Hi all,
Below is a small pybel script for Murcko framework generation, with or
without exocyclic double bonded heteroatoms.
Any comment on the programme structure, or how to improve it, are
welcome :) I'll need to run it on a ZINC subset, so the speedier the
better.
I plan to generate smaller Murcko scaffolds by deleting:
- in the initial molecule (if there is more than 3 cycles), all-carbon
and non-substituted (i.e. terminal) cycle(s) (yes, it could lead to
acyclic fragment, aborting the Murcko framework generation, e.g. for
tetraphenylmethane),
- in the Murcko framework, terminal cycle of 3 or 4 atoms
but not in the short term, and I'm not yet sure if I'll need such framework.
Regards,
Pascal
#!/usr/bin/env python
# encoding: utf-8
import sys
import os, pybel
import openbabel as ob
def checkIfIsOnlyOneNeighbor(mol, keepExo):
isAnAtomWithOneNeighbor = 0
atomWithOneNeighborList = []
if keepExo == "n" :
for atom in ob.OBMolAtomIter(mol.OBMol):
if not atom.IsInRing(): # Keep cycle anyway
neighborsCount = 0
for neighbor in ob.OBAtomAtomIter(atom):
neighborsCount = neighborsCount + 1
if (neighborsCount <= 1):
# only one neighbour : terminal atom, which
belongs not to the
Murcko framework
isAnAtomWithOneNeighbor = 1
atomWithOneNeighborList.append(atom) #
will be deleted
else:
for atom in ob.OBMolAtomIter(mol.OBMol):
if not atom.IsInRing():
neighborsCount = 0
for neighbor in ob.OBAtomAtomIter(atom):
neighborsCount = neighborsCount + 1
if (neighborsCount <= 1):
# Does atom have a double bond? Is this atom a
carbon? Is this
atom connected to a cycle?
if (atom.BOSum() < 2) | ((atom.BOSum()
== 2) & (atom.GetAtomicNum() == 6)):
# Delete if no double bond, or
if it's a carbon with a double bond
isAnAtomWithOneNeighbor = 1
atomWithOneNeighborList.append(atom) # will be deleted
else:
# It is a heteroatom with a
double bond...
for neighbor in
ob.OBAtomAtomIter(atom):
if not
neighbor.IsInRing():
# ... not
connected to a cycle
isAnAtomWithOneNeighbor = 1
atomWithOneNeighborList.append(atom) # will be deleted
# --> keep heteroatoms with exocyclic
double bond
return isAnAtomWithOneNeighbor, atomWithOneNeighborList
def stripStereo(mol):
smilesMurcko = mol.write("smi").split("\t")[0]
smilesMurckoNoStereo = smilesMurcko.replace("/","")
smilesMurckoNoStereo = smilesMurckoNoStereo.replace("\\","") # E/Z
stereochemistry is now reseted
molName = mol.OBMol.GetTitle()
molMurckoNoStereo = smilesMurckoNoStereo + "\t" + molName + "\n" #
The smiles to be written in the .smi file
return molMurckoNoStereo
def main():
if (len(sys.argv) < 3):
print "No input file provided and/or missing argument: Murcko.py
filetosprocess.ext KeepExocyclicCoubleBond:y/n"
print "The script will determine which file type to read from
by the
extension."
sys.exit(1)
elif ((sys.argv[2] != "n") & (sys.argv[2] != "y")):
print "Wrong argument: Murcko.py filetosprocess.ext
KeepExocyclicCoubleBond:y/n"
sys.exit(1)
keepExo = sys.argv[2]
molnum = 0
#murckoOutput = pybel.Outputfile("smi", "murckoFrameworks.smi", True)
# for writing smi file with Murcko framework - keeps E/Z
stereochemistry, see comment below
murckoNoStereoOutput = open("murckoFrameworksNoStereo.smi","w") # for
writing smi file with Murcko framework, without stereochemistry
for mol in pybel.readfile(sys.argv[1].split('.')[1], sys.argv[1]):
molnum += 1
#print mol.OBMol.GetTitle(), "- Molecules processed:", molnum
if not (molnum % 1000):
print "Molecules processed:", molnum
mol.OBMol.DeleteHydrogens()
haveAtomWithOneNeighbor,atomsWithOneNeighborList =
checkIfIsOnlyOneNeighbor(mol, keepExo)
while (haveAtomWithOneNeighbor):
for atomToDel in atomsWithOneNeighborList:
mol.OBMol.DeleteAtom(atomToDel) # delete atom
which are not part
of a cycle or a linker (terminal atoms) - Do it as long as necessary
haveAtomWithOneNeighbor,atomsWithOneNeighborList =
checkIfIsOnlyOneNeighbor(mol, keepExo)
## Molecule with no cycle have no Murcko framework
#smilesMurcko = mol.write("smi").split("\t")[0]
#if (smilesMurcko): # always true, because I always have at
least one cycle
#murckoOutput.write(mol)
#murckoOutput.write(mol) # E/Z stereochemistry conserved
noStereoMurcko = stripStereo(mol) # Need to delete "/" and "\"
from smiles
murckoNoStereoOutput.write(noStereoMurcko)
murckoNoStereoOutput.close()
#murckoOutput.close()
if __name__ == '__main__':
main()
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