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"
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_parseSSData(self):
"""Check that parseSSData() parses secondary structure"""
parser1 = MMCIFParser(filename='Data/1CRN.cif')
mols1 = parser1.parse()
ssDataForMol = parser1.parseSSData(mols1)
