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 convert_str(str_data, in_format, out_format):
mol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
conv.SetOutFormat(out_format)
conv.ReadString(mol, str_data)
return (conv.WriteString(mol), conv.GetOutFormat().GetMIMEType())
def cjson_to_ob_molecule(cjson):
cjson_str = json.dumps(cjson)
sdf_str = avo_convert_str(cjson_str, 'cjson', 'sdf')
conv = OBConversion()
conv.SetInFormat('sdf')
conv.SetOutFormat('sdf')
mol = OBMol()
conv.ReadString(mol, sdf_str)
return mol
def autodetect_bonds(cjson):
mol = cjson_to_ob_molecule(cjson)
mol.ConnectTheDots()
mol.PerceiveBondOrders()
conv = OBConversion()
conv.SetInFormat('sdf')
conv.SetOutFormat('sdf')
sdf_str = conv.WriteString(mol)
cjson_str = avo_convert_str(sdf_str, 'sdf', 'cjson')
return json.loads(cjson_str)
def to_inchi(str_data, in_format):
mol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
# Hackish for now, convert to xyz first...
conv.SetOutFormat('xyz')
conv.ReadString(mol, str_data)
xyz = conv.WriteString(mol)
# Now convert to inchi and inchikey.
mol = OBMol()
conv.SetInFormat('xyz')
conv.ReadString(mol, xyz)
conv.SetOutFormat('inchi')
inchi = conv.WriteString(mol).rstrip()
conv.SetOptions("K", conv.OUTOPTIONS)
inchikey = conv.WriteString(mol).rstrip()
return (inchi, inchikey)
def to_inchi(str_data, in_format):
mol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
conv.ReadString(mol, str_data)
conv.SetOutFormat('inchi')
inchi = conv.WriteString(mol).rstrip()
conv.SetOptions('K', conv.OUTOPTIONS)
inchikey = conv.WriteString(mol).rstrip()
return (inchi, inchikey)
class Converter:
def __init__(self, can=False):
self._OBconverter = OBConversion()
self._OBconverter.SetOutFormat('smi')
options = 'in'
if can:
options += 'c'
self._OBconverter.SetOptions(options, OBConversion.OUTOPTIONS)
def getSmiles(self, mol):
smiles = self._OBconverter.WriteString(mol.OBMol)[:-1]
if '@' in smiles:
smiles = self._OBconverter.WriteString(mol.OBMol)[:-1]
return smiles
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()
def write_ob_molecule(self, mol, format, f):
"""
Write an Open Babel molecule to file
:param mol: The molecule
:param format: The output format
:param f: The file to write output to
:param f_name: The file's name (for extension-finding purpose)
"""
conv = OBConversion()
if not conv.SetOutFormat(format):
raise ValueError("Error setting output format to " + format)
# write to file
try:
s = conv.WriteString(mol)
except (TypeError, ValueError, IOError):
raise ValueError("Error writing data file using OpenBabel")
if str.lower(format) == 'pdb':
s = s.replace("END", "ENDMDL")
f.write(s)
def convert_str(str_data,
in_format,
out_format,
gen3d=False,
add_hydrogens=False,
perceive_bonds=False,
out_options=None):
# Make sure that the start of InChI is valid before passing it to
# Open Babel, or Open Babel will crash the server.
if in_format.lower() == 'inchi':
validate_start_of_inchi(str_data)
if out_options is None:
out_options = {}
obMol = OBMol()
conv = OBConversion()
conv.SetInFormat(in_format)
conv.SetOutFormat(out_format)
conv.ReadString(obMol, str_data)
if add_hydrogens:
obMol.AddHydrogens()
if gen3d:
# Generate 3D coordinates for the input
mol = pybel.Molecule(obMol)
mol.make3D()
if perceive_bonds:
obMol.ConnectTheDots()
obMol.PerceiveBondOrders()
for option, value in out_options.items():
conv.AddOption(option, conv.OUTOPTIONS, value)
return (conv.WriteString(obMol), conv.GetOutFormat().GetMIMEType())