def set_aromaticity_mdl(self):
"""
Sets the aromaticity flags in this molecule to use the MDL model
"""
oechem.OEClearAromaticFlags(self.mol)
oechem.OEAssignAromaticFlags(self.mol, oechem.OEAroModel_MDL)
oechem.OEAssignHybridization(self.mol)
def CanSmi(mol, isomeric, kekule):
oechem.OEFindRingAtomsAndBonds(mol)
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModel_OpenEye)
smiflag = oechem.OESMILESFlag_Canonical
if isomeric:
smiflag |= oechem.OESMILESFlag_ISOMERIC
if kekule:
for bond in mol.GetBonds(oechem.OEIsAromaticBond()):
bond.SetIntType(5)
oechem.OECanonicalOrderAtoms(mol)
oechem.OECanonicalOrderBonds(mol)
oechem.OEClearAromaticFlags(mol)
oechem.OEKekulize(mol)
smi = oechem.OECreateSmiString(mol, smiflag)
return smi
def CanSmi(mol, isomeric, kekule):
"""
Returns the cannonical smile from the OEMol provided
:param mol: OEMolBase object
:param isomeric: force isometric
:param kekule: use kekule cleaning
:return: string of OESmiles
"""
oechem.OEFindRingAtomsAndBonds(mol)
oechem.OEAssignAromaticFlags(mol, oechem.OEAroModel_OpenEye)
smiflag = oechem.OESMILESFlag_Canonical
if isomeric:
smiflag |= oechem.OESMILESFlag_ISOMERIC
if kekule:
for bond in mol.GetBonds(oechem.OEIsAromaticBond()):
bond.SetIntType(5)
oechem.OECanonicalOrderAtoms(mol)
oechem.OECanonicalOrderBonds(mol)
oechem.OEClearAromaticFlags(mol)
oechem.OEKekulize(mol)
smi = oechem.OECreateSmiString(mol, smiflag)
return smi
def generateOEMolFromTopologyResidue(residue,
geometry=False,
tripos_atom_names=False):
"""
Generate an OpenEye OEMol molecule from an OpenMM Topology Residue.
Parameters
----------
residue : simtk.openmm.app.topology.Residue
The topology Residue from which an OEMol is to be created.
An Exception will be thrown if this residue has external bonds.
geometry : bool, optional, default=False
If True, will generate a single configuration with OEOmega.
Note that stereochemistry will be *random*.
tripos_atom_names : bool, optional, default=False
If True, will generate and assign Tripos atom names.
Returns
-------
molecule : openeye.oechem.OEMol
The OEMol molecule corresponding to the topology.
Atom order will be preserved and bond orders assigned.
The Antechamber `bondtype` program will be used to assign bond orders, and these
will be converted back into OEMol bond type assignments.
Note that there is no way to preserve stereochemistry since `Residue` does
not note stereochemistry in any way.
"""
# Raise an Exception if this residue has external bonds.
if len(list(residue.external_bonds())) > 0:
raise Exception(
"Cannot generate an OEMol from residue '%s' because it has external bonds."
% residue.name)
from openeye import oechem
# Create OEMol where all atoms have bond order 1.
molecule = oechem.OEMol()
molecule.SetTitle(residue.name) # name molecule after first residue
for atom in residue.atoms():
oeatom = molecule.NewAtom(atom.element.atomic_number)
oeatom.SetName(atom.name)
oeatom.AddData("topology_index", atom.index)
oeatoms = {oeatom.GetName(): oeatom for oeatom in molecule.GetAtoms()}
for (atom1, atom2) in residue.bonds():
order = 1
molecule.NewBond(oeatoms[atom1.name], oeatoms[atom2.name], order)
# Write out a mol2 file without altering molecule.
import tempfile
tmpdir = tempfile.mkdtemp()
mol2_input_filename = os.path.join(tmpdir,
'molecule-before-bond-perception.mol2')
ac_output_filename = os.path.join(tmpdir,
'molecule-after-bond-perception.ac')
ofs = oechem.oemolostream(mol2_input_filename)
m2h = True
substruct = False
oechem.OEWriteMol2File(ofs, molecule, m2h, substruct)
ofs.close()
# Run Antechamber bondtype
import subprocess
#command = 'bondtype -i %s -o %s -f mol2 -j full' % (mol2_input_filename, ac_output_filename)
command = 'antechamber -i %s -fi mol2 -o %s -fo ac -j 2' % (
mol2_input_filename, ac_output_filename)
[status, output] = getstatusoutput(command)
# Define mapping from GAFF bond orders to OpenEye bond orders.
order_map = {1: 1, 2: 2, 3: 3, 7: 1, 8: 2, 9: 5, 10: 5}
# Read bonds.
infile = open(ac_output_filename)
lines = infile.readlines()
infile.close()
antechamber_bond_types = list()
for line in lines:
elements = line.split()
if elements[0] == 'BOND':
antechamber_bond_types.append(int(elements[4]))
oechem.OEClearAromaticFlags(molecule)
for (bond, antechamber_bond_type) in zip(molecule.GetBonds(),
antechamber_bond_types):
#bond.SetOrder(order_map[antechamber_bond_type])
bond.SetIntType(order_map[antechamber_bond_type])
oechem.OEFindRingAtomsAndBonds(molecule)
oechem.OEKekulize(molecule)
oechem.OEAssignFormalCharges(molecule)
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
# Clean up.
os.unlink(mol2_input_filename)
os.unlink(ac_output_filename)
os.rmdir(tmpdir)
# Generate Tripos atom names if requested.
if tripos_atom_names:
oechem.OETriposAtomNames(molecule)
# Assign geometry
if geometry:
from openeye import oeomega
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetIncludeInput(False)
omega.SetStrictStereo(False)
omega(molecule)
return molecule
def _assign_am1bcc(cls, oe_molecule: OEMol):
"""Applies aromaticity flags based upon the aromaticity model
outlined in the original AM1BCC publications _[1].
Parameters
----------
oe_molecule
The molecule to assign aromatic flags to.
References
----------
[1] Jakalian, A., Jack, D. B., & Bayly, C. I. (2002). Fast, efficient generation
of high-quality atomic charges. AM1-BCC model: II. Parameterization and
validation. Journal of computational chemistry, 23(16), 1623–1641.
"""
from openeye import oechem
oechem.OEClearAromaticFlags(oe_molecule)
x_type = "[#6X3,#7X2,#15X2,#7X3+1,#15X3+1,#8X2+1,#16X2+1:N]"
y_type = "[#6X2-1,#7X2-1,#8X2,#16X2,#7X3,#15X3:N]"
z_type = x_type
# Case 1)
case_1_smirks = (f"{x_type.replace('N', '1')}1"
f"=@{x_type.replace('N', '2')}"
f"-@{x_type.replace('N', '3')}"
f"=@{x_type.replace('N', '4')}"
f"-@{x_type.replace('N', '5')}"
f"=@{x_type.replace('N', '6')}-@1")
case_1_matches = match_smirks(case_1_smirks, oe_molecule, unique=True)
case_1_atoms = {
match
for matches in case_1_matches for match in matches.values()
}
cls._set_aromatic(case_1_matches, oe_molecule)
# Track the ar6 assignments as there is no atom attribute to
# safely determine if an atom is in a six member ring when
# that same atom is also in a five member ring.
ar6_assignments = {*case_1_atoms}
# Case 2)
case_2_smirks = (f"{x_type.replace('N', '1')}1"
f"=@{x_type.replace('N', '2')}"
f"-@{x_type.replace('N', '3')}"
f"=@{x_type.replace('N', '4')}"
f"-@{x_type.replace('N', '5')}"
f":@{x_type.replace('N', '6')}-@1")
previous_case_2_atoms = None
case_2_atoms = {}
while previous_case_2_atoms != case_2_atoms:
case_2_matches = match_smirks(case_2_smirks,
oe_molecule,
unique=True)
# Enforce the ar6 condition
case_2_matches = [
case_2_match for case_2_match in case_2_matches
if case_2_match[4] in ar6_assignments
and case_2_match[5] in ar6_assignments
]
previous_case_2_atoms = case_2_atoms
case_2_atoms = {
match
for matches in case_2_matches for match in matches.values()
}
ar6_assignments.update(case_2_atoms)
cls._set_aromatic(case_2_matches, oe_molecule)
# Case 3)
case_3_smirks = (f"{x_type.replace('N', '1')}1"
f"=@{x_type.replace('N', '2')}"
f"-@{x_type.replace('N', '3')}"
f":@{x_type.replace('N', '4')}"
f"~@{x_type.replace('N', '5')}"
f":@{x_type.replace('N', '6')}-@1")
previous_case_3_atoms = None
case_3_atoms = {}
while previous_case_3_atoms != case_3_atoms:
case_3_matches = match_smirks(case_3_smirks,
oe_molecule,
unique=True)
# Enforce the ar6 condition
case_3_matches = [
case_3_match for case_3_match in case_3_matches
if case_3_match[2] in ar6_assignments and case_3_match[3] in
ar6_assignments and case_3_match[4] in ar6_assignments
and case_3_match[5] in ar6_assignments
]
previous_case_3_atoms = case_3_atoms
case_3_atoms = {
match
for matches in case_3_matches for match in matches.values()
}
ar6_assignments.update(case_3_atoms)
cls._set_aromatic(case_3_matches, oe_molecule)
# Case 4)
case_4_smirks = ("[#6+1:1]1"
f"-@{x_type.replace('N', '2')}"
f"=@{x_type.replace('N', '3')}"
f"-@{x_type.replace('N', '4')}"
f"=@{x_type.replace('N', '5')}"
f"-@{x_type.replace('N', '6')}"
f"=@{x_type.replace('N', '7')}-@1")
case_4_matches = match_smirks(case_4_smirks, oe_molecule, unique=True)
case_4_atoms = {
match
for matches in case_4_matches for match in matches.values()
}
cls._set_aromatic(case_4_matches, oe_molecule)
# Case 5)
case_5_smirks = (f"{y_type.replace('N', '1')}1"
f"-@{z_type.replace('N', '2')}"
f"=@{z_type.replace('N', '3')}"
f"-@{x_type.replace('N', '4')}"
f"=@{x_type.replace('N', '5')}-@1")
ar_6_ar_7_matches = {
*case_1_atoms,
*case_2_atoms,
*case_3_atoms,
*case_4_atoms,
}
case_5_matches = match_smirks(case_5_smirks, oe_molecule, unique=True)
case_5_matches = [
matches for matches in case_5_matches
if matches[1] not in ar_6_ar_7_matches
and matches[2] not in ar_6_ar_7_matches
]
cls._set_aromatic(case_5_matches, oe_molecule)
def set_aromaticity_mdl(self):
oechem.OEClearAromaticFlags(self.mol)
oechem.OEAssignAromaticFlags(self.mol, oechem.OEAroModel_MDL)
oechem.OEAssignHybridization(self.mol)
def main():
opt = parser.parse_args()
global which_gaff
if opt.gaff:
which_gaff = opt.gaff
else:
which_gaff = 1 # 2--> gaff2
global lig_input_mol2
if opt.lig:
lig_input_mol2 = opt.lig
else:
lig_input_mol2 = 'lig_in.mol2'
# ============== #
# new protocol:
# (1) amber bond typer --> ac file (2) openeye convert aromatic mol2 --> kekule form assignment with oechem.OEKekulize(mol)
# ============== #
command = '$AMBERHOME/bin/antechamber -i %s -fi mol2 -o lig.ac -fo ac -j 2 -dr n -pf y' % lig_input_mol2
print(command)
subprocess.call(command, shell=True)
molecule = oechem.OEGraphMol()
ifs = oechem.oemolistream(lig_input_mol2)
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMol2File(ifs, molecule)
print(molecule.GetTitle())
# Define mapping from GAFF bond orders to OpenEye bond orders.
order_map = {1: 1, 2: 2, 3: 3, 7: 1, 8: 2, 9: 5, 10: 5}
# Read bonds.
infile = open('lig.ac')
lines = infile.readlines()
infile.close()
antechamber_bond_types = list()
for line in lines:
elements = line.split()
if elements[0] == 'BOND':
antechamber_bond_types.append(int(elements[4]))
oechem.OEClearAromaticFlags(molecule)
for (bond, antechamber_bond_type) in zip(molecule.GetBonds(),
antechamber_bond_types):
#bond.SetOrder(order_map[antechamber_bond_type])
bond.SetIntType(order_map[antechamber_bond_type])
oechem.OEFindRingAtomsAndBonds(molecule)
oechem.OEKekulize(molecule)
oechem.OEAssignFormalCharges(molecule)
oechem.OEAssignAromaticFlags(molecule, oechem.OEAroModelOpenEye)
"""
charges = [ atom.GetFormalCharge() for atom in molecule.GetAtoms() ]
net_charge = np.array(charges).sum()
print("Net Charge:", net_charge)
"""
subprocess.call('grep CHARGE lig.ac', shell=True)
with open('lig.ac', "r") as f:
line = f.readline()
# if line.find("CHARGE") > -1 and len(line.split())> 2:
# net_charge = int( float( line.split()[1] ) )
if line.find("CHARGE") > -1:
net_charge = int(line[line.find("(") + 1:line.find(")")])
print("Net Charge:", net_charge)
# Write mol2 file for this molecule.
outmol = oechem.OEMol(molecule)
ofs = oechem.oemolostream()
filename = 'lig_oe.mol2'
ofs.open(filename)
oechem.OEWriteMolecule(ofs, outmol)
ofs.close()
if which_gaff == 1:
gaff = "gaff"
elif which_gaff == 2:
gaff = "gaff2"
command = "$AMBERHOME/bin/antechamber -i lig_oe.mol2 -fi mol2 -o lig_bcc.mol2 -fo mol2 -c bcc -at %s -nc %i -j 5 -pf y -dr n" \
% (gaff, net_charge)
print(command)
subprocess.call(command, shell=True)
command = "$AMBERHOME/bin/parmchk2 -i lig_bcc.mol2 -f mol2 -s %d -o lig.frcmod" % (
which_gaff)
print(command)
subprocess.call(command, shell=True)
#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
mol = oechem.OEGraphMol()
oechem.OEParseSmiles(mol, "n1ccncc1")
print("Canonical smiles :", oechem.OECreateCanSmiString(mol))
oechem.OEClearAromaticFlags(mol)
oechem.OEKekulize(mol)
print("Kekule smiles :", oechem.OECreateCanSmiString(mol))
# @ </SNIPPET>
