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r1461
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owl/ 1461 (8 years ago) by jmduarteg: Now really fixed the bug with DNA/RNA ASA calculations (there were a few other issues with atom nomenclature)
examples/ 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
writeSASAtoBFactor.java 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
writePerAtomDistancesToBFactor.java 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
unitCellVol.java 1181 (9 years ago) by jmduarteg: Now parsing the unit cell and crystal space group info when reading PDB sources. New simple script for unit cell volume.
testPymolServer.java 951 (9 years ago) by duarte: Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
testPyMol.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testJUNGframework.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
testDbRIGraph.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
testClusterConnection.java 1005 (9 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
testAICGraph.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
superimposeMult.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
scorePdbSet.java 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
scoreGeomOfPdbs.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
scoreDecoys.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
runMD.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
reconstruct.java 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
pir2fasta.java 1343 (8 years ago) by hstehr:
pairwiseSeqId.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
mirrorIt.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
mapMutations.java 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
genGraph.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
genDbGraph.java 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
enumerateInterfaces.java 1458 (8 years ago) by jmduarteg: Adapted to changes in PymolRunner
dumpseq.java 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
dumppdb.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
computeEnergies.java 1009 (9 years ago) by hstehr: refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
compareCMs.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
compareAlignments.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
clustal2fasta.java 1344 (8 years ago) by hstehr:
checkChirality.java 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
calculateGridDensity.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
calcVolsAndSurfs.java 1372 (8 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
calcMass.java 1407 (8 years ago) by jmduarteg: New methods and script to calculate mass of a protein/chain.
benchmarkGraphAlgorithm.java 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
averageGraph.java 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
alignSeq.java 1340 (8 years ago) by hstehr: Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta
addSeq2Mcma.java 1342 (8 years ago) by hstehr:
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