Paolo and Chris,
There actually is Rdkit function to do this very task: SplitMolByPDBChainId
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.SplitMolByPDBChainId
sob., 5 paź 2019, 14:42 użytkownik Paolo Tosco <paolo.tosco.m...@gmail.com>
napisał:
> Hi Chris,
>
> The following, though quite inefficient, will work:
>
> from rdkit import Chem
> mol = Chem.MolFromPDBFile("1CX2.pdb")
> chains = {a.GetPDBResidueInfo().GetChainId() for a in mol.GetAtoms()}
> chain_mols = {c: Chem.RWMol(mol) for c in chains}
> for c, m in chain_mols.items():
> bonds_to_remove = [(b.GetBeginAtomIdx(), b.GetEndAtomIdx()) for b in
> m.GetBonds() if b.GetBeginAtom().GetPDBResidueInfo().GetChainId() != c or
> b.GetEndAtom().GetPDBResidueInfo().GetChainId() != c]
> atoms_to_remove = [a.GetIdx() for a in m.GetAtoms() if
> a.GetPDBResidueInfo().GetChainId() != c]
> [m.RemoveBond(*b) for b in bonds_to_remove]
> [m.RemoveAtom(a) for a in sorted(atoms_to_remove, reverse=True)]
> Chem.MolToPDBFile(m, "{0:s}.pdb".format(c))
>
> Individual chains are saved to <chain_id.pdb>.
>
> As chains will be separate fragments, a more efficient way would to use
> rdmolops.GetMolFrags(asMols=True) which would avoid the bond/atom removal.
>
> Sorry for the poor formatting but this is what I could come up with
> IPython on the iPhone :-(
>
> p.
>
> > On 5 Oct 2019, at 12:46, Chris Swain via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
> >
> > Hi,
> >
> > I have a number of PDB files (foo.pdb.gz) and I want to separate each
> chain in each file out into a separate file. So if a file contains 4 chains
> it will generate 4 separate files.
> >
> > Can I do this using RDKit, if so how?
> >
> > Cheers
> >
> > Chris
> >
> > _______________________________________________
> > Rdkit-discuss mailing list
> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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