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r1228
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alignment/ 1009 (11 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
scoring/ 1127 (11 years ago) by matt4077: New Residuescoringfunctionimplementation
graphs/ 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.
features/ 1226 (11 years ago) by hstehr: Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
ContactType.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PdbLoadError.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PdbCodeNotFoundError.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PdbaseInconsistencyError.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
ConformationsNotSameSizeError.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PolResidue.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Polymer.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
AtomType.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PdbChainCodeNotFoundError.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
TemplateList.java 1009 (11 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
PdbSet.java 1009 (11 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
BackboneCoords.java 1009 (11 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
aapairsBounds.dat 1012 (11 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
contactTypes.dat 1012 (11 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
AAinfo.java 1012 (11 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
Template.java 1034 (11 years ago) by jmduarteg: Extracted Scop parsing code to its own connection class.
AminoAcid.java 1094 (11 years ago) by jmduarteg: Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
symop.lib 1179 (11 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
SymoplibParser.java 1180 (11 years ago) by jmduarteg: Now correctly parsing the right short name field
PdbfilePdb.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.
CrystalCell.java 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)
PdbUnitCell.java 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)
SpaceGroup.java 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.
PdbasePdb.java 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.
CiffilePdb.java 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.
Atom.java 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.
PdbAsymUnit.java 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.
Pdb.java 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.
ChainInterface.java 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.
InterfaceRimCore.java 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.
Residue.java 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.
ChainInterfaceList.java 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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