def log_new_clusters(output_file, n, leader_list):
print "log %d ligands. For change this number set the -n parameter" % n
str_info = "\t%s\t \t%20s\t %20s\t %20s\n" % ("File", "Model", "T.Energy",
"I.Energy")
for i in range(0, n):
str_info += "%s\t%20s\t%20s\t%20s\n" % (
leader_list[i].getFileBelow().split('/').pop(),
leader_list[i].getID(), leader_list[i].getTotalEnergy(),
leader_list[i].getInteractionEnergy())
out_log = file(output_file + ".log", "w")
out_log.write(str_info)
out_log.close()
conv = OBConversion()
conv.SetOutFormat("mol2")
conv.WriteFile(leader_list[0], output_file + ".mol2")
for i in range(1, n):
conv.Write(leader_list[i])
conv.CloseOutFile()
def type_mof(filename, output_dir, ff="uff", output_files=True):
obconversion = OBConversion()
obconversion.SetInAndOutFormats("cif", "xyz")
obmol = OBMol()
# Read MOF file and unit cell and write xyz file
obconversion.ReadFile(obmol, filename)
unitcell = openbabel.toUnitCell(obmol.GetData(openbabel.UnitCell))
uc = [
unitcell.GetA(),
unitcell.GetB(),
unitcell.GetC(),
unitcell.GetAlpha(),
unitcell.GetBeta(),
unitcell.GetGamma()
]
obconversion.WriteFile(obmol, 'mof_tmp.xyz')
# Replicate unit cell using angstrom
mol = Molecule(read='mof_tmp.xyz')
mol.set_cell(uc)
n_atoms = len(mol.atoms)
mol333 = mol.replicate([3, 3, 3], center=True)
print(mol333.cell)
mol333.write('mof333.cif', cell=mol333.cell.to_list())
# Type FF
obconversion.ReadFile(obmol, 'mof333.cif')
ff = OBForceField.FindForceField("UFF")
if not ff.Setup(obmol):
print("Error: could not setup force field")
ff.GetAtomTypes(obmol)
# Get atom types for the middle cell
types = []
for atom_idx, obatom in enumerate(OBMolAtomIter(obmol)):
if atom_idx >= n_atoms * 13 and atom_idx < n_atoms * 14:
ff_atom_type = obatom.GetData("FFAtomType").GetValue()
types.append(ff_atom_type)
if output_files:
mof_name = os.path.splitext(os.path.basename(filename))[0]
with open(os.path.join(output_dir, mof_name + "-obabel.log"),
'w') as f:
f.write("NOTE: types order is the same as the CIF input file.\n")
f.write("types= %s" % str(types))
uniq_types = sorted(set(types))
return [str(i) for i in uniq_types]
def log_new_clusters(output_file, n, leader_list, ref=None):
print "log %d ligands. For change this number set the -n parameter" % n
str_info = "\t%s\t %20s\t %20s\t %20s \t%15s\n" % (
"File", "Model", "T.Energy", "I.Energy", "RMSD")
if ref != None:
mol_ref = loadReferenceMolecule(ref)
if ref != None:
for i in range(0, n):
str_info += "%s\t%20s\t%20s\t%20s\t%15.3f\n" % (
leader_list[i].getFileBelow(), leader_list[i].getID(),
leader_list[i].getTotalEnergy(),
leader_list[i].getInteractionEnergy(),
getRMSD(leader_list[i], mol_ref))
else:
for i in range(0, n):
str_info += "%s\t%20s\t%20s\t%20s\t%15.3f\n" % (
leader_list[i].getFileBelow(), leader_list[i].getID(),
leader_list[i].getTotalEnergy(),
leader_list[i].getInteractionEnergy(),
getRMSD(leader_list[i], leader_list[0]))
out_log = file(output_file + ".log", "w")
out_log.write(str_info)
out_log.close()
conv = OBConversion()
conv.SetOutFormat("mol2")
conv.WriteFile(leader_list[0], output_file + ".mol2")
for i in range(1, n):
conv.Write(leader_list[i])
conv.CloseOutFile()