def test_parsePDBQS(): """ check that pdbqs format files can be read """ from MolKit.pdbParser import PdbqsParser parser = PdbqsParser("Data/1ent.pdbqs") m = parser.parse()[0] assert len(m.allAtoms)==2901
def test_parsePDBQS(): """ check that pdbqs format files can be read """ from MolKit.pdbParser import PdbqsParser parser = PdbqsParser("Data/1ent.pdbqs") m = parser.parse()[0] assert len(m.allAtoms) == 2901
def Read(filename=None, alllines=None, dataformat='pdb', modelsAs='molecules'): if not alllines and not filename: raise AssertionError("%s invalid molecule" % filename) elif alllines and filename: alllines = None elif filename: if not os.path.exists(filename): raise AssertionError("%s does't exist" % filename) if alllines: ext = dataformat args = [None, alllines] else: ext = filename.split('.')[1] args = [filename, None] if ext == 'pdb': parser = PdbParser(*args, modelsAs=modelsAs) elif ext == 'pdbq': parser = PdbqParser(*args, modelsAs=modelsAs) elif ext == 'pdbqt': parser = PdbqtParser(*args, modelsAs=modelsAs) elif ext == 'pdbqs': parser = PdbqsParser(*args, modelsAs=modelsAs) elif ext == 'pqr': parser = PQRParser(*args, modelsAs=modelsAs) # FIXME: pass all lines??? elif ext == 'mol2': parser = Mol2Parser( filename) # ??should modelsAs be available for mol2 format?? elif ext == 'cif': parser = MMCIFParser(filename) elif ext == 'f2d': parser = F2DParser(filename) else: print("File Format unknown can't parse it") return [] molecules = parser.parse() return molecules
def Read(filename, modelsAs='molecules'): if not os.path.exists(filename): raise AssertionError, "%s does't exist" % filename from MolKit.pdbParser import PdbParser, PdbqParser,PdbqsParser,\ PdbqtParser, PQRParser, F2DParser from MolKit.mol2Parser import Mol2Parser from MolKit.mmcifParser import MMCIFParser ext = string.split(filename, '.') if ext[-1] == 'pdb': parser = PdbParser(filename, modelsAs=modelsAs) elif ext[-1] == 'pdbq': parser = PdbqParser(filename, modelsAs=modelsAs) elif ext[-1] == 'pdbqt': parser = PdbqtParser(filename, modelsAs=modelsAs) elif ext[-1] == 'pdbqs': parser = PdbqsParser(filename, modelsAs=modelsAs) elif ext[-1] == 'pqr': parser = PQRParser(filename, modelsAs=modelsAs) elif ext[-1] == 'mol2': parser = Mol2Parser( filename) #??should modelsAs be available for mol2 format?? elif ext[-1] == 'cif': parser = MMCIFParser(filename, modelsAs=modelsAs) elif ext[-1] == 'f2d': parser = F2DParser(filename) else: print "File Format unknown can't parse it" return [] molecules = parser.parse() return molecules
def Read(filename): from MolKit.pdbParser import PdbParser, PdbqParser, PdbqsParser, PQRParser from MolKit.mol2Parser import Mol2Parser ext = string.split(filename, '.') if ext[-1] == 'pdb': parser = PdbParser(filename) elif ext[-1] == 'pdbq': parser = PdbqParser(filename) elif ext[-1] == 'pdbqs': parser = PdbqsParser(filename) elif ext[-1] == 'pqr': parser = PQRParser(filename) elif ext[-1] == 'mol2': parser = Mol2Parser(filename) else: print "File Format unknown can't parse it" return [] molecules = parser.parse() return molecules