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r1678
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src/ 1678 (6 years ago) by jmduarteg: Moved geometry related calculations to the GeometryTools class: rmsd, screw component, axis type, axis-angle etc. Like that the calculations can be used from anywhere. Introduced the OptSuperposition class as output of the rmsd calculation. Improved the rmsd calculation in PdbChain (and corrected some bugs). Also improved a lot the rmsd unit testing. All tests in PdbChainTest are now done with cif files and not anymore with pdbase. Implemented an optimal superposition method in ChainInterface and some output for that in enumerateInterfaces with the intention of finding the pseudo-symmetric relationship between NCS related chains in an interface. All tests passed.
jars/ 1647 (6 years ago) by jmduarteg: Fixing bug in jaligner: the NeedlemanWunschGotoh method used by owl.core.sequence.PairwiseSequenceAlignment had a bug causing infinite hanging when using very long sequences. The issue would happen when either of the 2 sequences to align was longer than 32768 (16 bit) and the other sequence would match it after the 32768 region, a test case is included in this commit to demonstrate it. The problem was an overflow: an array used for the traceback procedure was declared as short[] (16 bit), changing it to int[] (32 bit) the issue disappears. As the development in jaligner seems to be stopped I've simply downloaded the source, fixed the issue there (plus removing the loggers) and repackaged in a jar (jaligner-bugfixed.jar) that includes the sources.
scripts/ 1633 (6 years ago) by jmduarteg: Removing uniprot update script, doesn't belong in owl repo
modelit/ 1301 (8 years ago) by hstehr: overwriting default contactTypes.dat with the one needed for CMView release versions (only contains standard contact types). The old version with all esoteric contact types is renamed to contactTypes.all.dat
reconstruct/ 992 (9 years ago) by jmduarteg: Removed unneeded code
.classpath 1647 (6 years ago) by jmduarteg: Fixing bug in jaligner: the NeedlemanWunschGotoh method used by owl.core.sequence.PairwiseSequenceAlignment had a bug causing infinite hanging when using very long sequences. The issue would happen when either of the 2 sequences to align was longer than 32768 (16 bit) and the other sequence would match it after the 32768 region, a test case is included in this commit to demonstrate it. The problem was an overflow: an array used for the traceback procedure was declared as short[] (16 bit), changing it to int[] (32 bit) the issue disappears. As the development in jaligner seems to be stopped I've simply downloaded the source, fixed the issue there (plus removing the loggers) and repackaged in a jar (jaligner-bugfixed.jar) that includes the sources.
build.xml 1644 (6 years ago) by kumaran: 1)Javaversion variable is added in build.xml to change the version easily. 2)Pymol exited with error status 139 due to very long selection string written in the form of every residue(3+4+5+8+9+10). It is fixed by writing in the form of (3-5+8-10)
.project 1638 (6 years ago) by jmduarteg: Changing default eclipse project name to owl
gpl.txt 974 (9 years ago) by duarte: Adding license files
LICENSE 974 (9 years ago) by duarte: Adding license files
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svn:ignore .classpath .project .settings build