def hits(self): names = self.alignment.names[ 1 : self.max_count ] alignments = self.alignment.alignments[ 1 : self.max_count ] try: descriptions = self.alignment.descriptions[ 1 : self.max_count ] except AttributeError: descriptions = alignments base = self.alignment.alignments[0] for ( n, seq, desc ) in zip( names, alignments, descriptions ): pieces = n.split( "_" ) assert 0 < len( pieces ) if len( pieces ) == 1: pdb = pieces[0] chain = "" else: ( pdb, chain ) = pieces[:2] alignment = bioinformatics.clustal_alignment( names = [ "target", "%s_%s" % ( pdb, chain ) ], alignments = [ base, seq ], program = "<unknown>" ) yield bioinformatics.homology_search_hit( identifier = pdb, chain = chain, annotation = desc, alignment = alignment )
def hits(self): from iotbx import bioinformatics for h in self.root.hits: pieces = h.identifier.split("_") assert 0 < len(pieces) if len(pieces) == 1: pdb = pieces[0] chain = "" else: (pdb, chain) = pieces[:2] alignment = bioinformatics.clustal_alignment( names=["target", "%s_%s" % (pdb, chain)], alignments=[ h.alignments[0].query.seq, h.alignments[0].match.seq ], program="WU-BLAST") yield bioinformatics.homology_search_hit(identifier=pdb, chain=chain, annotation=h.description, alignment=alignment)
def hits(self): if not self.root.iterations: raise StopIteration from iotbx import bioinformatics for h in self.root.iterations[-1].hits: pieces = h.accession.split( "_" ) assert 0 < len( pieces ) if len( pieces ) == 1: pdb = pieces[0] chain = "" else: ( pdb, chain ) = pieces[:2] alignment = bioinformatics.clustal_alignment( names = [ "target", "%s_%s" % ( pdb, chain ) ], alignments = [ h.hsps[0].query.seq, h.hsps[0].hit.seq ], program = "NCBI-BLAST" ) yield bioinformatics.homology_search_hit( identifier = pdb, chain = chain, annotation = h.annotation, alignment = alignment )
def hits(self): if not self.root.iterations: raise StopIteration from iotbx import bioinformatics for h in self.root.iterations[-1].hits: pieces = h.accession.split("_") assert 0 < len(pieces) if len(pieces) == 1: pdb = pieces[0] chain = "" else: (pdb, chain) = pieces[:2] alignment = bioinformatics.clustal_alignment( names=["target", "%s_%s" % (pdb, chain)], alignments=[h.hsps[0].query.seq, h.hsps[0].hit.seq], program="NCBI-BLAST") yield bioinformatics.homology_search_hit(identifier=pdb, chain=chain, annotation=h.annotation, alignment=alignment)
def hits(self): from iotbx import bioinformatics for h in self.root.hits: pieces = h.identifier.split( "_" ) assert 0 < len( pieces ) if len( pieces ) == 1: pdb = pieces[0] chain = "" else: ( pdb, chain ) = pieces[:2] alignment = bioinformatics.clustal_alignment( names = [ "target", "%s_%s" % ( pdb, chain ) ], alignments = [ h.alignments[0].query.seq, h.alignments[0].match.seq ], program = "WU-BLAST" ) yield bioinformatics.homology_search_hit( identifier = pdb, chain = chain, annotation = h.description, alignment = alignment )