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r1678
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branches/ 1438 (8 years ago) by jmduarteg: An ant script for owl!
tags/ 1664 (6 years ago) by jmduarteg: Tagging for eppic release 2.0.2 - bug fix: null pointer in pdb file parsing when no TER records present or misplaced - many improvements in SpaceGroup and its testing - operators can now be classified into their types, including calculation of screw directions - bug fix: the axis vectors were wrongly calculated for some operators of some space groups, e.g. in H 3 2 or P 32 2 1 - bug fix in jaligner: sequences longer than 32768 characters were not aligning correctly when the match was occurring after character 32768. We fixed it ourselves in the jaligner source and repackaged the jar into owl. The jaligner developer has fixed it in git.
trunk/ 1678 (5 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.
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