def test_parseHYDBND_2():
"""
"""
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/smfx_goodHYDBND.pdb")
parser.parse()
mol = parser.mol
atmsInHBond = mol.allAtoms.get(lambda x: hasattr(x, 'hbonds'))
hbonds = atmsInHBond.hbonds
assert len(hbonds) == 21
def test_parseHYDBND_2():
"""
"""
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/smfx_goodHYDBND.pdb")
parser.parse()
mol = parser.mol
atmsInHBond = mol.allAtoms.get(lambda x: hasattr(x, 'hbonds'))
hbonds = atmsInHBond.hbonds
assert len(hbonds) == 21
def test_parseFileWrongFormat():
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/fakePDB.pdb")
mols = parser.parse()
assert mols is None or len(mols) == 0
parser = PdbParser("Data/hpi1s.mol2")
mols = parser.parse()
assert mols is None or len(mols) == 0
from MolKit.mol2Parser import Mol2Parser
parser = Mol2Parser("Data/1crn.pdb")
mols = parser.parse()
assert mols is None or len(mols) == 0
def test_parseHYDBND_1():
"""
"""
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/smfx_badHYDBND.pdb")
parser.PDBtags.remove("HYDBND")
del parser.pdbRecordParser['HYDBND']
parser.parse()
failure = False
hdbndLines = parser.getRecords(parser.allLines, "HYDBND")
try:
parser.parse_PDB_HYDBND(hbndLines)
except:
failure = True
assert failure
def test_parseFileWrongFormat():
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/fakePDB.pdb")
mols = parser.parse()
assert mols is None or len(mols)==0
parser = PdbParser("Data/hpi1s.mol2")
mols = parser.parse()
assert mols is None or len(mols)==0
from MolKit.mol2Parser import Mol2Parser
parser = Mol2Parser("Data/1crn.pdb")
mols=parser.parse()
assert mols is None or len(mols)==0
def test_parseHYDBND_1():
"""
"""
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/smfx_badHYDBND.pdb")
parser.PDBtags.remove("HYDBND")
del parser.pdbRecordParser['HYDBND']
parser.parse()
failure = False
hdbndLines = parser.getRecords(parser.allLines, "HYDBND")
try:
parser.parse_PDB_HYDBND(hbndLines)
except:
failure = True
assert failure
def test_parseMol_HelixRec():
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
parser.SetReadOptions('HELIX')
assert 'HELIX' in parser.pdbRecordParser.keys()
mols = parser.parse()
assert parser.recordInfo.has_key('HELIX')
def getTheMol(filename):
# from MolKit.protein import Protein
from MolKit.pdbParser import PdbParser
parser = PdbParser(filename=filename)
mol = parser.parse()
# mol.read( filename, PdbParser() )
return mol
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
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)
else:
print "File Format unknown can't parse it"
return []
molecules = parser.parse()
return molecules
def test_parseMol_HelixRec():
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
parser.SetReadOptions('HELIX')
assert 'HELIX' in parser.pdbRecordParser.keys()
mols = parser.parse()
assert parser.recordInfo.has_key('HELIX')
def getTheMol(filename):
# from MolKit.protein import Protein
from MolKit.pdbParser import PdbParser
parser = PdbParser(filename=filename)
mol = parser.parse()
# mol.read( filename, PdbParser() )
return mol
def test_parseHYDBND_3():
"""
check that HYDBND records are read correctly
when names start with a space (eg residue name " A1")
"""
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/bdna_HS.pdb")
m = parser.parse()[0]
assert len(m.allAtoms.get(lambda x: hasattr(x, 'hbonds')))==110
def test_parseHYDBND_3():
"""
check that HYDBND records are read correctly
when names start with a space (eg residue name " A1")
"""
from MolKit.pdbParser import PdbParser
parser = PdbParser("Data/bdna_HS.pdb")
m = parser.parse()[0]
assert len(m.allAtoms.get(lambda x: hasattr(x, 'hbonds'))) == 110
def test_parseSSData_2():
""" Calling parseSSData after setting the readOption to parse HELIX,
STRAND, TURN, etc..."""
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
parser.SetReadOptions('HELIX')
parser.SetReadOptions('SHEET')
parser.SetReadOptions('TURN')
mols = parser.parse()
assert parser.recordInfo.has_key('HELIX')
assert parser.recordInfo.has_key('SHEET')
assert parser.recordInfo.has_key('TURN')
ssDataForMol = parser.parseSSData(mols[0])
def test_parseSSData_2():
""" Calling parseSSData after setting the readOption to parse HELIX,
STRAND, TURN, etc..."""
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
parser.SetReadOptions('HELIX')
parser.SetReadOptions('SHEET')
parser.SetReadOptions('TURN')
mols = parser.parse()
assert parser.recordInfo.has_key('HELIX')
assert parser.recordInfo.has_key('SHEET')
assert parser.recordInfo.has_key('TURN')
ssDataForMol = parser.parseSSData(mols[0])
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
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
def test_parseMol_BasicRec():
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
mols = parser.parse()
def test_parseSSData():
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
mols = parser.parse()
ssDataForMol = parser.parseSSData(mols[0])
def test_parseMol_BasicRec():
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
mols = parser.parse()
def test_parseSSData():
from MolKit.pdbParser import PdbParser
parser = PdbParser('Data/1crn.pdb')
mols = parser.parse()
ssDataForMol = parser.parseSSData(mols[0])