If you turn off the sanitization the splitting should be super fast too. If
that is the only thing you would like to do.
pon., 7 paź 2019, 10:31 użytkownik Téletchéa Stéphane <
stephane.teletc...@univ-nantes.fr> napisał:
> Le 05/10/2019 à 12:46, Chris Swain via Rdkit-discuss a écrit :
> > Hi,
>
Le 05/10/2019 à 12:46, Chris Swain via Rdkit-discuss a écrit :
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?
On 10/5/2019 10:34 AM, Maciek Wójcikowski wrote:
Paolo and Chris,
There actually is Rdkit function to do this very task: SplitMolByPDBChainId
Why, though? -- It's a punch-card format with chain id in specific
column, you just read the lines and sort them into buckets on line[X].
Unless you
Thanks
Chris
> On 5 Oct 2019, at 16:34, Maciek Wójcikowski wrote:
>
> 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
>
>
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
napisał:
> Hi Chris,
>
> The following, though quite
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 =
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