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root/owl/trunk/src/owl/core/structure
r1180
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/ 1170 (12 years ago) by hstehr: adding secondary structure functions to RIGEnsemble and GraphAverager: GraphAverager can now use DSSP to get consensus secondary structure from underlying structures.
graphs/ 1177 (12 years ago) by cvehlow: actual version
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 1176 (12 years ago) by jmduarteg: Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
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 1176 (12 years ago) by jmduarteg: Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
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 1176 (12 years ago) by jmduarteg: Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
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 1176 (12 years ago) by jmduarteg: Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
PdbfilePdb.java 1176 (12 years ago) by jmduarteg: Now parsing the occupancy and bfactors from pdbfile, ciffile or pdbase. Tests passed (improved tests so that they can run straight from an pdb ftp mirror with gz files).
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 1138 (12 years ago) by cvehlow: Getter for Atoms-TreeMap.
SpaceGroup.java 1179 (12 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
SymoplibParser.java 1180 (12 years ago) by jmduarteg: Now correctly parsing the right short name field
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
symop.lib 1179 (12 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
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