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root/owl/trunk/src/owl/core/structure
r1367
File Last Change
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scoring/ 1287 (8 years ago) by matt4077:
graphs/ 1341 (8 years ago) by jmduarteg: Now parsing pdb titles in PDB, CIF and pdbase. Tests pass. Moved some constants from Pdb to PdbAsymUnit
features/ 1347 (8 years ago) by hstehr: moving project CCCP to this repository
alignment/ 1347 (8 years ago) by hstehr: moving project CCCP to this repository
PolResidue.java 1005 (9 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 (9 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 (9 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 (9 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 (9 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
vdw.radii 1247 (9 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
Asa.java 1255 (9 years ago) by jmduarteg: Minor changes to the test.
AtomRadii.java 1258 (9 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 (9 years ago) by jmduarteg: Added printing of rim and core residues methods.
SymoplibParser.java 1281 (8 years ago) by jmduarteg: Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.
PdbUnitCell.java 1284 (8 years ago) by cvehlow: Overrides removed
contactTypes.dat 1302 (8 years ago) by hstehr: adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
ConformationsNotSameSizeException.java 1305 (8 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 (8 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 (8 years ago) by jmduarteg: Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
CrystalCell.java 1306 (8 years ago) by jmduarteg: Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
ContactType.java 1316 (8 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
ChainInterface.java 1319 (8 years ago) by jmduarteg: Removed the serialize/deserialize methods (now in Goodies)
ChainInterfaceList.java 1319 (8 years ago) by jmduarteg: Removed the serialize/deserialize methods (now in Goodies)
Nucleotide.java 1321 (8 years ago) by jmduarteg: New enum for nucleotides
Atom.java 1324 (8 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
TemplateList.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbSet.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbLoadException.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
Template.java 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
AtomType.java 1327 (8 years ago) by jmduarteg: Some more atoms seen in pdb files
Residue.java 1331 (8 years ago) by jmduarteg: Another improvement to PdbfilePdb parsing: now we can also detect some ambiguous cases in alignments by checking the contiguity of the 3D chain. This fixes 2 cases from our test data set: 1dki and 2ofz. Now only 2 warnings for the whole dataset (both because of ambiguous assignment in HIS tags, safe to ignore. Could even be that CIF got them wrong)
PdbasePdb.java 1341 (8 years ago) by jmduarteg: Now parsing pdb titles in PDB, CIF and pdbase. Tests pass. Moved some constants from Pdb to PdbAsymUnit
CiffilePdb.java 1341 (8 years ago) by jmduarteg: Now parsing pdb titles in PDB, CIF and pdbase. Tests pass. Moved some constants from Pdb to PdbAsymUnit
PdbfilePdb.java 1341 (8 years ago) by jmduarteg: Now parsing pdb titles in PDB, CIF and pdbase. Tests pass. Moved some constants from Pdb to PdbAsymUnit
AminoAcid.java 1349 (8 years ago) by hstehr: moving info about reduced alphabets from main() to printReducedAlphabetInfo()
PdbAsymUnit.java 1363 (8 years ago) by jmduarteg: New class BoundingBox for bounds. Added bounds caching also to PdbAsymUnit. Fixed some issues with it in Pdb. Everything looks a lot cleaner thanks to new class.
Pdb.java 1363 (8 years ago) by jmduarteg: New class BoundingBox for bounds. Added bounds caching also to PdbAsymUnit. Fixed some issues with it in Pdb. Everything looks a lot cleaner thanks to new class.
contactTypes.all.dat 1367 (8 years ago) by hstehr: Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
contactTypes.cmview.dat 1367 (8 years ago) by hstehr: Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
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