Thanks.
I'd already tried Richard's suggestion, and it works, but just for
completeness, it seems that you need to collect the residues and the atoms
and then delete both (in that order) for it to work correctly.
Then I tried Noel's suggestion and that also seems to work, and is quite a
bit simpler
Also OBMol::CopySubstructure as described at
https://baoilleach.blogspot.com/2018/05/when-all-you-want-is-ring.html and
https://openbabel.github.io/api/3.0/classOpenBabel_1_1OBMol.shtml#a3271860ee44de0d38a27102c79913b1b
. Should be quite a bit faster I would think.
On Fri, 3 Mar 2023, 14:19 Richar
Hi Tim,
Deleting residues can be tricky. I've found the following to work well.
from openbabel import openbabel
obconversion = openbabel.OBConversion()
obconversion.SetInAndOutFormats("pdb", "pdb")
mol = openbabel.OBMol()
path = obconversion.ReadFile(mol, 'demo.pdb')
non_lig_atoms=[]
for i in
I'm trying to work out how to use openbabel from Python to perform
operations such as extracting out ligands from macromolecules in PDB or CIF
format. For instance, if I have a ligand that has the residue name of LIG,
how do I create a new molecule with just that ligand so that I can write it
out i
