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root/owl/trunk/src/owl/core/structure
r1130
File Last Change
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alignment/ 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
features/ 1067 (12 years ago) by hstehr: fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()
graphs/ 1129 (12 years ago) by cvehlow: Additional method for coordinate transversion.
scoring/ 1127 (12 years ago) by matt4077: New Residuescoringfunctionimplementation
AAinfo.java 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
AminoAcid.java 1094 (12 years ago) by jmduarteg: Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Atom.java 1109 (12 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.
AtomType.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
BackboneCoords.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
CiffilePdb.java 1032 (12 years ago) by jmduarteg: Extracted the calc-vol and calc-surf runner code to its own Runner class.
ConformationsNotSameSizeError.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
ContactType.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
Pdb.java 1118 (12 years ago) by cvehlow: RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.
PdbChainCodeNotFoundError.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
PdbCodeNotFoundError.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
PdbLoadError.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
PdbSet.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
PdbaseInconsistencyError.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
PdbasePdb.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
PdbfilePdb.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
PolResidue.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
Polymer.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
Residue.java 1109 (12 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.
Template.java 1034 (12 years ago) by jmduarteg: Extracted Scop parsing code to its own connection class.
TemplateList.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
aapairsBounds.dat 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
contactTypes.dat 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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