ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/core/structure
r1213
File Last Change
 ../
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
features/ 1170 (10 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/ 1211 (10 years ago) by jmduarteg: First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point.
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
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
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
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 (10 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
SymoplibParser.java 1180 (10 years ago) by jmduarteg: Now correctly parsing the right short name field
PdbasePdb.java 1181 (10 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.
CiffilePdb.java 1181 (10 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.
PdbfilePdb.java 1181 (10 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.
SpaceGroup.java 1209 (10 years ago) by jmduarteg: Fixed bug: was missing one operator in getTransformations
Atom.java 1211 (10 years ago) by jmduarteg: First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point.
Residue.java 1211 (10 years ago) by jmduarteg: First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point.
Pdb.java 1212 (10 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)
ChainInterface.java 1212 (10 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)
CrystalCell.java 1212 (10 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 (10 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)
PdbAsymUnit.java 1213 (10 years ago) by jmduarteg: Changed default cutoff to coincide with PISA, entry 1pmm was a good clue (one interface has a 1 atom contact with 6 cutoff). Now going to the negative side (instead of positive) when translating the unit cell to coincide with PISA operators.
         30 files shown