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r1610
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tests/ 1610 (9 years ago) by jmduarteg: Fixed bug: very strange PDB entries can have no atoms observed in a chain at all (e.g. 1oax) or all atoms of a chain in one alt location only (e.g. 3nji). We throw now exceptions for them as in my opinion they don't follow the data-modelling standards properly.
sadp/ 1305 (11 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.
ppi/ 1007 (12 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
mutanom/ 1392 (11 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.
litNet/ 1007 (12 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
graphAveraging/ 1392 (11 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 (11 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.
embed/ 1399 (11 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,...)
deltaRank/ 1314 (11 years ago) by jmduarteg: Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
decoyScoring/ 1392 (11 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.
core/ 1610 (9 years ago) by jmduarteg: Fixed bug: very strange PDB entries can have no atoms observed in a chain at all (e.g. 1oax) or all atoms of a chain in one alt location only (e.g. 3nji). We throw now exceptions for them as in my opinion they don't follow the data-modelling standards properly.
cccp/ 1399 (11 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 (9 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.
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