How do I deal with wild cards when creating reaction templates?

[gnsrivastava]

Hello,

I am trying to create reaction templates but there are some reactions that have wildcard notations for some of the atoms. I am not sure how to deal with them.
There is a paper that talks about converting them into C, N, P , S, Se, As if molecules is aromatic but doesn't say anything about aliphatic molecules.
Can you please guide me as to how to deal with them?

Gopal

[connorcoley]

Can you provide an example?

On Thu, Jan 14, 2021 at 05:44 Gopal Srivastava ***@***.***> wrote: Hello, I am trying to create reaction templates but there are some reactions that have wildcard notations for some of the atoms. I am not sure how to deal with them. There is a paper that talks about converting them into C, N, P , S, Se, As if molecules is aromatic but doesn't say anything about aliphatic molecules. Can you please guide me as to how to deal with them? Gopal — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#21>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAEXJWYTB4T4J7ZTOQKHWDSZ3DILANCNFSM4WCHK43Q> .

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[gnsrivastava]

These are smile strings. I am planning on converting them to SMARTS using Reaction Decoder.

1. *C@HCC(=O)SCCNC(=O)CCNC(=O)C@HC(C)(C)COP(=O)(O)OP(=O)(O)OC[C@H]1OC@@HC@H[C@@h]1OP(=O)
2. C(=O)CC(=O)SCCNC(=O)CCNC(=O)C@HC(C)(C)COP(=O)(O)OP(=O)(O)OC[C@H]1OC@@HC@H[C@@h]1OP(=O)(O)O>>C@HCC(=O)SCCNC(=O)CCNC(=O)C@HC(C)(C)COP(=O)(O)OP(=O)(O)OC[C@H]1OC@@HC@H[C@@h]1OP(=O)(O)O

*: Wildcards => can be R group or different substitution groups.
Thanks for the help.

Gopal

[connorcoley]

Hi Gopal,

These don't look like well-formed, valid SMILES and it's odd that you've got a mix of molecules and reactions there. Where did you get these from? I'm a little confused about what you're trying to do here, sorry

Reaction template extraction is outside of the scope of this repo, but is something that another one of our codes can do, rdchiral. The code isn't written to deal with these wildcards.

[gnsrivastava]

I am sorry for not properly posting the reaction. I think you answered my question. I have just one last question I was hoping you can help me with.
In [CH2:23]1[O:24][CH2:25][CH2:26][CH2:27]1.[F:1][c:2]1c:3[cH:4]c:5c:6[cH:7]1.[H-:22].[NH2:13][c:14]1[s:15][cH:16][cH:17][c:18]1[C:19]#[N:20].[Na+:21] | 1 | 2-13-1.0 | 2.196 | 1-2-0.0 | 1.877 what are 2.196 and 1.877. This line was taken from legend.csv in rexgen-master/template_comparison/cases.

[connorcoley]

These are scores associated with the graph edit they are adjacent to (i.e., a measure of how likely the model perceives them to be)

[gnsrivastava]

Thank you so much. These answers were a huge help.