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root/owl/trunk/src/owl/core/structure
r1117
File (rev) Last Change
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scoring/ 1084 (10 years ago) by matt4077: renamed conflicting ContactMap class.
graphs/ 1066 (10 years ago) by hstehr: new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
features/ 1067 (10 years ago) by hstehr: fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()
alignment/ 1009 (10 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
contactTypes.dat 1012 (10 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
aapairsBounds.dat 1012 (10 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
TemplateList.java 1009 (10 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
Template.java 1034 (10 years ago) by jmduarteg: Extracted Scop parsing code to its own connection class.
Residue.java 1109 (10 years ago) by jmduarteg: Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.
Polymer.java 1005 (10 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 (10 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PdbfilePdb.java 1009 (10 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
PdbasePdb.java 1009 (10 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
PdbaseInconsistencyError.java 1005 (10 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PdbSet.java 1009 (10 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
PdbLoadError.java 1005 (10 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 (10 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 (10 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Pdb.java 1111 (10 years ago) by jmduarteg: Now getPdbResSerFromResSer and getResSerFromPdbResSer will return null/-1 whenever there's no mapping. Allows then for checking from the caller.
ContactType.java 1005 (10 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 (10 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
CiffilePdb.java 1032 (10 years ago) by jmduarteg: Extracted the calc-vol and calc-surf runner code to its own Runner class.
BackboneCoords.java 1009 (10 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
AtomType.java 1005 (10 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Atom.java 1109 (10 years ago) by jmduarteg: Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.
AminoAcid.java 1094 (10 years ago) by jmduarteg: Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
AAinfo.java 1012 (10 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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