple distance bins, instead of just on contacts)
|
|
tools/
|
943
(12 years ago)
by winkelma:
contact map rainbows
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|
tinker/
|
940
(12 years ago)
by winkelma:
Delta Rank
|
|
features/
|
938
(12 years ago)
by stehr:
fixed bugs in getDescription()
|
|
embed/
|
937
(12 years ago)
by gmueller:
|
|
actionTools/
|
925
(12 years ago)
by winkelma:
merged tinker changes into trunk
|
|
tests/
|
919
(12 years ago)
by duarte:
Fixed bug: was not handling correctly sequences with 'X' in reconstruction
Fixed bug: Pdb.getPhi/Psi were failing because hasCoordinates(int,String) was NullPointing for unobserved residues.
Added test case for getAllPhiPsi
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sequence/
|
883
(12 years ago)
by stehr:
some cosmetic changes
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|
graphAveraging/
|
811
(13 years ago)
by duarte:
New options -e and -i in reconstruct (for forcing angle constraints)
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ppi/
|
788
(13 years ago)
by filippis:
white TO talyn
|
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litNet/
|
788
(13 years ago)
by filippis:
white TO talyn
|
|
sadp/
|
501
(14 years ago)
by duarte:
Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
|
scoreDecoys.java
|
945
(12 years ago)
by duarte:
Added new scoring method: atom distance based scoring (scoring based on multiple distance bins, instead of just on contacts)
|
|
writePerAtomDistancesToBFactor.java
|
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)
|
|
Manifest.txt
|
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
|
866
(12 years ago)
by duarte:
Refactored Residue->PolResidue. Now Residue will be the proper implementation of a residue as part of a Pdb
|
|
alignSeq.java
|
847
(13 years ago)
by stehr:
new executable for pairwise (global) sequence alignment
|
|
mirrorIt.java
|
844
(13 years ago)
by duarte:
New script to mirror a pdb
|
|
mapMutations.java
|
839
(13 years ago)
by stehr:
added option to keep pymol script
|
|
reconstruct.java
|
834
(13 years ago)
by duarte:
Now using file name as id for reports when reconstructing from cm files.
|
|
writeSASAtoBFactor.java
|
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
|
|
pairwiseSeqId.java
|
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
|
|
genGraph.java
|
794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
|
|
genDbGraph.java
|
794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
|
|
dumppdb.java
|
794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
|
|
dumpseq.java
|
794
(13 years ago)
by duarte:
Got rid of hard coded mysql server references in scripts.
|
|
testPdb.java
|
793
(13 years ago)
by duarte:
Cleaned up and updated the testPdb example code.
|
|
testMySQLConnection.java
|
792
(13 years ago)
by duarte:
Cleaned up and updated the mysql connection example
|
|
createGraphDb.sh
|
790
(13 years ago)
by filippis:
white TO talyn
|
|
doClassifySingleModels.sh
|
789
(13 years ago)
by filippis:
white TO talyn
|
|
benchmarkGraphAlgorithm.java
|
788
(13 years ago)
by filippis:
white TO talyn
|
|
testDbRIGraph.java
|
788
(13 years ago)
by filippis:
white TO talyn
|
|
calculateGridDensity.java
|
788
(13 years ago)
by filippis:
white TO talyn
|
|
averageGraph.java
|
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.
|
|
make-aglappe.sh
|
777
(13 years ago)
by duarte:
Added drmaa.jar to make file
|
|
superimposeMult.java
|
771
(13 years ago)
by stehr:
now taking command line parameters
|
|
addSeq2Mcma.java
|
769
(13 years ago)
by stehr:
added methods and executables to calculate 3d superimpositions using PolyposeRunner
|
|
compareAlignments.java
|
769
(13 years ago)
by stehr:
added methods and executables to calculate 3d superimpositions using PolyposeRunner
|
|
runMD.java
|
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)
|
|
testJUNGframework.java
|
660
(14 years ago)
by duarte:
Put another test: finding edges is independent of order of indices given for UNDIRECTED.
|
|
computeEnergies.java
|
573
(14 years ago)
by duarte:
Fixed script: was exiting after computing native energy!
|
|
testPymolServer.java
|
492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
testClusterConnection.java
|
492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
testGraph2Pml.java
|
492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
testPyMol.java
|
492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
compareCMs.java
|
492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
