def add_atom(mol, atomic_number, atom):
emol = EditableMol(mol)
new_index = emol.AddAtom(Chem.Atom(atomic_number))
emol.AddBond(atom.GetIdx(), new_index, Chem.BondType.SINGLE)
mol_ = emol.GetMol()
Chem.SanitizeMol(mol_)
return mol_
def graph(self, m):
from rdkit.Chem import EditableMol, Atom, rdchem
hcount = m.GetNumAtoms(False) - m.GetNumAtoms(True)
# create new molecule using single bonds only
em = EditableMol(Mol())
nbridx = [None] * m.GetNumAtoms()
iatom = 0
for atom in m.GetAtoms():
atnum = atom.GetAtomicNum()
if atnum == 1 and atom.GetIsotope() == 1:
#if atom.GetMass() > 1: pass
hcount += 1
else:
newatom = Atom(atnum)
#if atom.GetTotalDegree() == 0: newatom.SetNoImplicit(True) # otherwise [Na]. becomes [NaH].
#newatom.SetFormalCharge(atom.GetFormalCharge())
newatom.SetFormalCharge(0)
em.AddAtom(newatom)
aidx = atom.GetIdx()
nbridx[aidx] = iatom
iatom += 1
for a2 in atom.GetNeighbors():
a2idx = nbridx[a2.GetIdx()]
if a2idx != None:
em.AddBond(aidx, a2idx, rdchem.BondType.SINGLE)
#cansmi = self.cansmiles(em.GetMol())
cansmi = MolToSmiles(m, isomericSmiles=True)
#cansmi = cansmi.replace('+','').replace('-','').replace('[N]','N').replace('[O]','O').replace('[C]','C').replace('[I]','I').replace('[S]','S').replace('[P]','P').replace('[B]','B').replace('[Br]','Br').replace('[Cl]','Cl')
return "%s%s%d%+d" % (cansmi, ' H', hcount, GetFormalCharge(m))
def get_matching_parts(mol, *matches):
indices = reversed(range(mol.GetNumAtoms()))
for match in matches:
match = set(match)
part = EditableMol(mol)
for idx in indices:
if idx not in match:
part.RemoveAtom(idx)
yield part.GetMol()
def replace_dummy_with_h(m):
emol = EditableMol(m)
for atom in m.GetAtoms():
if atom.GetAtomicNum() == 1:
emol.ReplaceAtom(atom.GetIdx(), Chem.Atom(0))
m = emol.GetMol()
# for atom in m.GetAtoms():
# if atom.GetAtomicNum() == 0:
# for bond in atom.GetBonds():
# bond.SetBondType(Chem.BondType.UNSPECIFIED)
# atom.SetIsAromatic(False)
return m
def to_single_bond_remove_hs(mol):
atom_map = {}
emol = EditableMol(Chem.MolFromSmiles(""))
for atom in mol.GetAtoms():
if atom.GetAtomicNum() > 1:
new_idx = emol.AddAtom(Chem.Atom(atom.GetAtomicNum()))
atom_map[atom.GetIdx()] = new_idx
for bond in mol.GetBonds():
begin, end = bond.GetBeginAtom(), bond.GetEndAtom()
if begin.GetAtomicNum() <= 1:
continue
if end.GetAtomicNum() <= 1:
continue
new_idxs = atom_map[begin.GetIdx()], atom_map[end.GetIdx()]
emol.AddBond(new_idxs[0], new_idxs[1], Chem.BondType.SINGLE)
return emol.GetMol()
def convert_molecule(molecule):
from rdkit.Chem import Mol, EditableMol, Atom, Conformer
mol = Mol()
emol = EditableMol(mol)
conformer = Conformer()
atom_map = {}
for atom in molecule.atoms:
a = Atom(atom.element.number)
atom_map[atom] = i = emol.AddAtom(a)
conformer.SetAtomPosition(i, atom.coord().data())
for bond in molecule.bonds:
a1, a2 = bond.atoms
emol.AddBond(atom_map[a1], atom_map[a2])
mol = emol.GetMol()
mol.AddConformer(conformer)
return mol, atom_map
def remove_any_atom_bonds(m):
if not has_ring(m):
return m
emol = EditableMol(Chem.MolFromSmiles(""))
atom_map = {}
for atom in m.GetAtoms():
if atom.GetAtomicNum() == 0:
continue
new_idx = emol.AddAtom(Chem.Atom(atom.GetAtomicNum()))
atom_map[atom.GetIdx()] = new_idx
for bond in m.GetBonds():
start, end = bond.GetBeginAtom(), bond.GetEndAtom()
if start.GetAtomicNum() == 0:
continue
if end.GetAtomicNum() == 0:
continue
start, end = atom_map[start.GetIdx()], atom_map[end.GetIdx()]
emol.AddBond(start, end, bond.GetBondType())
return emol.GetMol()
def graph2(self, m):
from rdkit.Chem import EditableMol, RemoveHs, Atom, rdchem #, SanitizeMol, rdmolops
#natoms = m.GetNumAtoms()
# create new molecule using single bonds only
em = EditableMol(Mol())
hcount = 0
for atom in m.GetAtoms():
atnum = atom.GetAtomicNum()
hcount += atom.GetTotalNumHs(False)
newatom = Atom(atnum)
#newatom.SetFormalCharge(atom.GetFormalCharge())
em.AddAtom(newatom)
for bond in m.GetBonds():
em.AddBond(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
rdchem.BondType.SINGLE)
try:
mol = RemoveHs(em.GetMol())
except:
mol = em.GetMol()
#mol = em.GetMol()
#SanitizeMol(mol, SanitizeFlags.SANITIZE_ADJUSTHS)
#Chem.rdmolops.SanitizeFlags.SANITIZE_ADJUSTHS
cansmi = self.cansmiles(mol)
return "%s%s%d%+d" % (cansmi, ' H', hcount, GetFormalCharge(m))
def deprocess(vertices, edges):
from rdkit.Chem import EditableMol, MolFromSmiles, Atom, MolToSmiles, Bond, BondType, Mol
m = EditableMol(Mol())
for v in vertices:
if v != 0:
m.AddAtom(Atom(v))
for begin, end, type in edges:
if (begin, end) == (0, 0):
continue
if begin == end:
continue
if begin == len(vertices) - 1:
continue
if end == len(vertices) - 1:
continue
if begin > end:
begin, end = end, begin
if type == 0:
continue
if m.GetMol().GetBondBetweenAtoms(begin, end):
continue
m.AddBond(begin, end, BondType.values[type])
s = MolToSmiles(m.GetMol())
return s
def remove_isotopes(mol, sanitize=True):
edmol = EditableMol(mol)
for atom in mol.GetAtoms():
atom.SetIsotope(0)
if sanitize:
SanitizeMol(mol)
def add_bond_helper(mol, a1, a2, bond_type):
emol = EditableMol(mol)
emol.AddBond(a1.GetIdx(), a2.GetIdx(), bond_type)
return sanitize_emol(emol)
def create_emol(mol):
return EditableMol(mol)