 ../
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scoring/
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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.
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graphs/
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1561
(10 years ago)
by jmduarteg:
New method to calculate contact order
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features/
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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.
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alignment/
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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.
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vdw.radii
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1247
(11 years ago)
by jmduarteg:
Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
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symop.lib
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1179
(11 years ago)
by jmduarteg:
New classes to parse and store crystallographic space groups info.
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contactTypes.dat
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1302
(11 years ago)
by hstehr:
adding ALL_H contact type to contactTypes.dat because otherwise AAinfo.isValidAtomWithOXT() breaks with a NullPointerException
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contactTypes.cmview.dat
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1367
(11 years ago)
by hstehr:
Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
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contactTypes.all.dat
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1367
(11 years ago)
by hstehr:
Adding package 'mutanom' to OWL (previously in seperate repository 'structuralimpact')
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aapairsBounds.dat
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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
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TemplateList.java
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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.
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Template.java
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1472
(10 years ago)
by jmduarteg:
Fixed a couple of problems with ScopConnection. Added another atom type.
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SymoplibParser.java
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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
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SubunitId.java
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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
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SpaceGroup.java
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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
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SecStructureLine.java
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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.
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Residue.java
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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
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PdbxPolySeqLineList.java
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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.
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PdbxPolySeqLine.java
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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.
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PdbxPolySeqGroup.java
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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.
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PdbfileParser.java
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1641
(9 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
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PdbaseParser.java
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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
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PdbUnitCell.java
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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
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PdbLoadException.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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PdbCodeNotFoundException.java
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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.
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PdbChainSet.java
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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.
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PdbChain.java
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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
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PdbAsymUnit.java
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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
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Nucleotide.java
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1400
(11 years ago)
by jmduarteg:
Fixed some issues with writing of pdb files and wrote a test for write/read pdb files.
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NucResidue.java
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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
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InterfacesFinder.java
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1643
(9 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)
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InterfaceRimCore.java
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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
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InterfaceGraphEdge.java
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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.
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InterfaceGraph.java
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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
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HetResidue.java
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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
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CrystalTransform.java
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1583
(9 years ago)
by jmduarteg:
Made new CrystalTransform class serializable
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CrystalCell.java
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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.
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ContactType.java
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1316
(11 years ago)
by jmduarteg:
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
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ConformationsNotSameSizeException.java
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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.
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CiffileParser.java
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1623
(9 years ago)
by nikhilbiyani:
Bugfix: Check for nulls while reading QParams.
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ChainInterfaceList.java
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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
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ChainInterface.java
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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
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BackboneCoords.java
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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
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AtomType.java
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1624
(9 years ago)
by nikhilbiyani:
Added AtomTypes till atomic number 110
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AtomRadii.java
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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)
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AtomLineList.java
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1641
(9 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
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AtomLine.java
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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.
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Atom.java
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1626
(9 years ago)
by jmduarteg:
Another small fix related to last commit
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Asa.java
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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)
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AminoAcid.java
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1429
(10 years ago)
by jmduarteg:
Introduced calculation of relative ASAs.
A few new methods to calculate rim/core of interfaces using alternative definitions.
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AaResidue.java
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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
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