-
Notifications
You must be signed in to change notification settings - Fork 30
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Mol to SMARTS #59
Comments
Hi Christoph,
currently, we don't support SMARTS export nor import for two simple reasons:
* within Actelion/Idorsia there was only limited need, because our entire cheminformatics system is built on idcodes instead of SMILES/SMARTS, which are more powerful in certain aspects, e.g. stereo chemical representation or exclude groups, but on the other side don't support recursive fragments, which SMARTS do. People are never exposed to SMARTS or idcodes directly, because the always use chemical editors to define structures and query features.
* SMARTS and idcode query features are similar, but don't exactly match. Therefore, exporting and importing SMARTS automatically means to risk loosing precision of defined query features.
Supporting a limited set of SMARTS features, however, would not be very difficult, would suffice for many tasks, and is actually planned to do...
Thomas
…________________________________
Von: c-ruttkies <notifications@github.com>
Gesendet: Dienstag, 26. Mai 2020 10:38
An: Actelion/openchemlib <openchemlib@noreply.github.com>
Cc: Subscribed <subscribed@noreply.github.com>
Betreff: [Actelion/openchemlib] Mol to SMARTS (#59)
Hi,
is there a way to create a SMARTS out of a MolString that contains for example atom lists? The molString could be sth. like:
MJ191900
8 8 2 0 0 0 0 0 0 0999 V2000
-3.1250 2.2089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8395 1.7964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8395 0.9713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1250 0.5589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4105 0.9713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4105 1.7964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6258 2.0513 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
-4.6241 0.7163 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
3 8 1 0 0 0 0
7 F 2 7 8
8 T 2 9 17
M ALS 7 2 F N O
M ALS 8 2 T F Cl
M END
The string seems to be parsed correctly as StereoMolecule using the MolfileParser. With the SmilesCreator I can create the SMILES: C1(CC(CCC1[?])[?])
Is it also possible to get a valid SMARTS, e.g. C1CC[!F!Cl]CC[N,O]C1 ?
Best regards,
Christoph
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub<#59>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACNFEBXS75N7HIU36QQUAPLRTN5WVANCNFSM4NKDC5FQ>.
The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorized to state them to be the views of the sender's company.
|
Hi Thomas, thanks for the quick and helpful response. You already convinced me of looking into idcodes based structure representation and matching. Best regards, |
Hi @thsa, Any progress on supporting exporting a limited set of SMARTS features (aromatic/aliphatic state, ring membership, ring size membership, explicit/implicit hydrogen count, bond type, bond ring membership) ? It would make sense to have a similar class to This could be a very nice addition for many users. Emmanuel |
Hi Emmanuel,
thanks for reminding me. Currently the focus is on other topics, e.g. reaction mapping, but I agree that limited SMARTS features are important and I put that on the high priority agenda...
Thomas
…________________________________
Von: Emmanuel Noutahi ***@***.***>
Gesendet: Mittwoch, 28. Juli 2021 17:06
An: Actelion/openchemlib ***@***.***>
Cc: Thomas Sander ***@***.***>; Mention ***@***.***>
Betreff: Re: [Actelion/openchemlib] Mol to SMARTS (#59)
Hi @thsa<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fthsa&data=04%7C01%7Cthomas.sander%40idorsia.com%7C070f4b77e1204af9d3c408d951d9416e%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637630815807256891%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=BT%2Fdmxg9wWMHMcJl9Lf0CfNORR9j3n0w5xiSq5SibHE%3D&reserved=0>,
Any progress on supporting exporting a limited set of SMARTS features (aromatic/aliphatic state, ring membership, ring size membership, explicit/implicit hydrogen count, bond type, bond ring membership) ? This could be a very nice addition for many users.
Emmanuel
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FActelion%2Fopenchemlib%2Fissues%2F59%23issuecomment-888386947&data=04%7C01%7Cthomas.sander%40idorsia.com%7C070f4b77e1204af9d3c408d951d9416e%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637630815807266848%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Iw7mo9e99QGQ676Y7c%2FF9v7NhPRkIW%2FC654cuNhYAiQ%3D&reserved=0>, or unsubscribe<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACNFEBRCJ4DRILE3IJ3W6GLT2AMGVANCNFSM4NKDC5FQ&data=04%7C01%7Cthomas.sander%40idorsia.com%7C070f4b77e1204af9d3c408d951d9416e%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637630815807266848%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=W%2FTAYsLQyWPdXzL1iUFCQSVc1r7mMIgbTDc3ltH30bg%3D&reserved=0>.
The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorized to state them to be the views of the sender's company.
|
Hi,
is there a way to create a SMARTS out of a MolString that contains for example atom lists? The molString could be sth. like:
MJ191900
8 8 2 0 0 0 0 0 0 0999 V2000
-3.1250 2.2089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8395 1.7964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8395 0.9713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1250 0.5589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4105 0.9713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4105 1.7964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6258 2.0513 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
-4.6241 0.7163 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
3 8 1 0 0 0 0
7 F 2 7 8
8 T 2 9 17
M ALS 7 2 F N O
M ALS 8 2 T F Cl
M END
The string seems to be parsed correctly as StereoMolecule using the MolfileParser. With the SmilesCreator I can create the SMILES: C1(CC(CCC1[?])[?])
Is it also possible to get a valid SMARTS, e.g. C1CC[!F!Cl]CC[N,O]C1 ?
Best regards,
Christoph
The text was updated successfully, but these errors were encountered: