def test_compute_charge_dictionary(self):
for fname in (self.ligand_file, self.protein_file):
_, mol = rgf.load_molecule(fname)
ComputeGasteigerCharges(mol)
charge_dict = rgf.compute_charge_dictionary(mol)
self.assertEqual(len(charge_dict), mol.GetNumAtoms())
for i in range(mol.GetNumAtoms()):
self.assertIn(i, charge_dict)
self.assertIsInstance(charge_dict[i], (float, int))
def partialcharge(self):
if self.Atom.HasProp('_TriposPartialCharge'):
return float(self.Atom.GetProp('_TriposPartialCharge'))
if not self.Atom.HasProp('_GasteigerCharge'):
ComputeGasteigerCharges(self.Atom.GetOwningMol())
return float(self.Atom.GetProp('_GasteigerCharge').replace(',','.'))
def MolToMol2Block(mol, confId=-1, addHs=False, addCharges=False):
"""Returns a Mol2 string block for a molecule
ARGUMENTS:
- mol: the molecule
- confId: (optional) selects which conformation to output (-1 = default)
if set to None will return all conformers
RETURNS:
a string
"""
#
# References
# - Format specs http://www.tripos.com/data/support/mol2.pdf
# - Atom typing http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html
#
confIds = (confId, )
if confId == None:
confIds = Chem.Mol.GetNumConformers()
blocks = []
# add explicit hydrogens (since mol2 reader requires them)
if addHs:
h_coords = mol.GetNumConformers() > 0 and mol.GetConformer(-1).Is3D()
try:
mol = AddHs(mol, addCoords=h_coords)
except RuntimeError:
mol = AddHs(mol, addCoords=False)
# compute charges
if addCharges:
ComputeGasteigerCharges(mol)
for confId in confIds:
molecule = """@<TRIPOS>MOLECULE
{}
{} {} 0 0 0
SMALL
GASTEIGER\n\n""".format(
mol.GetProp("_Name") if mol.HasProp("_Name") else "UNK",
mol.GetNumAtoms(), mol.GetNumBonds())
# FIXME "USER_CHARGES" could become 'Gasteiger charges'
# FIXME "SMALL" means small molecule but could become "PROTEIN"
pos = _get_positions(mol, confId)
atom_lines = [
"{:>4} {:>4} {:>13.4f} {:>9.4f} {:>9.4f} {:<5} {} {} {:>7.4f}".
format(a.GetIdx() + 1,
a.GetSymbol(),
float(pos[a.GetIdx()][0]),
float(pos[a.GetIdx()][1]),
float(pos[a.GetIdx()][2]),
_sybyl_atom_type(a), 1, "UNL",
float(a.GetProp('_GasteigerCharge').replace(',', '.'))
if a.HasProp('_GasteigerCharge') else 0.0)
for a in mol.GetAtoms()
]
atom_lines = ["@<TRIPOS>ATOM"] + atom_lines
atom_lines = "\n".join(atom_lines) + "\n"
bond_lines = [
"{:>5} {:>5} {:>5} {:>2}".format(
bid + 1,
b.GetBeginAtomIdx() + 1,
b.GetEndAtomIdx() + 1, "ar"
if b.GetBondTypeAsDouble() == 1.5 else "am"
if _amide_bond(b) else str(int(b.GetBondTypeAsDouble())))
for bid, (b) in enumerate(mol.GetBonds())
]
bond_lines = ["@<TRIPOS>BOND"] + bond_lines + ["\n"]
bond_lines = "\n".join(bond_lines)
block = molecule + atom_lines + bond_lines
blocks.append(block)
return "".join(blocks)