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root/owl/trunk/src/owl/core/structure
r1265
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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
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
vdw.radii 1247 (11 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
symop.lib 1179 (11 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
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
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
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
Template.java 1034 (11 years ago) by jmduarteg: Extracted Scop parsing code to its own connection class.
SymoplibParser.java 1180 (11 years ago) by jmduarteg: Now correctly parsing the right short name field
SpaceGroup.java 1258 (11 years ago) by jmduarteg: Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators. Added a test for SpaceGroup to test for proper parsing of algebraic strings
Residue.java 1256 (11 years ago) by jmduarteg: Now reporting on percent burial too
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
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
PdbfilePdb.java 1262 (11 years ago) by jmduarteg: Fixed bug: some PDB files (like those output by phenix) don't write the Z number at the end of the CRYST1 record, thus not having enough trailing spaces, we have to take care of this.
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.
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
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)
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
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
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
PdbAsymUnit.java 1265 (11 years ago) by jmduarteg: Now keeping track of ASA calc method
Pdb.java 1258 (11 years ago) by jmduarteg: Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators. Added a test for SpaceGroup to test for proper parsing of algebraic strings
InterfaceRimCore.java 1264 (11 years ago) by jmduarteg: Added printing of rim and core residues methods.
CrystalCell.java 1258 (11 years ago) by jmduarteg: Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators. Added a test for SpaceGroup to test for proper parsing of algebraic strings
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
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
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.
ChainInterfaceList.java 1265 (11 years ago) by jmduarteg: Now keeping track of ASA calc method
ChainInterface.java 1264 (11 years ago) by jmduarteg: Added printing of rim and core residues methods.
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
AtomType.java 1247 (11 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
AtomRadii.java 1258 (11 years ago) by jmduarteg: Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators. Added a test for SpaceGroup to test for proper parsing of algebraic strings
Atom.java 1248 (11 years ago) by jmduarteg: Now using our own ASA calculation instead of NACCESS for the interface areas calculation. We are slower than NACCESS but at least don't depend on it anymore, old NACCESS methods can still be used.
Asa.java 1255 (11 years ago) by jmduarteg: Minor changes to the test.
AminoAcid.java 1094 (11 years ago) by jmduarteg: Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
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
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