 ../
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alignment/
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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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features/
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1226
(11 years ago)
by hstehr:
Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
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scoring/
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1287
(11 years ago)
by matt4077:
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graphs/
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1292
(11 years ago)
by cvehlow:
Control database access! for CGAP
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ContactType.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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PdbLoadError.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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PdbCodeNotFoundError.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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PdbaseInconsistencyError.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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ConformationsNotSameSizeError.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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PolResidue.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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Polymer.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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PdbChainCodeNotFoundError.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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TemplateList.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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PdbSet.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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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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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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contactTypes.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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AAinfo.java
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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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Template.java
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1034
(12 years ago)
by jmduarteg:
Extracted Scop parsing code to its own connection class.
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AminoAcid.java
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1094
(11 years ago)
by jmduarteg:
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
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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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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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AtomType.java
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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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Atom.java
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1248
(11 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.
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Asa.java
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1255
(11 years ago)
by jmduarteg:
Minor changes to the test.
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Residue.java
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1256
(11 years ago)
by jmduarteg:
Now reporting on percent burial too
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AtomRadii.java
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1258
(11 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
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InterfaceRimCore.java
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1264
(11 years ago)
by jmduarteg:
Added printing of rim and core residues methods.
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CrystalCell.java
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1269
(11 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
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SpaceGroup.java
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1270
(11 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"
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PdbAsymUnit.java
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1280
(11 years ago)
by jmduarteg:
Now enumerateInterfaces takes file from local cif file PDB repo. Fixed some docs.
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SymoplibParser.java
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1281
(11 years ago)
by jmduarteg:
Now checking that the space group read from file/db is correct, if not PdbLoadError thrown.
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PdbasePdb.java
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1282
(11 years ago)
by jmduarteg:
Fixed formatting of the exception message
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CiffilePdb.java
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1282
(11 years ago)
by jmduarteg:
Fixed formatting of the exception message
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PdbfilePdb.java
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1282
(11 years ago)
by jmduarteg:
Fixed formatting of the exception message
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ChainInterface.java
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1284
(11 years ago)
by cvehlow:
Overrides removed
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ChainInterfaceList.java
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1284
(11 years ago)
by cvehlow:
Overrides removed
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PdbUnitCell.java
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1284
(11 years ago)
by cvehlow:
Overrides removed
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Pdb.java
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1286
(11 years ago)
by hstehr:
calling readStructureOrNull was exiting rather than returning null
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