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root/owl/trunk/src/owl/core/connections/pisa
r1217
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PisaConnection.java 1077 (11 years ago) by jmduarteg: Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case. Some new functionality in PISA classes
PisaInterface.java 1217 (10 years ago) by jmduarteg: First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison. New test class to compare automatically to PISA output.
PisaInterfaceXMLParser.java 1215 (10 years ago) by jmduarteg: Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side. Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa. Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct. Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.
PisaMolecule.java 1215 (10 years ago) by jmduarteg: Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side. Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa. Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct. Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.
PisaResidue.java 1101 (11 years ago) by jmduarteg: Now serializable (to be able to write them to file)
PisaRimCore.java 1101 (11 years ago) by jmduarteg: Now serializable (to be able to write them to file)
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