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r1647
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alignment/ 1372 (11 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
features/ 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
graphs/ 1561 (9 years ago) by jmduarteg: New method to calculate contact order
scoring/ 1372 (11 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
AaResidue.java 1428 (10 years ago) by jmduarteg: Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation
AminoAcid.java 1429 (10 years ago) by jmduarteg: Introduced calculation of relative ASAs. A few new methods to calculate rim/core of interfaces using alternative definitions.
Asa.java 1619 (9 years ago) by jmduarteg: Fixed bug in ASA calculation: was taking in finding neighbours procedure the default vdw element radius rather thatn the one set in setRadius: NOTE this changes slightly the area values we are getting. Fixed issue in parsing of atoms when no atom type can be guessed: now whenever we can't guess we write a warning, also setRadius will use default radius if element not known (instead of null pointing)
Atom.java 1626 (9 years ago) by jmduarteg: Another small fix related to last commit
AtomLine.java 1448 (10 years ago) by jmduarteg: Fixed bug in PDB file parsing: wasn't parsing correctly PDB files with no TER records and non-poly HETATMs. They were both merged together into one chain.
AtomLineList.java 1641 (8 years ago) by jmduarteg: Fixed bug: was null pointing on pdb files with a TER record positioned just before a HETATM record in the middle of a poly chain, now added more checks for duplicated PDB chain codes assignments which will catch that problem plus possibly others
AtomRadii.java 1619 (9 years ago) by jmduarteg: Fixed bug in ASA calculation: was taking in finding neighbours procedure the default vdw element radius rather thatn the one set in setRadius: NOTE this changes slightly the area values we are getting. Fixed issue in parsing of atoms when no atom type can be guessed: now whenever we can't guess we write a warning, also setRadius will use default radius if element not known (instead of null pointing)
AtomType.java 1624 (9 years ago) by nikhilbiyani: Added AtomTypes till atomic number 110
BackboneCoords.java 1009 (12 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 1613 (9 years ago) by jmduarteg: Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering
ChainInterfaceList.java 1613 (9 years ago) by jmduarteg: Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering
CiffileParser.java 1623 (9 years ago) by nikhilbiyani: Bugfix: Check for nulls while reading QParams.
ConformationsNotSameSizeException.java 1305 (11 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.
ContactType.java 1316 (11 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
CrystalCell.java 1590 (9 years ago) by jmduarteg: Now also checking the translation component of the SCALE matrix, and if different from (0,0,0) throwing an exception. Some entries still have a shifted origin (e.g. 1hga, 1hgb, 1hgc). Let's hope they fix this in next remediation.
CrystalTransform.java 1583 (9 years ago) by jmduarteg: Made new CrystalTransform class serializable
HetResidue.java 1620 (9 years ago) by jmduarteg: Minor issue fix: now heavy water (deuterated water) treated as water, i.e. not read. Also extracted the constants to HetResidue
InterfaceGraph.java 1582 (9 years ago) by jmduarteg: Important fix to interface calculation: finally total symmetry redundancy elimination is working! - fixed a bug present since rev 1573: translation vectors of transforms were not stored properly and thus wasn't comparing the right operators - extracted TransformIdTransform private class to new class CrystalTransform. Rationalise some of the code thanks to that (still more to be done) - better debug output in interface calculation to show duplicates info
InterfaceGraphEdge.java 1471 (10 years ago) by jmduarteg: Introduced some more experimental code for enumeration of assemblies. BEWARE many things are UNFINISHED, namely in InterfaceGraph class the code to find induced and symmetry related interfaces is just a draft. There are many fundamental issues not solved yet. Be careful especially with implementations of equals and hashCode methods in InterfaceGraph, SubunitId, InterfaceGraphEdge etc. They alter "quietly" the behaviour of everything.
InterfaceRimCore.java 1613 (9 years ago) by jmduarteg: Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering
InterfacesFinder.java 1643 (8 years ago) by jmduarteg: Fixed bug CRK-128: in a non-crystallographic entry with cofactors it was crashing at getCofactors because we weren't checking for non-crystallographic entry there. The crash was a "cannot invert matrix" error, happening because the cell parameters where 0,0,0. Funnily enough this would not happen in my local machine (OpenJDK java 1.6.0_27), but it did happen in merlin (OpenJDK java1.6.0_24)
NucResidue.java 1428 (10 years ago) by jmduarteg: Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation
Nucleotide.java 1400 (10 years ago) by jmduarteg: Fixed some issues with writing of pdb files and wrote a test for write/read pdb files.
PdbAsymUnit.java 1627 (9 years ago) by jmduarteg: Several fixes: - bug fix: was always throwing exception in pdb parser for no secondary structure when not protein - new reasonable-crystal-cell check when loading PDB entries - safer pdb file parsing: now all substrings should be checked. For instance now swiss-model output files are parseable
PdbChain.java 1613 (9 years ago) by jmduarteg: Changing output options for some classes to be able to output residues with PDB residue numbering as well as CIF residue numbering
PdbChainSet.java 1372 (11 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
PdbCodeNotFoundException.java 1305 (11 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.
PdbLoadException.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbUnitCell.java 1582 (9 years ago) by jmduarteg: Important fix to interface calculation: finally total symmetry redundancy elimination is working! - fixed a bug present since rev 1573: translation vectors of transforms were not stored properly and thus wasn't comparing the right operators - extracted TransformIdTransform private class to new class CrystalTransform. Rationalise some of the code thanks to that (still more to be done) - better debug output in interface calculation to show duplicates info
PdbaseParser.java 1620 (9 years ago) by jmduarteg: Minor issue fix: now heavy water (deuterated water) treated as water, i.e. not read. Also extracted the constants to HetResidue
PdbfileParser.java 1641 (8 years ago) by jmduarteg: Fixed bug: was null pointing on pdb files with a TER record positioned just before a HETATM record in the middle of a poly chain, now added more checks for duplicated PDB chain codes assignments which will catch that problem plus possibly others
PdbxPolySeqGroup.java 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
PdbxPolySeqLine.java 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
PdbxPolySeqLineList.java 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Residue.java 1428 (10 years ago) by jmduarteg: Fixed bug: was calculating ASAs/BSAs with Hydrogen atoms when they were present. Calculating without them is more common practice and most importantly makes more comparable prots with/without hydrogens. Now removing Hydrogens before interfaces calculation
SecStructureLine.java 1392 (11 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
SpaceGroup.java 1639 (9 years ago) by jmduarteg: Fixed 'I 1 2 1' issue: it was actually a bug rather than a "feature", we were parsing everything in symoplib but some space groups happened to have alternative names and 'I 1 2 1' is the alternative name of 'I 2" which we were allowing. Now parsing and storing in lookup map both names. Fixed also a bug by which the last space group in file was not added to the lookup-by-name map
SubunitId.java 1582 (9 years ago) by jmduarteg: Important fix to interface calculation: finally total symmetry redundancy elimination is working! - fixed a bug present since rev 1573: translation vectors of transforms were not stored properly and thus wasn't comparing the right operators - extracted TransformIdTransform private class to new class CrystalTransform. Rationalise some of the code thanks to that (still more to be done) - better debug output in interface calculation to show duplicates info
SymoplibParser.java 1639 (9 years ago) by jmduarteg: Fixed 'I 1 2 1' issue: it was actually a bug rather than a "feature", we were parsing everything in symoplib but some space groups happened to have alternative names and 'I 1 2 1' is the alternative name of 'I 2" which we were allowing. Now parsing and storing in lookup map both names. Fixed also a bug by which the last space group in file was not added to the lookup-by-name map
Template.java 1472 (10 years ago) by jmduarteg: Fixed a couple of problems with ScopConnection. Added another atom type.
TemplateList.java 1372 (11 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
aapairsBounds.dat 1012 (12 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.all.dat 1367 (11 years ago) by hstehr: Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
contactTypes.cmview.dat 1367 (11 years ago) by hstehr: Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
contactTypes.dat 1302 (11 years ago) by hstehr: adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
symop.lib 1179 (11 years ago) by jmduarteg: New classes to parse and store crystallographic space groups info.
vdw.radii 1247 (11 years ago) by jmduarteg: Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
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