Dear all,
I'm tryting to delete a ring atom with the following script:
--------------------Start of the Script-------------------------
#!/usr/bin/env python
import pybel
import openbabel as ob
obconversion = ob.OBConversion()
obconversion.SetInAndOutFormats('smi','can')
def main():
m=pybel.readstring('smi',"c1ccccc1O RingMol")
print obconversion.WriteString(m.OBMol)
for i in m.atoms:
print i,i.OBAtom.IsInRing()
print
m.OBMol.BeginModify()
atom_d=m.atoms[2].OBAtom ##randomly pick an atom of ring to delete
m.OBMol.DeleteAtom(atom_d)
m.OBMol.SetTitle('NoRingMol')
m.OBMol.EndModify()
print obconversion.WriteString(m.OBMol)
for i in m.atoms:
print i,i.OBAtom.IsInRing()
if __name__ == '__main__':
main()
---------------------End of the Script-------------------------------
It gives the following output:
>>>
Oc1ccccc1 RingMol
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 8 (0.00 0.00 0.00) False
C/C=C(/O)\C=C NoRingMol
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 6 (0.00 0.00 0.00) True
Atom: 8 (0.00 0.00 0.00) False
From the output SMILES, we can find the final molecule "C/C=C(/O)\C=C
NoRingMol"
contains no ring after we remove a ring atom of the initial molecule. That is
what I'm expecting.
However, when I retrieved the atom information of the final molecule, I found
that all carbon atoms
are still ring atoms. I guess there might be some flags should be updated when
a molecule is
modified. An easy but expensive solution is to parse the output SMILES again to
get the correct
ring information of each atom, but I wonder if there is a better way to do
that.
Thanks in advance!
2010-12-16
------------------------------------------------
Mingyue Zheng, Ph.D.
Drug Discovery and Design Center (DDDC)
Box 1201, Shanghai Institute of Materia Medica.
No. 555 Rd. Zuchongzhi, Shanghai, China
Tel: 86-021-50806600-1308
Email: [email protected]
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