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 Richard Overstreet, <reoverstr...@charter.net>
wrote:
> 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 range(mol.NumAtoms()):
> atom=mol.GetAtom(i+1)
> resname=atom.GetResidue().GetName()
> if resname != 'LIG':
> print(resname)
> non_lig_atoms.append(atom)
>
> for atom in non_lig_atoms:
> mol.DeleteAtom(atom)
>
> obconversion.WriteFile(mol,'nolig_demo.pdb')
>
> $ cat demo.pdb
> ATOM 1 N ALA A 1 -0.525 1.362 0.000 1.00
> 0.00 N
> ATOM 2 CA ALA A 1 0.000 0.000 0.000 1.00
> 0.00 C
> ATOM 3 C ALA A 1 1.520 0.000 0.000 1.00
> 0.00 C
> ATOM 4 O ALA A 1 2.152 0.808 -0.678 1.00
> 0.00 O
> ATOM 5 CB ALA A 1 -0.507 -0.774 -1.206 1.00
> 0.00 C
> ATOM 6 O LIG A 2 4.957 -2.553 -0.341 1.00
> 0.00 O
> ATOM 7 N LIG A 2 2.116 -0.911 0.764 1.00
> 0.00 N
> ATOM 8 CB LIG A 2 4.075 -0.753 2.287 1.00
> 0.00 C
> ATOM 9 CA LIG A 2 3.571 -1.003 0.842 1.00
> 0.00 C
> ATOM 10 C6 LIG A 2 5.566 -0.553 2.346 1.00
> 0.00 C
> ATOM 11 C7 LIG A 2 6.420 -1.538 2.843 1.00
> 0.00 C
> ATOM 12 C8 LIG A 2 6.121 0.622 1.833 1.00
> 0.00 C
> ATOM 13 C LIG A 2 3.965 -2.393 0.368 1.00
> 0.00 C
> ATOM 14 C10 LIG A 2 7.800 -1.358 2.825 1.00
> 0.00 C
> ATOM 15 C11 LIG A 2 7.500 0.804 1.811 1.00
> 0.00 C
> ATOM 16 C12 LIG A 2 8.342 -0.187 2.305 1.00
> 0.00 C
> ATOM 17 N ALA A 3 3.188 -3.399 0.759 1.00
> 0.00 N
> ATOM 18 CA ALA A 3 3.470 -4.776 0.365 1.00
> 0.00 C
> ATOM 19 C ALA A 3 3.451 -4.925 -1.148 1.00
> 0.00 C
> ATOM 20 O ALA A 3 3.668 -6.018 -1.670 1.00
> 0.00 O
> ATOM 21 CB ALA A 3 2.461 -5.731 0.981 1.00
> 0.00 C
> ATOM 22 OXT ALA A 3 3.219 -3.956 -1.868 1.00
> 0.00 O
> TER 23 ALA A
> 3
> END
>
> The trick is to store a list of atoms to delete. This way is the more
> stable.
> On 3/3/23 03:34, Tim Dudgeon wrote:
>
> 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 in, for instance, molfile format.
>
> If found that I can iterate through the residues and filter them with
> something like this:
>
> for obres in openbabel.OBResidueIter(obmol_from_cif_file):
> if obres.GetName() == 'LIG':
> print('ligand res')
> else:
> print('other res')
>
> But it's not clear to me how to create a new mol or to delete the residues
> I don't want. If I just use obmol_from_cif_file.DeleteResidue(obres) I
> end up getting a Segmentation fault.
>
> Thanks
> Tim
>
>
>
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