 ../
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alignment/
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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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scoring/
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1127
(11 years ago)
by matt4077:
New Residuescoringfunctionimplementation
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graphs/
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1225
(11 years ago)
by jmduarteg:
Now elimination of redundant interfaces not based only on count of edges, but also on identity of each of the contacts (atom's serials, atom codes, residue serials, residue types). Added more test cases. Seems to be working fine.
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features/
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1226
(11 years ago)
by hstehr:
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
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ContactType.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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PdbLoadError.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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PdbCodeNotFoundError.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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PdbaseInconsistencyError.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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ConformationsNotSameSizeError.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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PolResidue.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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Polymer.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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AtomType.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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PdbChainCodeNotFoundError.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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TemplateList.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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PdbSet.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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BackboneCoords.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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aapairsBounds.dat
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1012
(12 years ago)
by hstehr:
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
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contactTypes.dat
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1012
(12 years ago)
by hstehr:
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
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AAinfo.java
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1012
(12 years ago)
by hstehr:
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
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Template.java
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1034
(12 years ago)
by jmduarteg:
Extracted Scop parsing code to its own connection class.
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AminoAcid.java
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1094
(11 years ago)
by jmduarteg:
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
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symop.lib
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1179
(11 years ago)
by jmduarteg:
New classes to parse and store crystallographic space groups info.
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SymoplibParser.java
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1180
(11 years ago)
by jmduarteg:
Now correctly parsing the right short name field
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PdbfilePdb.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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CrystalCell.java
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1212
(11 years ago)
by jmduarteg:
First fully working implementation of interface enumeration!! WAn exact copy of PISA's interface enumeration! (only tested with very few examples so far)
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PdbUnitCell.java
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1212
(11 years ago)
by jmduarteg:
First fully working implementation of interface enumeration!! WAn exact copy of PISA's interface enumeration! (only tested with very few examples so far)
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SpaceGroup.java
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1215
(11 years ago)
by jmduarteg:
Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side.
Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa.
Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct.
Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.
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PdbasePdb.java
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1218
(11 years ago)
by jmduarteg:
Fixed bug: was null pointing in parsing NMR cif files because they don't have crystal parameter fields. Now skipping that properly. Added NMR test entry to test cases.
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CiffilePdb.java
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1218
(11 years ago)
by jmduarteg:
Fixed bug: was null pointing in parsing NMR cif files because they don't have crystal parameter fields. Now skipping that properly. Added NMR test entry to test cases.
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Pdb.java
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1228
(11 years ago)
by jmduarteg:
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
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InterfaceRimCore.java
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1228
(11 years ago)
by jmduarteg:
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
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Residue.java
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1228
(11 years ago)
by jmduarteg:
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
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ChainInterfaceList.java
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1228
(11 years ago)
by jmduarteg:
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
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Atom.java
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1230
(11 years ago)
by jmduarteg:
Fixed bug: bsa values were wrongly calculated.
Now sort of interfaces is always descending.
Some more testing for individual residues asa and bsa values.
Still an issue: individual bsas are not matching pisa's even though total interface areas are fine.
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PdbAsymUnit.java
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1242
(11 years ago)
by jmduarteg:
Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).
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ChainInterface.java
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1242
(11 years ago)
by jmduarteg:
Fixed bug: NACCESS (weirdly) calculates slightly different ASA values for same molecule in different orientation (i.e. it depends on the choice of axes)!! That produces then some strange BSA values (including some negative) and slight discrepancies. Thus now we run NACCESS always for each of the 2 isolated molecules of the interface and then the complex (and so losing efficiency).
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