 ../
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examples/
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1399
(10 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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owl/
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1625
(9 years ago)
by jmduarteg:
Fixed issue: now setting unknown atom type whenever we can't guess the element. If we read from PDB file and there is an unguesseable atom that we then have to write out again the code would fail because in writeAtoms we assume we have atom types for everything.
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addSeq2Mcma.java
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1342
(11 years ago)
by hstehr:
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alignSeq.java
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1594
(9 years ago)
by jmduarteg:
Now will also take uniprot codes as input
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averageGraph.java
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1399
(10 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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benchmarkGraphAlgorithm.java
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1392
(10 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.
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calcMass.java
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1407
(10 years ago)
by jmduarteg:
New methods and script to calculate mass of a protein/chain.
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calcVolsAndSurfs.java
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1372
(11 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.
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calculateGridDensity.java
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1372
(11 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.
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checkChirality.java
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1392
(10 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.
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clustal2fasta.java
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1344
(11 years ago)
by hstehr:
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compareAlignments.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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compareCMs.java
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1372
(11 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.
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computeEnergies.java
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1009
(12 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
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dumppdb.java
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1372
(11 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.
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dumpseq.java
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1392
(10 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.
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enumerateAssemblies.java
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1587
(9 years ago)
by jmduarteg:
Now using a minimum threshold value for considering a residue at surface (instead of 0 before)
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enumerateInterfaces.java
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1613
(9 years ago)
by jmduarteg:
Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering
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genDbGraph.java
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1472
(10 years ago)
by jmduarteg:
Fixed a couple of problems with ScopConnection. Added another atom type.
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genGraph.java
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1372
(11 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.
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getPisaAssemblyPreds.java
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1480
(10 years ago)
by jmduarteg:
Minor fix
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mapMutations.java
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1399
(10 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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mirrorIt.java
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1372
(11 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.
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pairwiseSeqId.java
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1009
(12 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
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pir2fasta.java
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1343
(11 years ago)
by hstehr:
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reconstruct.java
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1399
(10 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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runMD.java
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1009
(12 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
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scoreDecoys.java
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1372
(11 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.
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scoreGeomOfPdbs.java
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1372
(11 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.
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scorePdbSet.java
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1392
(10 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.
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superimposeMult.java
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1372
(11 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.
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testAICGraph.java
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1372
(11 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.
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testClusterConnection.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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testDbRIGraph.java
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1009
(12 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
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testJUNGframework.java
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1372
(11 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.
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testPyMol.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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unitCellVol.java
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1181
(11 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.
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writePerAtomDistancesToBFactor.java
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1399
(10 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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writeSASAtoBFactor.java
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1399
(10 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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