def __get_all_heteroatoms__(self, template_pir):
template_PirFormat = AlignFile(template_pir)
return template_PirFormat.get_all_heteroatoms()
# if __name__ == '__main__':
# x = AlignmentBuilder("1bdm.pdb", "aligned.m", 'template.pir')
# alingFile = file('ali.ali','w')
# alingFile.write(x.__get_template_sequence__() + "\n\n")
# alingFile.write(x.__get_target_sequence__())
# alingFile.close()
# print x.templatePIR.get_all_heteroatoms(0)
def __init__(self, modeldir, templatePDBFile, alignmentfile, template_pir): # self.hmmr3file = hmmr3file self.workdir = modeldir self.templatePDBFile = templatePDBFile self.alignmentfile = alignmentfile self.fastaAlignment = self.__get_fasta_alignment_str__() self.templatePIR = AlignFile(template_pir)
class AlignmentBuilder():
def __init__(self, modeldir, templatePDBFile, alignmentfile, template_pir):
# self.hmmr3file = hmmr3file
self.workdir = modeldir
self.templatePDBFile = templatePDBFile
self.alignmentfile = alignmentfile
self.fastaAlignment = self.__get_fasta_alignment_str__()
self.templatePIR = AlignFile(template_pir)
def __get_fasta_alignment_str__(self):
fastaAlignmentFile = AlignIO.read(self.alignmentfile, "fasta")
fastaAlignmentList = []
for record in fastaAlignmentFile:
fastaAlignmentList.append(record.seq)
return fastaAlignmentList
def __get_target_sequence__(self):
structureName = "seq.ali"
structureType = "sequence"
description = ""
start = ""
chain_start = ""
stop = ""
chain_stop = ""
sequence = str(self.fastaAlignment[1]).upper() + self.templatePIR.get_all_heteroatoms(0)
return PirFormat(structureName, structureType, description, start, chain_start, stop, chain_stop, sequence).get()
def __get_template_sequence__(self):
#env = environ()
#mdl = model(env, file=self.templatePDBFile)
structureName = os.path.basename(self.templatePDBFile).partition(".")[0] #melhorar isso
parser = PDBParser()
structure = parser.get_structure(structureName, self.workdir + "/" + self.templatePDBFile)
model = structure[0] #get model from structure
listOfChains = model.get_list()
# structureType = mdl.prottyp
# description = mdl.name
# start = mdl.range[0].partition(":")[0]
#chain_start = mdl.range[0].partition(":")[2]
# stop = mdl.range[0].partition(":")[0]
#chain_stop = mdl.range[1].partition(":")[2]
# structureType = mdl.prottyp
structureType = "StructureX"
description = ""
start = "FIRST"
chain_start = listOfChains[0].id
stop = "END"
chain_stop = listOfChains[-1].id
sequence = str(self.fastaAlignment[0]).upper() + self.templatePIR.get_all_heteroatoms(0)
return PirFormat(structureName, structureType, description, start, chain_start, stop, chain_stop, sequence).get()
def __get_all_heteroatoms__(self, template_pir):
template_PirFormat = AlignFile(template_pir)
return template_PirFormat.get_all_heteroatoms()
# if __name__ == '__main__':
# x = AlignmentBuilder("1bdm.pdb", "aligned.m", 'template.pir')
# alingFile = file('ali.ali','w')
# alingFile.write(x.__get_template_sequence__() + "\n\n")
# alingFile.write(x.__get_target_sequence__())
# alingFile.close()
# print x.templatePIR.get_all_heteroatoms(0)
