def test_smiles_from_adjacent_matrix(smiles):
charged_fragments = True
quick = True
# Cut apart the smiles
mol = get_mol(smiles)
atoms = get_atoms(mol)
charge = Chem.GetFormalCharge(mol)
adjacent_matrix = Chem.GetAdjacencyMatrix(mol)
#
mol = Chem.RemoveHs(mol)
canonical_smiles = Chem.MolToSmiles(mol)
# Define new molecule template from atoms
new_mol = x2m.get_proto_mol(atoms)
# reconstruct the molecule from adjacent matrix, atoms and total charge
new_mols = x2m.AC2mol(new_mol, adjacent_matrix, atoms, charge,
charged_fragments, quick)
new_mol_smiles_list = []
for new_mol in new_mols:
new_mol = Chem.RemoveHs(new_mol)
new_mol_smiles = Chem.MolToSmiles(new_mol)
new_mol_smiles_list.append(new_mol_smiles)
assert canonical_smiles in new_mol_smiles_list
return
def take_elementary_step(mol, charge, E_cutoff, heterolytic, quick):
chiral_parent = Chem.FindMolChiralCenters(mol, includeUnassigned=True)
parent_is_chiral = len(chiral_parent) > 0
if parent_is_chiral:
atom2chirality = {key: value for (key, value) in chiral_parent}
atomicNumList = [a.GetAtomicNum() for a in mol.GetAtoms()]
proto_mol = xyz2mol.get_proto_mol(atomicNumList)
AC = Chem.GetAdjacencyMatrix(mol)
num_atoms = len(atomicNumList)
I_elementary = get_I_elementary(AC, num_atoms, atomicNumList)
smiles_list = []
molecules = []
raw_smiles_list = []
raw_molecules = []
for I in I_elementary:
newmol = xyz2mol.AC2mol(proto_mol, I, atomicNumList, charge,
heterolytic, quick)
if parent_is_chiral:
newmol = set_chirality(mol, newmol, atom2chirality)
raw_smiles = Chem.MolToSmiles(newmol, isomericSmiles=True)
if raw_smiles not in raw_smiles_list:
raw_smiles_list.append(raw_smiles)
raw_molecules.append(newmol)
energy_of_reactant = get_BO_energy(mol)
for smiles, raw_mol in zip(raw_smiles_list, raw_molecules):
try:
test_mol = Chem.MolFromSmiles(smiles)
except:
continue
if test_mol != None:
energy = get_BO_energy(raw_mol)
if smiles not in smiles_list and energy_of_reactant - energy < E_cutoff:
smiles_list.append(smiles)
molecules.append(raw_mol)
smiles_list.insert(0, Chem.MolToSmiles(mol, isomericSmiles=True))
molecules.insert(0, mol)
return smiles_list, molecules
def take_elementary_step(mol, charge, E_cutoff, heterolytic):
atomicNumList = [a.GetAtomicNum() for a in mol.GetAtoms()]
proto_mol = xyz2mol.get_proto_mol(atomicNumList)
AC = Chem.GetAdjacencyMatrix(mol)
num_atoms = len(atomicNumList)
I_elementary = get_I_elementary(AC, num_atoms, atomicNumList)
smiles_list = []
molecules = []
raw_smiles_list = []
raw_molecules = []
for I in I_elementary:
newmol = xyz2mol.AC2mol(proto_mol, I, atomicNumList, charge,
heterolytic)
raw_smiles = Chem.MolToSmiles(newmol)
if raw_smiles not in raw_smiles_list:
raw_smiles_list.append(raw_smiles)
raw_molecules.append(newmol)
energy_of_reactant = get_BO_energy(mol)
for smiles, raw_mol in zip(raw_smiles_list, raw_molecules):
try:
test_mol = Chem.MolFromSmiles(smiles)
except:
continue
if test_mol != None:
energy = get_BO_energy(raw_mol)
if smiles not in smiles_list and energy_of_reactant - energy < E_cutoff:
smiles_list.append(smiles)
molecules.append(raw_mol)
smiles_list.insert(0, Chem.MolToSmiles(mol))
molecules.insert(0, mol)
return smiles_list, molecules
#smiles_list = ['C1(CC2=CC=CC=C2)=CC=CC=C1']
#smiles_list = ['[O-]c1ccccc1[O-]']
#smiles_list = ['C[N+](=O)[O-]']
#smiles_list = ['N#CC(C#N)=CC=C1C=CC=CC(=C1)c1ccc(cc1)[N+](=O)[O-]']
#smiles_list = ['CNC([O-])=C([NH+]=C/CC(O)=O)C']
#smiles_list = ['Cc1cn(C2CC(O)C(COP(=O)([O-])OP(=O)([O-])OC3OC(C)C([NH3+])C(O)C3O)O2)c(=O)[nH]c1=O']
for smiles in smiles_list:
#print(smiles)
mol = Chem.MolFromSmiles(smiles)
Chem.Kekulize(mol, clearAromaticFlags = True)
charge = Chem.GetFormalCharge(mol)
mol = Chem.AddHs(mol)
atomicNumList = [a.GetAtomicNum() for a in mol.GetAtoms()]
proto_mol = x2m.get_proto_mol(atomicNumList)
AC = Chem.GetAdjacencyMatrix(mol)
newmol = x2m.AC2mol(proto_mol,AC,atomicNumList,charge,charged_fragments,quick)
#print Chem.MolToSmiles(newmol)
newmol = Chem.RemoveHs(newmol)
newmol_smiles = Chem.MolToSmiles(newmol)
#print (newmol_smiles)
mol = Chem.RemoveHs(mol)
canonical_smiles = Chem.MolToSmiles(mol)
if newmol_smiles != canonical_smiles:
print("uh,oh", smiles, newmol_smiles)