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core/ 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.
owl_test_paths.dat 1030 (12 years ago) by jmduarteg: Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere. 1254 (11 years ago) by jmduarteg: Made conf file path a resource path so that it is readable from jar file too.
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