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root/owl/trunk/src/owl/core/structure
r1287
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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
features/ 1226 (10 years ago) by hstehr: Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
graphs/ 1287 (10 years ago) by matt4077:
scoring/ 1287 (10 years ago) by matt4077:
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
AminoAcid.java 1094 (11 years ago) by jmduarteg: Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Asa.java 1255 (10 years ago) by jmduarteg: Minor changes to the test.
Atom.java 1248 (10 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.
AtomRadii.java 1258 (10 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
AtomType.java 1247 (10 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
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
ChainInterface.java 1284 (10 years ago) by cvehlow: Overrides removed
ChainInterfaceList.java 1284 (10 years ago) by cvehlow: Overrides removed
CiffilePdb.java 1282 (10 years ago) by jmduarteg: Fixed formatting of the exception message
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
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
CrystalCell.java 1269 (10 years ago) by jmduarteg: Fixed bug in SpaceGroupTest. Now it works and test passes. Introduced checking for clashes in interfaces. Added it to the PdbAsymUnitTest
InterfaceRimCore.java 1264 (10 years ago) by jmduarteg: Added printing of rim and core residues methods.
Pdb.java 1286 (10 years ago) by hstehr: calling readStructureOrNull was exiting rather than returning null
PdbAsymUnit.java 1280 (10 years ago) by jmduarteg: Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.
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
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
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
PdbUnitCell.java 1284 (10 years ago) by cvehlow: Overrides removed
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
PdbasePdb.java 1282 (10 years ago) by jmduarteg: Fixed formatting of the exception message
PdbfilePdb.java 1282 (10 years ago) by jmduarteg: Fixed formatting of the exception message
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
Residue.java 1256 (10 years ago) by jmduarteg: Now reporting on percent burial too
SpaceGroup.java 1270 (10 years ago) by jmduarteg: Fixed bug: was still not converting well algebraic transformations to matrix: was failing for transformations with terms like "X-Y+1/3"
SymoplibParser.java 1281 (10 years ago) by jmduarteg: Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.
Template.java 1034 (11 years ago) by jmduarteg: Extracted Scop parsing code to its own connection class.
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
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
symop.lib 1179 (10 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
vdw.radii 1247 (10 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
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