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root/owl/trunk/src/owl/core/structure
r1327
File Last Change
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scoring/ 1287 (10 years ago) by matt4077:
features/ 1306 (10 years ago) by jmduarteg: Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
alignment/ 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
graphs/ 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
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
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
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!
Asa.java 1255 (10 years ago) by jmduarteg: Minor changes to the test.
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
InterfaceRimCore.java 1264 (10 years ago) by jmduarteg: Added printing of rim and core residues methods.
SymoplibParser.java 1281 (10 years ago) by jmduarteg: Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.
PdbUnitCell.java 1284 (10 years ago) by cvehlow: Overrides removed
contactTypes.dat 1302 (10 years ago) by hstehr: adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
PdbChainCodeNotFoundException.java 1305 (10 years ago) by jmduarteg: Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
ConformationsNotSameSizeException.java 1305 (10 years ago) by jmduarteg: Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
PdbaseInconsistencyException.java 1305 (10 years ago) by jmduarteg: Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
PdbCodeNotFoundException.java 1305 (10 years ago) by jmduarteg: Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
SpaceGroup.java 1306 (10 years ago) by jmduarteg: Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
CrystalCell.java 1306 (10 years ago) by jmduarteg: Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
ContactType.java 1316 (10 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
AminoAcid.java 1316 (10 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
Residue.java 1316 (10 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
ChainInterface.java 1319 (10 years ago) by jmduarteg: Removed the serialize/deserialize methods (now in Goodies)
ChainInterfaceList.java 1319 (10 years ago) by jmduarteg: Removed the serialize/deserialize methods (now in Goodies)
Nucleotide.java 1321 (10 years ago) by jmduarteg: New enum for nucleotides
Atom.java 1324 (10 years ago) by jmduarteg: A few bug fixes and improvements in pdb data parsing. - bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files - improved very slightly the cif file parser moving out of loops the index getters - drop fullLength as a field in Pdb, now we have only getFullLength() - pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster) - now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
PdbAsymUnit.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
TemplateList.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
Pdb.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbSet.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbLoadException.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
Template.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbasePdb.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
CiffilePdb.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbfilePdb.java 1326 (10 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
AtomType.java 1327 (10 years ago) by jmduarteg: Some more atoms seen in pdb files
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