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r1625
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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
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.
graphAveraging/ 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
gmbp/ 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
mutanom/ 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
decoyScoring/ 1392 (8 years ago) by jmduarteg: MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
cccp/ 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
embed/ 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
casp/ 1597 (7 years ago) by jmduarteg: Several changes related to blast: - now supporting blast+ blastp. - blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired - refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+ Also updated uniprot jar.
tests/ 1612 (6 years ago) by jmduarteg: Fixed bug: was null pointing in parsing 2bi6 mmCIF file. It had a multi-line quoted value in a _struct_conf non-loop element. We weren't handling that correctly. Also added a new peptide-linked 3-letter code het residue
core/ 1625 (6 years ago) by jmduarteg: Fixed issue: now setting unknown atom type whenever we can't guess the element. If we read from PDB file and there is an unguesseable atom that we then have to write out again the code would fail because in writeAtoms we assume we have atom types for everything.
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