Hi all,
I would like to generate the Murcko framework for a library.
CDK should be able to do this, but the code should be updated and the
function is currently not fully usable - if I understood well.
If anybody is aware of an other solution...?
So, I'm beginning to do a script with pybel. First, I just want to
remove atoms which have only one neighbour.
If there less than 2 neighbours, I do this:
for atom in ob.OBMolAtomIter(mol.OBMol):
(...)
if (neighborsCount <= 1):
mol.OBMol.DeleteAtom(atom)
But it scans only 13 atoms, with 2 atom deleted, instead of 14 in the
test molecule (and theorically 3 deletion).
If I don't delete atoms, all is doing well (i.e., it scans all 14 atoms).
Any advice for doing it in the right manner?
Full code below, Open Babel 2.2.3.
Smiles used:
c1(n(c2c(cccc2)o1)C[C@@H](N)C)=O ART12966845
Thanks,
Regards,
Pascal
#!/usr/bin/env python
# encoding: utf-8
import sys
import os, pybel
import openbabel as ob
def main():
if len(sys.argv) < 2:
print "No input file provided: Murcko.py filetosprocess.ext"
sys.exit(1)
for mol in pybel.readfile(sys.argv[1].split('.')[1], sys.argv[1]):
mol.OBMol.DeleteHydrogens()
atomCount = 0
for atom in ob.OBMolAtomIter(mol.OBMol):
atomCount = atomCount + 1
print "Atom count:", atomCount
atomCount = 0
for atom in ob.OBMolAtomIter(mol.OBMol):
atomCount = atomCount + 1
if not atom.IsInRing():
neighborsCount = 0
for neighbor in ob.OBAtomAtomIter(atom):
neighborsCount = neighborsCount + 1
if (neighborsCount <= 1):
print "Idx:", atom.GetIdx(), "Type:",
atom.GetType(),"Deleted"
mol.OBMol.DeleteAtom(atom)
print "Atom count:", atomCount
smilesMurcko = mol.write("smi")
print "Current smiles:", smilesMurcko
if __name__ == '__main__':
main()
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