ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl
r1331
File Last Change
 ../
litNet/ 1007 (9 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
ppi/ 1007 (9 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
graphAveraging/ 1305 (8 years ago) by jmduarteg: Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
sadp/ 1305 (8 years ago) by jmduarteg: Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
deltaRank/ 1314 (8 years ago) by jmduarteg: Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
gmbp/ 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
casp/ 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
embed/ 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
decoyScoring/ 1326 (8 years ago) by jmduarteg: Renamed xxxxError classes to xxxxException as they should be.
tests/ 1330 (8 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.
core/ 1331 (8 years ago) by jmduarteg: Another improvement to PdbfilePdb parsing: now we can also detect some ambiguous cases in alignments by checking the contiguity of the 3D chain. This fixes 2 cases from our test data set: 1dki and 2ofz. Now only 2 warnings for the whole dataset (both because of ambiguous assignment in HIS tags, safe to ignore. Could even be that CIF got them wrong)
         0 files shown