 ../
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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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1568
(9 years ago)
by jmduarteg:
Bug fix: was null pointing when a Deuterium atom was present in a standard amino acid (not clear anyway whether that is standard PDB practice). Now checking for unknown atoms in standard amino acids when getting their radii. Will output error and continue with their standard vdw radius.
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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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1340
(11 years ago)
by hstehr:
Fixed bugs in method for reading from PIR file; added script to convert from PIR to Fasta
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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
(11 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
(11 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
(11 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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1471
(10 years ago)
by jmduarteg:
Introduced some more experimental code for enumeration of assemblies. BEWARE many things are UNFINISHED, namely in InterfaceGraph class the code to find induced and symmetry related interfaces is just a draft. There are many fundamental issues not solved yet. Be careful especially with implementations of equals and hashCode methods in InterfaceGraph, SubunitId, InterfaceGraphEdge etc. They alter "quietly" the behaviour of everything.
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enumerateInterfaces.java
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1513
(10 years ago)
by jmduarteg:
Implemented some basic symmetry redundancy elimination in interfaces search. Moved interfaces-search to a separate class.
New pymol output file in enumerateInterfaces with all interfaces in a single session
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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
(11 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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