rdkit-molecular-descriptors

Name: rdkit-molecular-descriptors
Author: ma-compbio-lab

36stars5forks

How to install rdkit-molecular-descriptors?

ma-compbio-lab/skillfoundry/rdkit-molecular-descriptors

$npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-molecular-descriptors

Installs into the current project.

Summary

Use this skill to compute compact cheminformatics descriptors from one SMILES string with RDKit. Do not use it for docking, quantum chemistry, or large library screening.

Files · 1

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SKILL.md

1	## Purpose
2	Turn a SMILES string into a compact descriptor summary suitable for quick triage, featurization, and metadata enrichment.
3
4	## When to use
5	- You need a local RDKit-backed molecular summary from a SMILES string.
6	- You want canonical SMILES, formula, weight, and simple physicochemical descriptors.
7
8	## When not to use
9	- You need conformer generation, docking, or reaction modeling.
10	- You need batch-scale descriptor computation for millions of compounds.
11
12	## Inputs
13	- One SMILES string
14	- Optional molecule name
15	- Optional JSON output path
16
17	## Outputs
18	- JSON summary with canonical SMILES, formula, exact mass, logP, TPSA, HBA/HBD, rotatable bonds, ring count, and heavy-atom count
19
20	## Requirements
21	- `slurm/envs/chem-tools` with RDKit available
22
23	## Procedure
24	1. Run `slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-molecular-descriptors/scripts/compute_rdkit_descriptors.py --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --name aspirin`.
25	2. Inspect `canonical_smiles`, `formula`, `molecular_weight`, and `tpsa`.
26	3. Reuse the JSON payload for downstream filtering or reporting.
27
28	## Validation
29	- The command exits successfully.
30	- `canonical_smiles` is non-empty for a known valid molecule.
31	- Descriptor fields are numeric where expected.
32
33	## Failure modes and fixes
34	- Invalid SMILES: verify the input string and quoting.
35	- Missing RDKit environment: run the script with `slurm/envs/chem-tools/bin/python`.
36
37	## Safety and limits
38	- Descriptor calculation only.
39	- No medicinal-chemistry or safety interpretation is implied.
40
41	## Provenance
42	- RDKit docs: https://www.rdkit.org/docs/index.html
43	- RDKit repository: https://github.com/rdkit/rdkit
44
45	## Related skills
46	- `chembl-molecule-search`

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rdkit-molecular-descriptors

36stars5forks

View on GitHub

How to install rdkit-molecular-descriptors?

ma-compbio-lab/skillfoundry/rdkit-molecular-descriptors

$npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-molecular-descriptors

Installs into the current project.

Summary

Use this skill to compute compact cheminformatics descriptors from one SMILES string with RDKit. Do not use it for docking, quantum chemistry, or large library screening.

Files · 1

View on GitHub

SKILL.md

1	## Purpose
2	Turn a SMILES string into a compact descriptor summary suitable for quick triage, featurization, and metadata enrichment.
3
4	## When to use
5	- You need a local RDKit-backed molecular summary from a SMILES string.
6	- You want canonical SMILES, formula, weight, and simple physicochemical descriptors.
7
8	## When not to use
9	- You need conformer generation, docking, or reaction modeling.
10	- You need batch-scale descriptor computation for millions of compounds.
11
12	## Inputs
13	- One SMILES string
14	- Optional molecule name
15	- Optional JSON output path
16
17	## Outputs
18	- JSON summary with canonical SMILES, formula, exact mass, logP, TPSA, HBA/HBD, rotatable bonds, ring count, and heavy-atom count
19
20	## Requirements
21	- `slurm/envs/chem-tools` with RDKit available
22
23	## Procedure
24	1. Run `slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-molecular-descriptors/scripts/compute_rdkit_descriptors.py --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --name aspirin`.
25	2. Inspect `canonical_smiles`, `formula`, `molecular_weight`, and `tpsa`.
26	3. Reuse the JSON payload for downstream filtering or reporting.
27
28	## Validation
29	- The command exits successfully.
30	- `canonical_smiles` is non-empty for a known valid molecule.
31	- Descriptor fields are numeric where expected.
32
33	## Failure modes and fixes
34	- Invalid SMILES: verify the input string and quoting.
35	- Missing RDKit environment: run the script with `slurm/envs/chem-tools/bin/python`.
36
37	## Safety and limits
38	- Descriptor calculation only.
39	- No medicinal-chemistry or safety interpretation is implied.
40
41	## Provenance
42	- RDKit docs: https://www.rdkit.org/docs/index.html
43	- RDKit repository: https://github.com/rdkit/rdkit
44
45	## Related skills
46	- `chembl-molecule-search`

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