 ../
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examples/
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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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owl/
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1577
(7 years ago)
by jmduarteg:
Important change in interface calculation:
- another massive gain in run-time and memory usage: we first use the bounding boxes translations to see if it is worth translating the whole unit cells
- thanks to that we now go to 2nd neighbors! (still performance is better than before with only 1st neighbors!). With that we fixed the long-standing bug by which we miss interfaces beyond the 1st neighbor
- included a few examples of 2nd neighbor problem in test
- re-done the symmetry redundancy elimination, it is there but it has a very little effect on overall performance. Now we only don't use an operator when we are very sure its partner was in the right place. In effect we could get rid of it because it wouldn't really affect the performance, we rather keep it as it is good to remember that there is a lot of symmetry redundancy
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testClusterConnection.java
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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
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testPyMol.java
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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
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computeEnergies.java
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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
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testDbRIGraph.java
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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
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runMD.java
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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
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pairwiseSeqId.java
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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
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unitCellVol.java
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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.
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compareAlignments.java
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1326
(8 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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alignSeq.java
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1340
(8 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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addSeq2Mcma.java
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1342
(8 years ago)
by hstehr:
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pir2fasta.java
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1343
(8 years ago)
by hstehr:
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clustal2fasta.java
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1344
(8 years ago)
by hstehr:
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genGraph.java
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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.
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superimposeMult.java
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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.
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calcVolsAndSurfs.java
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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.
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scoreGeomOfPdbs.java
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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.
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mirrorIt.java
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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.
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testAICGraph.java
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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.
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testJUNGframework.java
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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.
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dumppdb.java
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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.
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scoreDecoys.java
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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.
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calculateGridDensity.java
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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.
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compareCMs.java
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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.
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scorePdbSet.java
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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.
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checkChirality.java
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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.
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benchmarkGraphAlgorithm.java
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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.
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dumpseq.java
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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.
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reconstruct.java
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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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averageGraph.java
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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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writeSASAtoBFactor.java
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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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mapMutations.java
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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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writePerAtomDistancesToBFactor.java
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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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calcMass.java
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1407
(8 years ago)
by jmduarteg:
New methods and script to calculate mass of a protein/chain.
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enumerateAssemblies.java
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1471
(8 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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genDbGraph.java
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1472
(8 years ago)
by jmduarteg:
Fixed a couple of problems with ScopConnection. Added another atom type.
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getPisaAssemblyPreds.java
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1480
(8 years ago)
by jmduarteg:
Minor fix
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enumerateInterfaces.java
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1573
(7 years ago)
by jmduarteg:
IMPORTANT changes and fixes in interface calculation:
- very important bug fix: BoundingBox was not always telling properly whether 2 boxes overlap. This not only fixes the important bug but also boosts the speed of interface calculation
- optimisation of PdbChain.getAICGraph not to return an empty graph whenever no overlap of boxes is found (instead of generating empty distance matrix and checking its emptiness): this alone gives the biggest performance boost to interface calculation, around 5x faster thanks to this alone
- fine optimisation of max/min calculation in BoundingBox
- made sure that bounds caching is done properly
- introduced the right solution for symmetry redundancy elimination: operators multiplication is the identity. Before we had an ad-hoc solution that wasn't comprehensive at all
- in any case the symmetry redundancy elimination is right now almost turned off because we introduced new conditions to re-check equivalent operators to fix cases like 2gsg, 3ka0, 1vzi, 1g3p and 1eaq, where some interfaces are missed due to an equivalent operator making the molecule fall in a cell where there's no contacts
All in all this totally changes the interface calculation: 1) by a massive boost in performance 2) by making it more correct, surely there were cases with missing interfaces, we were just lucky not to find them in testing
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