 ../
|
examples/
|
1399
(11 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/
|
1599
(9 years ago)
by jmduarteg:
Fixed important issues with searching and alignment of homologs:
- ids and coverage were calculated wrongly, based on all BlastHsps for a hit. Now based on single Hsps
- fixed bug in BlastHsp.getQueryCoverage: was miscalculating the coverage by 1 unit
- the useHspsOnly parameter in alignment didn't make much sense. We need always to use the hsp segments only, extending to the full sequence is dangerous and in any case does not make sense at all if the clustering is done in hsps only
|
addSeq2Mcma.java
|
1342
(11 years ago)
by hstehr:
|
|
alignSeq.java
|
1594
(9 years ago)
by jmduarteg:
Now will also take uniprot codes as input
|
|
averageGraph.java
|
1399
(11 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
(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.
|
|
calcMass.java
|
1407
(10 years ago)
by jmduarteg:
New methods and script to calculate mass of a protein/chain.
|
|
calcVolsAndSurfs.java
|
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.
|
|
calculateGridDensity.java
|
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.
|
|
checkChirality.java
|
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.
|
|
clustal2fasta.java
|
1344
(11 years ago)
by hstehr:
|
|
compareAlignments.java
|
1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
|
|
compareCMs.java
|
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.
|
|
computeEnergies.java
|
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
|
|
dumppdb.java
|
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.
|
|
dumpseq.java
|
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.
|
|
enumerateAssemblies.java
|
1587
(9 years ago)
by jmduarteg:
Now using a minimum threshold value for considering a residue at surface (instead of 0 before)
|
|
enumerateInterfaces.java
|
1588
(9 years ago)
by jmduarteg:
New feature: now we can take cofactors into account for calculation of ASA in interfaces
|
|
genDbGraph.java
|
1472
(10 years ago)
by jmduarteg:
Fixed a couple of problems with ScopConnection. Added another atom type.
|
|
genGraph.java
|
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.
|
|
getPisaAssemblyPreds.java
|
1480
(10 years ago)
by jmduarteg:
Minor fix
|
|
mapMutations.java
|
1399
(11 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
(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.
|
|
pairwiseSeqId.java
|
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
|
|
pir2fasta.java
|
1343
(11 years ago)
by hstehr:
|
|
reconstruct.java
|
1399
(11 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
(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
|
|
scoreDecoys.java
|
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.
|
|
scoreGeomOfPdbs.java
|
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.
|
|
scorePdbSet.java
|
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.
|
|
superimposeMult.java
|
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.
|
|
testAICGraph.java
|
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.
|
|
testClusterConnection.java
|
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
|
|
testDbRIGraph.java
|
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
|
|
testJUNGframework.java
|
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.
|
|
testPyMol.java
|
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
|
|
unitCellVol.java
|
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.
|
|
writePerAtomDistancesToBFactor.java
|
1399
(11 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
(11 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,...)
|
