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SMILES Depiction Generator

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Dear all, is aromatic display (like `DepictionGenerator.withAromaticDisplay()`) available in the CDK Depict web app? By default, it seems to be turned off (see below) and I could not find a...

smiles: N1C2C(=S3c4c1ccc(c4)N=Cc1ccc(SO3)cc1)C=CC=C2 smiles: c12cc3C4c5cc6ccccc6cc5C(c3cc1cccc2)Oc1ccc(cc1)O4 The sulphur here should be bonded to the benzene, other drawers confirm this smiles is correct! (although if its not, please school me!) ![#1](https://user-images.githubusercontent.com/78424742/236647014-144a4bc0-c704-442a-adbe-300dbdd3343d.png) ![#1 (1)](https://user-images.githubusercontent.com/78424742/236648060-ebd8d0b8-ddeb-4c8d-950f-51c7a9cd7839.png)

Nice app! But what are the query parameters that the endpoint accepts? I'm wanting to make use of the SVG generation by calling the API.

Salt placement is usually great but I came across the following where the Br- overlaps a bond. ``` C=C(C[N+](C)(C)C)OC(=O).[Br-] ``` ![png](https://user-images.githubusercontent.com/45337/96236220-a7843280-0f93-11eb-9902-1bf1fdf5a9df.png)

bug

Highlighting via SMARTS is possible, but having an extra checkbox to say "align" would be great. I've missed this multiple times. Not sure how much work this would be for...

enhancement

Would it be possible to have API documentation? In particular, I'm wondering how to depict MOL files which someone in a pub told me was possible.

enhancement

Would it be possible to display atom mapping and colour map at the same time? I have had a few tries but haven't found a workaround yet, I would like...

enhancement

Would be nice to be able to use webservice for SMI->MOL.

Hi @johnmay with increasing dark (but not always black) mode use cases ... is it possible to consider adding a "white on clear" and/or "neon on clear" option? ![image](https://github.com/cdk/depict/assets/4070141/e26ab0f7-6908-45be-a092-19c37e9bd3cb) Thanks!

Bumps [org.springframework:spring-webmvc](https://github.com/spring-projects/spring-framework) from 5.3.34 to 6.1.13. Release notes Sourced from org.springframework:spring-webmvc's releases. v6.1.13 :star: New Features Errors thrown from SmartLifeycle#stop results in (unnecessary) waiting for the shutdown timeout #33442 Updates...

dependencies
java