def loadCDFMolecule(fname):
mol = Chem.BasicMolecule()
cdf_reader = Chem.FileCDFMoleculeReader(fname)
if not cdf_reader.read(mol):
return None
Chem.calcImplicitHydrogenCounts(mol, False)
Chem.perceiveHybridizationStates(mol, False)
Chem.setAtomSymbolsFromTypes(mol, False)
Chem.perceiveSSSR(mol, False)
Chem.setRingFlags(mol, False)
Chem.setAromaticityFlags(mol, False)
return mol
def process():
if len(sys.argv) < 3:
print >> sys.stderr, 'Usage:', sys.argv[
0], '[input.cdf] [output directory]'
sys.exit(2)
in_fname = path.splitext(path.basename(sys.argv[1]))[0]
mol = Chem.BasicMolecule()
cdf_reader = Chem.FileCDFMoleculeReader(sys.argv[1])
pvd_file = open(path.join(sys.argv[2], in_fname + '.pvd'), 'w')
Util.writePVDHeader(pvd_file)
print >> sys.stderr, '- Processing CDF-file:', sys.argv[1], '...'
if not cdf_reader.read(mol):
print '!! Could not read file'
sys.exit(2)
backbone_atoms = []
for atom in mol.atoms:
if Biomol.isPDBBackboneAtom(atom) and Biomol.getResidueAtomName(
atom) == 'C':
backbone_atoms.append(atom)
bond_list = []
for bond in mol.bonds:
if Biomol.getResidueCode(
bond.getAtom(0)) == 'HOH' or Biomol.getResidueCode(
bond.getAtom(1)) == 'HOH':
continue
if Chem.getType(bond.getAtom(0)) == Chem.AtomType.H or Chem.getType(
bond.getAtom(1)) == Chem.AtomType.H:
continue
bond_list.append(bond)
num_confs = Chem.getNumConformations(mol)
num_coords = len(bond_list) * 4 + (
len(backbone_atoms) * SPLINE_POINTS_PER_BB_ATOM - 1) * 2
bond_ctr = Math.Vector3D()
i = 0
while i < num_confs:
line_x_coords = numpy.ndarray(num_coords, numpy.float32)
line_y_coords = numpy.ndarray(num_coords, numpy.float32)
line_z_coords = numpy.ndarray(num_coords, numpy.float32)
atom_types = numpy.ndarray(num_coords, numpy.uint32)
spline_ctrl_points = numpy.ndarray((len(backbone_atoms), 3),
numpy.float32)
j = 0
for atom in backbone_atoms:
atom_pos = Chem.getConformer3DCoordinates(atom, i)
spline_ctrl_points[j, 0] = atom_pos(0)
spline_ctrl_points[j, 1] = atom_pos(1)
spline_ctrl_points[j, 2] = atom_pos(2)
j += 1
spline_pts = spline(spline_ctrl_points,
len(backbone_atoms) * SPLINE_POINTS_PER_BB_ATOM)
j = 0
k = 0
while k < (len(backbone_atoms) * SPLINE_POINTS_PER_BB_ATOM - 1):
line_x_coords[j] = spline_pts[0][k]
line_y_coords[j] = spline_pts[1][k]
line_z_coords[j] = spline_pts[2][k]
atom_types[j] = 0
j += 1
line_x_coords[j] = spline_pts[0][k + 1]
line_y_coords[j] = spline_pts[1][k + 1]
line_z_coords[j] = spline_pts[2][k + 1]
atom_types[j] = 0
j += 1
k += 1
for bond in bond_list:
atom1 = bond.getAtom(0)
atom2 = bond.getAtom(1)
atom1_pos = Chem.getConformer3DCoordinates(atom1, i)
atom2_pos = Chem.getConformer3DCoordinates(atom2, i)
atom1_type = Chem.getType(atom1)
atom2_type = Chem.getType(atom2)
bond_ctr.assign(atom1_pos)
bond_ctr += atom2_pos
bond_ctr *= 0.5
line_x_coords[j] = atom1_pos(0)
line_y_coords[j] = atom1_pos(1)
line_z_coords[j] = atom1_pos(2)
atom_types[j] = atom1_type
j += 1
line_x_coords[j] = bond_ctr(0)
line_y_coords[j] = bond_ctr(1)
line_z_coords[j] = bond_ctr(2)
atom_types[j] = atom1_type
j += 1
line_x_coords[j] = bond_ctr(0)
line_y_coords[j] = bond_ctr(1)
line_z_coords[j] = bond_ctr(2)
atom_types[j] = atom2_type
j += 1
line_x_coords[j] = atom2_pos(0)
line_y_coords[j] = atom2_pos(1)
line_z_coords[j] = atom2_pos(2)
atom_types[j] = atom2_type
j += 1
line_x_coords.resize(j)
line_y_coords.resize(j)
line_z_coords.resize(j)
atom_types.resize(j)
out_fname = in_fname + '_frame_no_' + str(i)
out_path = path.join(sys.argv[2], out_fname)
line_data = {'atom_type': atom_types}
print >> sys.stderr, '- Writing structure data for frame', i, '...'
if not pyevtk.hl.linesToVTK(out_path,
line_x_coords,
line_y_coords,
line_z_coords,
pointData=line_data):
print '!! Could not write output file'
sys.exit(2)
Util.writePVDEntry(pvd_file, i, out_fname, 'vtu')
i += 1
Util.writePVDFooter(pvd_file)
