def GetFrame(mol, mode='Scaff'):
'''return a ganeric molecule defining the reduced scaffold of the input mol.
mode can be 'Scaff' or 'RedScaff':
Scaff -> chop off the side chains and return the scaffold
RedScaff -> remove all linking chains and connect the rings
directly at the atoms where the linker was
'''
ring = mol.GetRingInfo()
RingAtoms = flatten(ring.AtomRings())
NonRingAtoms = [atom.GetIdx() for atom in mol.GetAtoms() if atom.GetIdx() not in RingAtoms]
RingNeighbors = []
Paths = []
for NonRingAtom in NonRingAtoms:
for neighbor in mol.GetAtomWithIdx(NonRingAtom).GetNeighbors():
if neighbor.GetIdx() in RingAtoms:
RingNeighbors.append(NonRingAtom)
#The ring Atoms having a non ring Neighbor will be the start of a walk
Paths.append([neighbor.GetIdx(), NonRingAtom])
break
PosConnectors = [x for x in NonRingAtoms if x not in RingNeighbors
] #Only these Atoms are potential starting points of a Linker chain
#print 'PosConnectors:'
#print PosConnectors
Framework = [x for x in RingAtoms]
#Start a list of pathways which we will have to walk
#print 'Path atoms:'
#print Paths
Linkers = []
while len(Paths) > 0:
NewPaths = []
for P in Paths:
if P == None:
print('ooh')
else:
for neighbor in mol.GetAtomWithIdx(P[-1]).GetNeighbors():
if neighbor.GetIdx() not in P:
if neighbor.GetIdx() in NonRingAtoms:
n = P[:]
n.append(neighbor.GetIdx())
NewPaths.append(n[:])
elif neighbor.GetIdx() in RingAtoms:
#print 'adding the following path to Framework:'
#print P
n = P[:]
n.append(neighbor.GetIdx())
Linkers.append(n)
Framework = Framework + P[:]
Paths = NewPaths[:]
#print 'Linkers:',Linkers
#print 'RingAtoms:',RingAtoms
#em.AddBond(3,4,Chem.BondType.SINGLE)
if mode == 'RedScaff':
Framework = list(set(Framework))
todel = []
NonRingAtoms.sort(reverse=True)
em = Chem.EditableMol(mol)
BondsToAdd = [sorted([i[0], i[-1]]) for i in Linkers]
mem = []
for i in BondsToAdd:
if i not in mem:
em.AddBond(i[0], i[1], Chem.BondType.SINGLE)
mem.append(i)
for i in NonRingAtoms:
todel.append(i)
for i in todel:
em.RemoveAtom(i)
m = em.GetMol()
#===================================#
# Now do the flattening of atoms and bonds!
# Any heavy atom will become a carbon and any bond will become a single bond! #
#===================================#
# for atom in m.GetAtoms(): #
# atom.SetAtomicNum(6) #
# atom.SetFormalCharge(0) #
# for bond in m.GetBonds(): #
# bond.SetBondType(Chem.BondType.SINGLE) #
# Chem.SanitizeMol(m) #
#===================================#
return m
if mode == 'Scaff':
Framework = list(set(Framework))
todel = []
NonRingAtoms.sort(reverse=True)
for i in NonRingAtoms:
if i != None:
if i not in Framework:
todel.append(i)
em = Chem.EditableMol(mol)
for i in todel:
em.RemoveAtom(i)
m = em.GetMol()
#===================================#
# Now do the flattening of atoms and bonds!
# Any heavy atom will become a carbon and any bond will become a single bond!! #
#===================================#
# for atom in m.GetAtoms(): #
# atom.SetAtomicNum(6) #
# atom.SetFormalCharge(0) #
# for bond in m.GetBonds(): #
# bond.SetBondType(Chem.BondType.SINGLE) #
# Chem.SanitizeMol(m) #
#===================================#
return m
# for atom in m.GetAtoms(): #
# atom.SetAtomicNum(6) #
# atom.SetFormalCharge(0) #
# for bond in m.GetBonds(): #
# bond.SetBondType(Chem.BondType.SINGLE) #
# Chem.SanitizeMol(m) #
#===================================#
return m
if __name__ == '__main__':
if len(sys.argv) < 2:
print("No input file provided: Frames.py filetosprocess.ext")
sys.exit(1)
suppl = Chem.SDMolSupplier(sys.argv[1])
FrameDict = {}
for mol in suppl:
m = GetFrame(mol)
cansmiles = Chem.MolToSmiles(m, isomericSmiles=True)
if cansmiles in FrameDict:
FrameDict[cansmiles].append(mol)
else:
FrameDict[cansmiles] = [mol, ]
counter = 0
w = open('frames.smi', 'w')
for key, item in FrameDict.items():
counter += 1
d = Chem.SDWriter(str(counter) + '.sdf')