Wikidata:Property proposal/SMIRKS
SMIRKS
[edit]Originally proposed at Wikidata:Property proposal/Natural science
| Description | A superset of "reaction SMILES" and a subset of "reaction SMARTS", is a line notation for specifying reaction transforms. |
|---|---|
| Represents | SMIRKS (Q124450357) |
| Data type | String |
| Domain | group or class of chemical entities (Q72070508) |
| Example 1 | Amide reduction (Q4746154)→[C:1](=[O:2])[N:3]>>[C:1]([H])[N:3] |
| Example 2 | Claisen condensation (Q898501)→[#6:1]-[#6:2]-[#6:3](=[O:4])-[#8:5]-[#6:6].[#6:7]-[#6:8]-[#6:9](=[O:10])-[#8:11]-[#6:12]>>[#6:1]-[#6:2]-[#6:3](=[O:4])-[#6:8](-[#6:7])-[#6:9](=[O:10])-[#8:11]-[#6:12].[#6:6]-[#8:5] |
| Example 3 | L-leucine transaminase activity (Q21109559)→[O:1]=[C:2]([O:3])[CH2:4][CH2:5][C:6](=[O:7])[OH:8].[CH3:9][C:10]([CH3:11])([CH:12][C@H:13]([C:14](=[O:15])[OH:16])[NH2:17])>>[O:1]=[C:2]([O:3])[CH2:4][CH2:5][C:6](=[O:18])[OH:19].[CH3:9][C:10]([CH3:11])([CH:12][C@H:13]([C:14](=[O:15])[O:20])=[NH:17][C:6]) |
| Formatter URL | https://smarts.plus/smartsview/download_rest?smarts=$1;filetype=png;vmode=0;textdesc=1;depsymbols=1;smartsheading=0 (cf. https://smartsview.zbh.uni-hamburg.de/rest for more details; as this should be a string-datatype property, use of [[MediaWiki:Gadget-AuthorityControl.js]] would be necessary) |
| See also | SMARTS notation (P8533) |
Motivation
[edit]SMIRKS, by integrating the expressive capabilities of SMILES for molecules with the pattern matching features of SMARTS, offers a powerful language for describing generic chemical reactions. This includes the specification of atom and bond changes in a reaction, making it a versatile tool for chemical information processing. The inclusion of a SMIRKS property on Wikidata would facilitate the detailed encoding of chemical reactions and biosynthetic mechanisms.
Notified participants of WikiProject Chemistry
- Note
- I am not expert in the topic of encoding chemical reactions and it doesn't seems to be a particularly easy one. For example the RDKit doc describes a Reaction SMARTS which is not SMIRKS, not reaction SMILES, derived from SMARTS. [1] Their is also a blog post [2] and a github issue [3] on the topic of reaction SMARTS.
- I reused the formatter URL proposed by Wostr in https://www.wikidata.org/wiki/Wikidata:Property_proposal/SMARTS. Using https://smarts.plus/smartsview, the three examples above are nicely rendered. This is not the case using the URL (only the first one is rendered correctly). Didn't find out why ... (edit) some special characters need to be escaped [4] I do not know how to reflect this in the URL formatter field.
ChemAxon's MarvinSketch https://chemaxon.com/marvin can be used to prepare SMIRKS.
Any help welcomed ! – The preceding unsigned comment was added by GrndStt (talk • contribs).
References
- ↑ https://www.rdkit.org/docs/RDKit_Book.html#reaction-smarts
- ↑ http://efficientbits.blogspot.com/2018/04/rdkit-reaction-smarts.html
- ↑ https://github.com/rdkit/rdkit/discussions/5168
- ↑ https://smarts.plus/rest
Discussion
[edit]
Support Sounds good to me. I will come back on the formatter field aspects and talk to John Mayfield to see about the CDK Depict support. --Egon Willighagen (talk) 07:11, 8 February 2024 (UTC)- 'Support' Clearly a plus. Would also help in regards to Wikidata talk:WikiProject Chemistry#Chemical Reactions AdrianoRutz (talk) 10:37, 8 February 2024 (UTC)
- @GrndStt, Egon Willighagen, AdrianoRutz:
Done: SMIRKS (P12491). Regards Kirilloparma (talk) 15:34, 21 February 2024 (UTC)
