def FindAllAdsorbateGraphsOfLengthN(mol1,
SurfaceAtomSymbols,
NMaxEdge,
NMinEdge=0,
valence_based=False,
debug=False):
"""
Adsorbate Graph mining Tool. Molecular graph of the surface and adsorbate
are inputed. Graphs of any shape with lengths specified are obtained
Input List
mol1: RdKit Mol object of surface and adsorbate
SurfaceAtomSymbols: Surface atom symbols
NMaxEdge: Maximum number of edges. if -1, find everything
NMinEdge: Minimum number of edges
valence_based: Valence based graphs obtained
debug: Debugging function
Output List
SMILES_count: dictionary of SMILES -> count
"""
# AdsorbateSMILES of length N is found. Not radial.
# if NMaxEdge = -1, find everything
# mol2 is copied, then surface atoms are removed, and the enumeration is performed
# check if mol is rdkit mol
assert isinstance(mol1, Chem.rdchem.Mol)
mol1 = LumpH(mol1)
mol2 = mol1.__copy__() # mol without surface atoms
mol2 = Chem.RWMol(mol2)
# Go through the molecule, add non-surface atoms to relevant atom list
Mol2toMol1Map = dict()
NSAL = list() # (N)on(S)urface (A)tom (L)ist
SAL = list() # (S)urface (A)tom (L)ist
mol2i = 0
for mol1i in xrange(0, mol1.GetNumAtoms()):
atom = mol1.GetAtomWithIdx(mol1i)
if atom.GetSymbol() not in SurfaceAtomSymbols:
NSAL.append(mol1i)
Mol2toMol1Map[mol2i] = mol1i
mol2i += 1
else:
SAL.append(mol1i)
mol2.RemoveAtom(mol2i)
# check N
if NMaxEdge >= mol2.GetNumBonds():
NMaxEdge = mol2.GetNumBonds()
if NMinEdge >= mol2.GetNumBonds():
NMinEdge = mol2.GetNumBonds()
if NMaxEdge == -1:
NMaxEdge = mol2.GetNumBonds()
# (S)ubgraph (B)ond (I)ndex (L)ist(s)
SBILs = list()
if NMaxEdge > 0:
SBILs = Chem.FindAllSubgraphsOfLengthMToN(mol2, NMinEdge, NMaxEdge)
# valence_based
if valence_based:
bonds = mol1.GetBonds()
# remove surface atom - surface atom bond
for i in xrange(len(bonds) - 1, -1, -1):
if bonds[i].GetBeginAtom().GetSymbol() in SurfaceAtomSymbols and \
bonds[i].GetEndAtom().GetSymbol() in SurfaceAtomSymbols:
mol1.RemoveBond(bonds[i].GetBeginAtomIdx(),
bonds[i].GetEndAtomIdx())
atoms = mol1.GetAtoms()
# Separate binding sites
for i in xrange(len(atoms) - 1, -1, -1):
if atoms[i].GetSymbol() in SurfaceAtomSymbols:
neighbors = atoms[i].GetNeighbors()
neighboridx = list()
for neighbor_atom in neighbors:
neighboridx.append(neighbor_atom.GetIdx())
if len(neighboridx) > 1: # it has connection to organic atoms
for j in xrange(1, len(neighboridx)):
# add valence
mol1.RemoveBond(atoms[i].GetIdx(), neighboridx[j])
new_surf_atom = Chem.Atom(SurfaceAtomSymbols)
new_surf_atom_idx = mol1.AddAtom(new_surf_atom)
mol1.AddBond(new_surf_atom_idx, neighboridx[j],
Chem.rdchem.BondType.ZERO)
# debug
if debug:
print Chem.MolToSmiles(mol1)
# Get finger prints
smiless = list() # (F)inger(p)rint(s). It's in atom index, and will be
# converted to SMILES later. This is done to remove duplicates
## length = 0 case
if NMinEdge == 0:
for idx in NSAL:
smiless.append([idx])
## Radius > 1 cases
# add organic atoms
for SBIL in SBILs:
for SBI in SBIL:
AL = set() # (A)tom (L)ist
for BI in SBI:
B = mol2.GetBondWithIdx(BI)
AL.add(Mol2toMol1Map[B.GetBeginAtomIdx()])
AL.add(Mol2toMol1Map[B.GetEndAtomIdx()])
smiless.append(list(AL))
# Add surface atom that is neighbor to SMILES
# add surface atoms
for smiles in smiless:
RSAL = list() # (R)elevant (S)urface (A)tom (L)ist
for SA in SAL:
for NeighborAtom in mol1.GetAtomWithIdx(SA).GetNeighbors():
NeighborAtomIdx = NeighborAtom.GetIdx()
if NeighborAtomIdx in smiles:
RSAL.append(SA)
smiles += RSAL
# convert atom indexes to SMILES
SMILES_count = defaultdict(int)
for smiles in smiless:
SMILES_count[_GetSMILES(mol1, smiles)] += 1
return SMILES_count
