def test_writer_1(self):
"""
Checks that MMCIFParser can read the file written by MMCIFWriter
"""
parser = MMCIFParser(filename='Data/1CRN.cif')
mol = parser.parse()
writer = MMCIFWriter()
writer.write('Data/1CRN_.cif', mol)
new_parser = MMCIFParser(filename='Data/1CRN_.cif')
mol = parser.parse()
os.remove('Data/1CRN_.cif')
def test_writer_1(self):
"""
Checks that MMCIFParser can read the file written by MMCIFWriter
"""
parser = MMCIFParser(filename='Data/1CRN.cif')
mol = parser.parse()
writer = MMCIFWriter()
writer.write('Data/1CRN_.cif',mol)
new_parser = MMCIFParser(filename='Data/1CRN_.cif')
mol = parser.parse()
os.remove('Data/1CRN_.cif')
def test_write_2(self):
"""
Tests that PdbWriter can write molecule parsed by MMCIFParser
"""
# read a molecule
parser = MMCIFParser(filename='Data/1CRN.cif')
mol = parser.parse()
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_mmcifwriter.pdb', mol)
os.remove('Data/1crn_mmcifwriter.pdb')
def test_write_2(self):
"""
Tests that PdbWriter can write molecule parsed by MMCIFParser
"""
# read a molecule
parser = MMCIFParser(filename='Data/1CRN.cif')
mol = parser.parse()
# instanciate a PdbWriter and call the write method with the
# default arguments
from MolKit.pdbWriter import PdbWriter
writer = PdbWriter()
writer.write('Data/1crn_mmcifwriter.pdb', mol)
os.remove('Data/1crn_mmcifwriter.pdb')
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
file_out.write("HETATM")
file_out.write(" %6s" % Atom.number) #2
file_out.write(" " + Atom.element) #3
file_out.write(" %5s" % Atom.name) #4
file_out.write(" " + Atom.parent.type) #5
if Atom.parent.parent.name == ' ':
file_out.write(" ?") #6
else:
file_out.write(" " + Atom.parent.parent.name)
file_out.write(" %5d" % int(Atom.parent.number)) #7
file_out.write(" %7.3f" % Atom._coords[0][0]) #8
file_out.write(" %7.3f" % Atom._coords[0][1]) #9
file_out.write(" %7.3f" % Atom._coords[0][2]) #10
file_out.write(" %6.2f" % float(Atom.occupancy)) #11
file_out.write(" %6.2f" % float(Atom.temperatureFactor)) #12
file_out.write("\n")
file_out.close()
if __name__ == '__main__':
from MolKit.mmcifParser import MMCIFParser
parser = MMCIFParser(filename='Tests/Data/1CRN.cif')
print "Reading molecule"
mol = parser.parse()
print "Done parsing"
SS_Data = parser.parseSSData(mol)
print "Done parsing secondary structure"
writer = MMCIFWriter()
writer.write('Tests/Data/1CRN_.cif', mol)
print "Done"
else:
file_out.write("HETATM")
file_out.write(" %6s"%Atom.number) #2
file_out.write(" " + Atom.element) #3
file_out.write(" %5s"%Atom.name) #4
file_out.write(" " + Atom.parent.type) #5
if Atom.parent.parent.name == ' ':
file_out.write(" ?") #6
else:
file_out.write(" " + Atom.parent.parent.name)
file_out.write(" %5d"%int(Atom.parent.number)) #7
file_out.write(" %7.3f"%Atom._coords[0][0]) #8
file_out.write(" %7.3f"%Atom._coords[0][1]) #9
file_out.write(" %7.3f"%Atom._coords[0][2]) #10
file_out.write(" %6.2f"%float(Atom.occupancy)) #11
file_out.write(" %6.2f"%float(Atom.temperatureFactor)) #12
file_out.write("\n")
file_out.close()
if __name__ == '__main__':
from MolKit.mmcifParser import MMCIFParser
parser = MMCIFParser( filename='Tests/Data/1CRN.cif' )
print "Reading molecule"
mol = parser.parse()
print "Done parsing"
SS_Data = parser.parseSSData( mol )
print "Done parsing secondary structure"
writer = MMCIFWriter()
writer.write('Tests/Data/1CRN_.cif',mol)
print "Done"
def test_parseNAD(self):
parser1 = MMCIFParser("Data/1GGA_.cif")
mol1 = parser1.parse()
P = mol1.chains[-1].residues.atoms[0].chemElem
assert P is 'P'
def test_parseFileWrongFormat(self):
parser1 = MMCIFParser("Data/fakePDB.pdb")
mols1 = parser1.parse()
assert mols1 is None or len(mols1)==0
def test_parseSSData(self):
"""Check that parseSSData() parses secondary structure"""
parser1 = MMCIFParser(filename='Data/1CRN.cif')
mols1 = parser1.parse()
ssDataForMol = parser1.parseSSData(mols1)
def initParser(self):
global mols
if mols is None:
parser = MMCIFParser(filename='./Data/2PLV.cif')
mols = parser.parse()
self.mols = mols
