def graph2mol(graph):
emol = Chem.RWMol()
for v in graph.vs():
emol.AddAtom(Chem.AtomFromSmiles(v["name"]))
for e in graph.es():
emol.AddBond(e.source, e.target, rank2bond(e['bond']))
mol = emol.GetMol()
return mol
def edit_RCO2H(em, pm, match_combo, L=None):
'''
Should return a list of mols
Source: Reynolds Class Notes, 9-24-20, p.3
Test SMILES: *c1ccc(*)cc1
'''
o_inds = [em.AddAtom(Chem.AtomFromSmiles('O')) for _ in range(L)]
c_inds = [em.AddAtom(Chem.AtomFromSmiles('C')) for _ in range(L)]
dbl_o_inds = [em.AddAtom(Chem.AtomFromSmiles('O')) for _ in range(L)]
methyl_c_inds = [em.AddAtom(Chem.AtomFromSmiles('C')) for _ in range(L)]
for i in range(L):
em.AddBond(o_inds[i], match_combo[i][1], Chem.BondType.SINGLE)
em.AddBond(c_inds[i], o_inds[i], Chem.BondType.SINGLE)
em.AddBond(c_inds[i], dbl_o_inds[i], Chem.BondType.DOUBLE)
em.AddBond(c_inds[i], methyl_c_inds[i], Chem.BondType.SINGLE)
em = retro.pm_to_lp_em(em, pm)
new_mol = em.GetMol()
for x in match_combo:
new_mol.GetAtomWithIdx(x[1]).SetNumExplicitHs(
pm.mol.GetAtomWithIdx(x[1]).GetNumImplicitHs())
new_mol.GetAtomWithIdx(x[0]).SetNumExplicitHs(
pm.mol.GetAtomWithIdx(x[0]).GetNumImplicitHs() + 1)
return [new_mol]
def edit_HCl(em, pm, match_combo, L=None):
'''
Should return a list of mols
Source: Reynolds Class Notes, 9-24-20, p.5
Test SMILES: '*/C(C#N)=C/C1C=CC(*)CC1'
'''
match_arr = np.array(match_combo)
new_mols = []
for i in range(2):
em = Chem.EditableMol(pm.mol)
cl_inds = [em.AddAtom(Chem.AtomFromSmiles('Cl')) for _ in range(L)]
c_inds = match_arr[:, i]
for i in range(L):
em.RemoveBond(match_combo[i][0], match_combo[i][1])
em.AddBond(match_combo[i][0], match_combo[i][1],
Chem.BondType.SINGLE)
em.AddBond(int(c_inds[i]), cl_inds[i], Chem.BondType.SINGLE)
em = retro.pm_to_lp_em(em, pm)
new_mols.append(em.GetMol())
return new_mols
def ring_close_retro(lp, pm=None):
'''
Reverse of Ring-closing which will occur after addition of heat
Source: Reynolds Class Notes, 8-25-20, p.2
Test SMILES: '*c5ccc(Oc4ccc(n3c(=O)c2cc1c(=O)n(*)c(=O)c1cc2c3=O)cc4)cc5'
'''
if type(lp) == str or type(
lp
) == Chem.rdchem.Mol: #only for convenience. Pass in LinearPol object when possible
lp = ru.LinearPol(lp)
start_match = Chem.MolFromSmarts('[c,C;!R0;!R1](=O)[n,N;!R0;!R1]')
end_match = Chem.MolFromSmarts('[#6R0](=O)([OH])[C,c][C,c][CR1](=O)[NR1]')
if pm is None:
pm = lp.PeriodicMol()
if pm is not None:
pm.GetSSSR()
if pm is None:
return []
mols = []
if pm.HasSubstructMatch(
start_match) and not pm.HasSubstructMatch(end_match):
lp_no_connect_inds = np.array(
[x for x in range(lp.mol.GetNumAtoms()) if x not in lp.star_inds])
def lp_to_pm_ind(lp_ind):
return int(np.argwhere(lp_no_connect_inds == lp_ind))
ar_atom_idx = [a.GetIdx() for a in lp.mol.GetAromaticAtoms()]
if len(
ar_atom_idx
) != 0: #only execute below for aromatic polymers. There for speed.
ri = lp.mol.GetRingInfo()
ar = ri.AtomRings()
atom_aromaticity = {a: 0 for a in ar_atom_idx}
for ring in ar:
ar_ring = 1
for a in ring:
if a not in atom_aromaticity.keys():
ar_ring = 0
if ar_ring == 1:
for a in ring:
atom_aromaticity[a] += 1
all_matches = pm.mol.GetSubstructMatches(start_match)
seen = set()
matches = [] #unique matches
for match in all_matches:
ms = set(match) #match set
#print(seen.difference(ms))
#print(ms.difference(seen))
if len(ms.intersection(seen)) == 0:
seen = seen.union(ms)
matches.append(match)
#matches = pm.mol.GetSubstructMatches(start_match)
for L in range(1, len(matches) + 1):
#for L in range(2,3):
for match_combo in itertools.combinations(matches, L):
em = Chem.EditableMol(pm.mol)
#print('Match combo:', match_combo)
for i_c, i_o, i_n in match_combo: #indices of atoms in pm
#print('Matches: %s %s %s' %(i_c,i_o,i_n) )
fix_aromaticity = False
if pm.mol.GetBondBetweenAtoms(
i_c, i_n).GetBondType() == Chem.BondType.AROMATIC:
fix_aromaticity = True
ring_atoms = None
ring_size = 100
for i in range(len(ar)):
ring = ar[i]
if lp_no_connect_inds[
i_c] in ring and lp_no_connect_inds[
i_n] in ring and len(
ring
) < ring_size: #assume correct ring is the smallest one
ring_atoms = set(ring)
ring_size = len(ring)
o = em.AddAtom(Chem.AtomFromSmiles('O'))
em.AddBond(i_c, o, Chem.BondType.SINGLE)
#print('bond between %s and %s' %(i_c,o))
em.RemoveBond(i_c, i_n)
#print('Bond removed between %s and %s' %(i_c,i_n))
med_mol = em.GetMol()
if fix_aromaticity:
try:
i_n_aromaticity = atom_aromaticity[lp_to_pm_ind(
i_n)]
except:
i_n_aromaticity = 0
for i in ring_atoms:
if atom_aromaticity[
i] == i_n_aromaticity: #if an atom was part of same number of aromatic rings as the N atom, it shouldn't be aromatic
#print('Ring atom lp:',i)
pm_i = lp_to_pm_ind(i)
#print('Ring atom pm:',pm_i)
med_mol.GetAtomWithIdx(pm_i).SetIsAromatic(
False)
#remove all aromatic bonds
neighs = [
x.GetIdx() for x in med_mol.GetAtoms()
[pm_i].GetNeighbors()
]
aromatic_neighs = [
x for x in neighs
if med_mol.GetBondBetweenAtoms(pm_i, x).
GetBondType() == Chem.BondType.AROMATIC
]
#print('Aromatic neighs of %s: %s' %(pm_i,aromatic_neighs))
em = Chem.EditableMol(med_mol)
for x in aromatic_neighs:
em.RemoveBond(x, pm_i)
em.AddBond(x, pm_i, Chem.BondType.SINGLE)
med_mol = em.GetMol()
em = Chem.EditableMol(med_mol)
star1 = em.AddAtom(Chem.AtomFromSmiles('*'))
star2 = em.AddAtom(Chem.AtomFromSmiles('*'))
em.RemoveBond(pm.connector_inds[0], pm.connector_inds[1])
em.AddBond(pm.connector_inds[0], star1, Chem.BondType.SINGLE)
em.AddBond(pm.connector_inds[1], star2, Chem.BondType.SINGLE)
new_mol = em.GetMol()
try:
Chem.SanitizeMol(new_mol)
mols.append(ru.mol_without_atom_index(new_mol))
except:
return []
return mols
else:
return []
def set_atm_list(self, str_atm_list):
atm_list = []
for str_atm in str_atm_list:
atm_list.append(Chem.AtomFromSmiles("["+str_atm+"]"))
self.prepare_atm(atm_list)
