Hi, Are these not intended to be query strings so rather than SMILES they should be regarded as SMARTS?
If so you can perhaps just use a text editor to do a find and replace using schema shown here https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html <https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html> Cheers, Chris > > Message: 1 > Date: Mon, 22 Jun 2020 17:09:36 +0200 > From: Goutam Mukherjee <cyz078...@gmail.com> > To: rdkit-discuss <rdkit-discuss@lists.sourceforge.net> > Subject: [Rdkit-discuss] Query about creating SMILES string of small > chemical fragment > Message-ID: > <CAA2G6bLW0VJupAEeqJG6pGDxAR7PVQpZ2hMxk4U=m8aqwnn...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Members, > > I want to generate a list of SMILES strings of these following chemical > fragments (pseudo SMILES notation): > > [R]N([R])C(=S)N([R])C([R])=O > [R]N([R])C(=O)C([R])=O > [R]SS[R] > [R]N([R])N([R])C([R])=O > [R]P(O)(O)=O > [R]C([Nar])=O > [R]N([R])C(=O)N([R])C([R])=O > [R]C=O > [R][N+]([R])([R])[R] > [R]N([R])C(=S)N([R])[R] > [R]N1CC(=O)N([R])C1=O > [R]N([R])S(=O)(=O)N([R])[R] > [R]S([R])=O > [R]S([Nar])(=O)=O > [R]OP(O)(O)=O > [R]SCN([R])C([R])=O > [R]N([R])C(=S)N([R])N=C > [R]N([R])CN([R])C([R])=O > O=[Nar] > > Where R is a substitution that may be carbon or hydrogen and ar is aromatic > one. > > A detail of such moieties can be found in the following links: > https://static-content.springer.com/esm/art%3A10.1186%2Fs13321-017-0225-z/MediaObjects/13321_2017_225_MOESM1_ESM.txt. > > Could anyone please help me how to convert these pseudo-SMILES to a > SMILES notation. > > > Thanks and Best Regards, > > Goutam > -------------- next part -------------- > An HTML attachment was scrubbed... >
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