Hi Goutam,
I assume you are typing the first example interactively in the Python
interpreter or in a ipython shell or Jupyter notebook.
In that case you only need to enter the same commands in a text editor, save
the script with a name (e.g., substructure.py) and run it from a shell;
python substructure.py
If this is not what you are after please get back to me off-list such that we
keep the mailing list traffic to a minimum.
Cheers,
p.
> On 28 Jun 2019, at 19:10, Goutam Mukherjee <cyz078...@gmail.com> wrote:
>
> Hi All,
>
> I have one query about Substructure matching using RDKit.
> I have a target SMILES codes (Required to convert Canonical SMILES format)
> which may content 1 or more than one SMILES code
> I have one more file, a query file, which content just one SMILES code of a
> small fragment. Say,
> Target file: Brc1ccc(cc1)C(=O)Nc1n[nH]c(c1)C1CCCCC1
> Query file format: c1cn[nH]c1
> I have to compare whether the query fragment is present in the target file or
> not.
>
> I able to do it in command line
> Here is the command
> from __future__ import print_function
> from rdkit import Chem
> m = Chem.MolFromSmiles('Brc1ccc(cc1)C(=O)Nc1n[nH]c(c1)C1CCCCC1')
> m.HasSubstructMatch(Chem.MolFromSmarts('c1cn[nH]c1'))
> True
>
> However, I want to do this substructure search using command line (say,
> python script).
> Could you please help me to do this.
> Your help will be highly appreciated.
>
> Thanks and Kind Regards,
> Goutam
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