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connections/ 1598 (9 years ago) by jmduarteg: New classes to parse PiQSi annotation file
features/ 1372 (11 years ago) by jmduarteg: MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
runners/ 1599 (9 years ago) by jmduarteg: Fixed important issues with searching and alignment of homologs: - ids and coverage were calculated wrongly, based on all BlastHsps for a hit. Now based on single Hsps - fixed bug in BlastHsp.getQueryCoverage: was miscalculating the coverage by 1 unit - the useHspsOnly parameter in alignment didn't make much sense. We need always to use the hsp segments only, extending to the full sequence is dangerous and in any case does not make sense at all if the clustering is done in hsps only
sequence/ 1603 (9 years ago) by jmduarteg: Small fix to allow for underscore in blast query id
structure/ 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.
util/ 1586 (9 years ago) by jmduarteg: Now using more headers for guessing PDB files, for instance modeller uses EXPDTA as first line of their output files
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