def load_pdb(filename):
"""
Loads a single molecule from a pdb file.
This function does support only a small fragment from the pdb specification.
It assumes that there is only one molecular geometry in the pdb file.
"""
f = file(filename)
numbers = []
coordinates = []
occupancies = []
betas = []
for line in f:
if line.startswith("ATOM"):
symbol = line[76:78].strip()
numbers.append(periodic[symbol].number)
coordinates.append(
[float(line[30:38]),
float(line[38:46]),
float(line[46:54])])
occupancies.append(float(line[54:60]))
betas.append(float(line[60:66]))
f.close()
if len(numbers) > 0:
molecule = Molecule(numbers, coordinates)
molecule.occupancies = numpy.array(occupancies)
molecule.betas = numpy.array(betas)
return molecule
else:
raise IOError("No molecule found in pdb file %s" % filename)
def load_pdb(filename):
"""Loads a single molecule from a pdb file.
This function does support only a small fragment from the pdb specification.
It assumes that there is only one molecular geometry in the pdb file.
"""
f = file(filename)
numbers = []
coordinates = []
occupancies = []
betas = []
for line in f:
if line.startswith("ATOM"):
symbol = line[76:78].strip()
numbers.append(periodic[symbol].number)
coordinates.append([float(line[30:38])*angstrom, float(line[38:46])*angstrom, float(line[46:54])*angstrom])
occupancies.append(float(line[54:60]))
betas.append(float(line[60:66]))
f.close()
if len(numbers) > 0:
molecule = Molecule(numbers, coordinates)
molecule.occupancies = numpy.array(occupancies)
molecule.betas = numpy.array(betas)
return molecule
else:
raise FileFormatError("No molecule found in pdb file %s" % filename)
