SKETCH-2631: Provide ability to mutate monomers from toolbar by JarrettSJohnson · Pull Request #254 · schrodinger/sketcher

JarrettSJohnson · 2026-02-27T02:15:50Z

Linked Case: SKETCH-2631

Description

This revision supports the mutation of monomers from the sketcher monomer toolbar. Each of the following criteria from the jira ticket was addressed:

Mutation by clicking on monomer button
Toolbar button background changes for compatible changes (similar to what the atomistic tools do)
Mixed-selections (selecting amino-acid and peptides) will enable buttons that are compatible with any individual monomer type, but performing the selection will only mutate similar monomer types (e.g. you can't mutate a peptide to a nucleic acid even when other nucleic acids are in the mixed selection)
Selections disable the "full" nucleic acid buttons.

I'm not too comfortable with HELM/SMILES, so the the changes w.r.t. bool is_smiles (which didn't seem to be monomer-friendly) might need extra scrutiny. Without this change, the monomer's display would show '***' (SMILES_PLACEHOLDER_TEXT).

Testing Done

Added some boost tests and e2e tests (which this PR is diff'd against) to validate the criteria above.

KevKeating

Looks good to me. I just had a few very minor comments.

ethan-schrodinger

As long as @KevKeating's comments are addressed, this LGTM.

ethan-schrodinger · 2026-02-27T17:19:44Z

 {
 #ifdef __EMSCRIPTEN__
-    throw std::logic_error("Monomers are not yet supported in WASM Sketcher");
+    return std::nullopt;


Why this change?

This was in response to Rachel's comment about using the MonomerDB to verify if a helm symbol is a standard monomer. For wasm-sketcher, since there's no DB, throws this exception and upstream catches the wrong exception type. Upstream call converts nullopt to using the default monomer DB (which is what the else part does..We could just drop this ifdef altogether probably...but maybe I don't have enough background knowledge as to why the monomer DB was kept out of wasm-sketcher in the first place).

I assume since we're now supporting monomers for wasm-sketcher, we probably want to support a monomer DB for it? Lemme know if that's not the case.

Conferred with Rachel; change is fine for default monomers. Custom monomers for sketcher will be supported in another ticket.

You could also get rid of the catch block here here, since it shouldn't have any effect any more.

This might be the relevant case for enabling custom monomers in wasm sketcher https://schrodinger.atlassian.net/browse/SKETCH-2655

KevKeating · 2026-02-27T20:14:17Z

 {
 #ifdef __EMSCRIPTEN__
-    throw std::logic_error("Monomers are not yet supported in WASM Sketcher");
+    return std::nullopt;


You could also get rid of the catch block here here, since it shouldn't have any effect any more.

KevKeating · 2026-02-27T20:31:02Z

@@ -216,9 +216,6 @@ QColor get_color_for_monomer(
    try {


You could get rid of lines 216 and 219 as well.

rachelnwalker

rdkit_

rachelnwalker · 2026-03-04T19:17:52Z

rdkit_

oops not sure how I did that

…nger#254) * Linked Case: SKETCH-2631 ### Description This revision supports the mutation of monomers from the sketcher monomer toolbar. Each of the following criteria from the jira ticket was addressed: 1. Mutation by clicking on monomer button 2. Toolbar button background changes for compatible changes (similar to what the atomistic tools do) 3. Mixed-selections (selecting amino-acid and peptides) will enable buttons that are compatible with any individual monomer type, but performing the selection will only mutate similar monomer types (e.g. you can't mutate a peptide to a nucleic acid even when other nucleic acids are in the mixed selection) 4. Selections disable the "full" nucleic acid buttons. I'm not too comfortable with HELM/SMILES, so the the changes w.r.t. `bool is_smiles` (which didn't seem to be monomer-friendly) might need extra scrutiny. Without this change, the monomer's display would show '***' (`SMILES_PLACEHOLDER_TEXT`). ### Testing Done Added some boost tests and e2e tests (which this PR is diff'd against) to validate the criteria above.

…sing (#266) * Linked Case: NOJIRAID ### Description This might be more of a discussion than a proposal if this is controversial. It's something that will affect how my tests should be made for SKETCH-2707. If this revision is agreed on, I'll file a JIRA ticket for it. Currently, molecules with undefined monomers could be imported from helm strings, but AFAICT, this doesn't serve much value and should be treated as an error when imported into the sketcher instead? This PR proposes to enforce validation of monomers in a helm string against an available monomer database, and invalid monomers will prevent importing a molecule. For tests, we can bypass validation with `helm::helm_to_rdkit`, if we're just checking for things like attachment points, etc. (This is a stacked PR on top #254 since this requires the monomer database to be available in the wasm sketcher.) ### Testing Done Added new tests which ensures proper exception is thrown with invalid monomers.

…nger#254) * Linked Case: SKETCH-2631 ### Description This revision supports the mutation of monomers from the sketcher monomer toolbar. Each of the following criteria from the jira ticket was addressed: 1. Mutation by clicking on monomer button 2. Toolbar button background changes for compatible changes (similar to what the atomistic tools do) 3. Mixed-selections (selecting amino-acid and peptides) will enable buttons that are compatible with any individual monomer type, but performing the selection will only mutate similar monomer types (e.g. you can't mutate a peptide to a nucleic acid even when other nucleic acids are in the mixed selection) 4. Selections disable the "full" nucleic acid buttons. I'm not too comfortable with HELM/SMILES, so the the changes w.r.t. `bool is_smiles` (which didn't seem to be monomer-friendly) might need extra scrutiny. Without this change, the monomer's display would show '***' (`SMILES_PLACEHOLDER_TEXT`). ### Testing Done Added some boost tests and e2e tests (which this PR is diff'd against) to validate the criteria above.

JarrettSJohnson requested review from KevKeating and cdvonbargen February 27, 2026 02:15

JarrettSJohnson requested review from ethan-schrodinger, juzerzarif and rachelnwalker as code owners February 27, 2026 02:15

rachelnwalker reviewed Feb 27, 2026

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Comment thread src/schrodinger/rdkit_extensions/monomer_mol.cpp Outdated

JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch from e24d72e to 9ecb6e3 Compare February 27, 2026 04:06

JarrettSJohnson requested a review from rachelnwalker February 27, 2026 04:07

JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch from 9ecb6e3 to 0bee87e Compare February 27, 2026 06:13

KevKeating reviewed Feb 27, 2026

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Comment thread src/schrodinger/sketcher/sketcher_widget.cpp

ethan-schrodinger reviewed Feb 27, 2026

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ethan-schrodinger approved these changes Feb 27, 2026

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JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch from 0bee87e to 5713b37 Compare February 27, 2026 18:51

JarrettSJohnson requested a review from KevKeating February 27, 2026 18:51

JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch from 5713b37 to 8a054b3 Compare February 27, 2026 18:56

KevKeating approved these changes Feb 27, 2026

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JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch from 8a054b3 to 41e3287 Compare February 27, 2026 20:29

KevKeating reviewed Feb 27, 2026

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JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch 2 times, most recently from 13b635b to 8054386 Compare February 27, 2026 20:37

KevKeating approved these changes Feb 27, 2026

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cdvonbargen approved these changes Mar 4, 2026

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JarrettSJohnson force-pushed the e2e_tests branch from e8390e6 to 825ca40 Compare March 4, 2026 18:32

rachelnwalker approved these changes Mar 4, 2026

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JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch from 8054386 to 6d0e1cf Compare March 6, 2026 06:25

JarrettSJohnson mentioned this pull request Mar 6, 2026

SKETCH-2707: Provide ability to validate monomer against DB while parsing #266

Merged

JarrettSJohnson force-pushed the e2e_tests branch 2 times, most recently from f0c91a9 to d3a6614 Compare March 19, 2026 15:09

Base automatically changed from e2e_tests to main March 19, 2026 16:11

SKETCH-2631: Provide ability to mutate monomers from toolbar

0caeaa3

JarrettSJohnson force-pushed the SKETCH-2631_monomer_mutation branch from 6d0e1cf to 0caeaa3 Compare March 19, 2026 23:13

JarrettSJohnson added this pull request to the merge queue Mar 19, 2026

Merged via the queue into main with commit 9ccee18 Mar 20, 2026
6 checks passed

JarrettSJohnson deleted the SKETCH-2631_monomer_mutation branch March 20, 2026 00:22

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JarrettSJohnson commented Feb 27, 2026

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