epam / epam/Indigo

Interested in resolving issues from the SMILES benchmark?

Open
#129 10 comments 0 reactions 0 assignees View on GitHub
Core Priority: Medium question
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

I've put together a benchmark to compare the ability of different tools to read SMILES. The goal is to identify corner cases and improve SMILES reading across the board. Initial results were reported at the recent ICCS:
https://nextmovesoftware.com/blog/2018/06/06/can-we-agree-on-the-structure-represented-by-a-smiles-string/
...and the benchmark itself is available at:
https://github.com/nextmovesoftware/smilesreading

In the benchmark, each toolkit reports the number of hydrogens on each atom in the molecule represented by an aromatic SMILES string, or whether there was an error reading it. If you are interested in working through some of the issues raised by the benchmark, let me know and I am happy to describe them and how they might be solved. I have already done this with a number of toolkits.

Contributor guide

No contributing guide indexed for this repository

Research direction

Review the SMILES benchmark at github.com/nextmovesoftware/smilesreading and the linked ICCS report to understand the reported corner cases. Ask the maintainer which benchmark discrepancies apply to Indigo and how they should be addressed; done means improving SMILES reading so the relevant benchmark cases report the expected hydrogens or errors.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
testing
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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