rdkit-molecule-standardization

Name: rdkit-molecule-standardization
Author: ma-compbio-lab

36stars5forks

How to install rdkit-molecule-standardization?

ma-compbio-lab/skillfoundry/rdkit-molecule-standardization

$npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-molecule-standardization

Installs into the current project.

Summary

Use this skill to standardize one small-molecule SMILES string with RDKit MolStandardize. It is for local cleanup, salt stripping, uncharging, and tautomer canonicalization, not docking or batch-library processing.

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SKILL.md

1	## Purpose
2	Turn a single SMILES string into a deterministic standardization summary using `RDKit` `MolStandardize`.
3
4	## When to use
5	- You need a local starter for the taxonomy leaf `molecule-standardization`.
6	- You want to strip salts or counterions before downstream featurization.
7	- You want a compact JSON summary with fragment-parent, uncharged, and canonical-tautomer SMILES.
8
9	## When not to use
10	- You need conformers, docking, or quantum chemistry.
11	- You need bulk normalization across large compound libraries.
12
13	## Inputs
14	- One SMILES string passed by `--smiles` or a single-line file passed by `--smiles-file`
15	- Optional molecule name
16	- Optional JSON output path
17
18	## Outputs
19	- JSON summary with cleaned, fragment-parent, uncharged, and canonical-tautomer SMILES
20	- Charge before and after standardization
21	- Formula and heavy-atom count for the standardized molecule
22
23	## Requirements
24	- `slurm/envs/chem-tools` with `RDKit` and `MolStandardize`
25
26	## Procedure
27	1. Run `slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization/scripts/standardize_rdkit_molecule.py --smiles-file skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization/examples/sodium_acetate.smiles --name sodium-acetate`.
28	2. Inspect `fragment_parent_smiles` to confirm salt stripping.
29	3. Inspect `uncharged_smiles` and `canonical_tautomer_smiles` before reusing the molecule downstream.
30
31	## Validation
32	- The script exits successfully with the `chem-tools` prefix.
33	- The sodium acetate example standardizes to `CC(=O)O`.
34	- The runtime output matches `assets/sodium_acetate_standardized.json`.
35
36	## Failure modes and fixes
37	- Invalid SMILES: verify the input string or the first non-empty line in the SMILES file.
38	- Missing RDKit environment: run the script with `slurm/envs/chem-tools/bin/python`.
39
40	## Safety and limits
41	- This is a molecule-cleanup helper only.
42	- It does not imply medicinal-chemistry, ADMET, or synthesis interpretation.
43
44	## Provenance
45	- RDKit documentation: https://www.rdkit.org/docs/
46	- RDKit MolStandardize API: https://www.rdkit.org/docs/source/rdkit.Chem.MolStandardize.rdMolStandardize.html
47
48	## Related skills
49	- `rdkit-molecular-descriptors`
50	- `chembl-molecule-search`

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rdkit-molecule-standardization

36stars5forks

View on GitHub

How to install rdkit-molecule-standardization?

ma-compbio-lab/skillfoundry/rdkit-molecule-standardization

$npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-molecule-standardization

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	## Purpose
2	Turn a single SMILES string into a deterministic standardization summary using `RDKit` `MolStandardize`.
3
4	## When to use
5	- You need a local starter for the taxonomy leaf `molecule-standardization`.
6	- You want to strip salts or counterions before downstream featurization.
7	- You want a compact JSON summary with fragment-parent, uncharged, and canonical-tautomer SMILES.
8
9	## When not to use
10	- You need conformers, docking, or quantum chemistry.
11	- You need bulk normalization across large compound libraries.
12
13	## Inputs
14	- One SMILES string passed by `--smiles` or a single-line file passed by `--smiles-file`
15	- Optional molecule name
16	- Optional JSON output path
17
18	## Outputs
19	- JSON summary with cleaned, fragment-parent, uncharged, and canonical-tautomer SMILES
20	- Charge before and after standardization
21	- Formula and heavy-atom count for the standardized molecule
22
23	## Requirements
24	- `slurm/envs/chem-tools` with `RDKit` and `MolStandardize`
25
26	## Procedure
27	1. Run `slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization/scripts/standardize_rdkit_molecule.py --smiles-file skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization/examples/sodium_acetate.smiles --name sodium-acetate`.
28	2. Inspect `fragment_parent_smiles` to confirm salt stripping.
29	3. Inspect `uncharged_smiles` and `canonical_tautomer_smiles` before reusing the molecule downstream.
30
31	## Validation
32	- The script exits successfully with the `chem-tools` prefix.
33	- The sodium acetate example standardizes to `CC(=O)O`.
34	- The runtime output matches `assets/sodium_acetate_standardized.json`.
35
36	## Failure modes and fixes
37	- Invalid SMILES: verify the input string or the first non-empty line in the SMILES file.
38	- Missing RDKit environment: run the script with `slurm/envs/chem-tools/bin/python`.
39
40	## Safety and limits
41	- This is a molecule-cleanup helper only.
42	- It does not imply medicinal-chemistry, ADMET, or synthesis interpretation.
43
44	## Provenance
45	- RDKit documentation: https://www.rdkit.org/docs/
46	- RDKit MolStandardize API: https://www.rdkit.org/docs/source/rdkit.Chem.MolStandardize.rdMolStandardize.html
47
48	## Related skills
49	- `rdkit-molecular-descriptors`
50	- `chembl-molecule-search`

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