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r1330
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data/ 1308 (11 years ago) by jmduarteg: Fixed important bug that broke the reconstruction programs. Tinker output files don't contain occupancy/bfactors. Thus we have to make their parsing optional. Added a test case for this.
AminoAcidTest.java 1316 (11 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
PdbAsymUnitTest.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
PdbParsersTest.java 1330 (11 years ago) by jmduarteg: Now the re-numbering of residue serials in PDB files has been improved. Instead of aligning the sequences whenever the serials don't match SEQRES, we first try to see if there is a shift in the serials with respect to SEQRES (happens in many cases). Only if we can't find a shift that fully matches SEQRES we proceed to re-aligning. We also treat properly now the ins codes. Mapping is as close to CIF as possible. The parsers test passes for the whole cullpdb20. For some entries like 2ofz the mapping does not coincide 100% with CIF as there are ambiguities in the alignment.
PdbTest.java 1326 (11 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
SpaceGroupTest.java 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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