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r1428
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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,...)
owl/ 1428 (8 years ago) by jmduarteg: Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation
addSeq2Mcma.java 1342 (8 years ago) by hstehr:
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
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,...)
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.
calcMass.java 1407 (8 years ago) by jmduarteg: New methods and script to calculate mass of a protein/chain.
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.
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.
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.
clustal2fasta.java 1344 (8 years ago) by hstehr:
compareAlignments.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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.
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
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.
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.
enumerateInterfaces.java 1428 (8 years ago) by jmduarteg: Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation
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.
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.
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,...)
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.
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
pir2fasta.java 1343 (8 years ago) by hstehr:
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,...)
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
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.
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.
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.
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.
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.
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
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
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.
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
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.
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.
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,...)
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,...)
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