rdkit-scaffold-analysis-starter

Name: rdkit-scaffold-analysis-starter
Author: ma-compbio-lab

36stars5forks

How to install rdkit-scaffold-analysis-starter?

ma-compbio-lab/skillfoundry/rdkit-scaffold-analysis-starter

$npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-scaffold-analysis-starter

Installs into the current project.

Summary

Use this skill to compute Murcko scaffold summaries for a small local molecule set with RDKit. Prefer it for deterministic scaffold grouping and smoke-scale cheminformatics checks.

Files · 1

View on GitHub

SKILL.md

1	## Purpose
2	Analyze a small local TSV of SMILES strings with RDKit Murcko scaffolds and emit a compact JSON summary that can feed later smoke integration or scaffold triage workflows.
3
4	## When to use
5	- You need a local scaffold grouping summary for a small curated molecule set.
6	- You want canonical SMILES, Murcko scaffolds, generic scaffolds, and group counts from one deterministic run.
7
8	## When not to use
9	- You need large library clustering, matched molecular pair analysis, or SAR interpretation.
10	- You need remote compound lookup or medicinal-chemistry recommendations.
11
12	## Inputs
13	- A TSV file with columns `name` and `smiles`
14	- Optional JSON output path
15
16	## Outputs
17	- JSON with per-molecule canonical SMILES, Murcko scaffold, generic scaffold, scaffold groups, generic scaffold groups, and summary counts
18
19	## Requirements
20	- `slurm/envs/chem-tools/bin/python`
21	- RDKit available in that environment
22
23	## Procedure
24	1. Inspect `examples/molecules.tsv`.
25	2. Run `slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-scaffold-analysis-starter/scripts/run_rdkit_scaffold_analysis.py --input skills/drug-discovery-and-cheminformatics/rdkit-scaffold-analysis-starter/examples/molecules.tsv`.
26	3. Review `molecules`, `scaffold_groups`, and `summary`.
27
28	## Validation
29	- The bundled example returns at least one scaffold group with count `>= 2`.
30	- Invalid SMILES input returns a non-zero exit code with a clear error message.
31
32	## Failure modes and fixes
33	- Invalid SMILES: fix the offending row in the input TSV.
34	- Missing RDKit environment: rerun with `slurm/envs/chem-tools/bin/python`.
35	- Missing `name` or `smiles` columns: use a header row with exactly those field names.
36
37	## Safety and limits
38	- Local scaffold computation only.
39	- No medicinal-chemistry conclusions are implied by the grouping.
40
41	## Provenance
42	- RDKit docs: https://www.rdkit.org/docs/index.html
43	- RDKit Murcko scaffold API: https://www.rdkit.org/docs/source/rdkit.Chem.Scaffolds.MurckoScaffold.html
44	- RDKit repository: https://github.com/rdkit/rdkit
45
46	## Related skills
47	- `rdkit-molecular-descriptors`
48	- `rdkit-molecule-standardization`

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rdkit-scaffold-analysis-starter

36stars5forks

View on GitHub

How to install rdkit-scaffold-analysis-starter?

ma-compbio-lab/skillfoundry/rdkit-scaffold-analysis-starter

$npx -y skills add ma-compbio-lab/SkillFoundry --skill rdkit-scaffold-analysis-starter

Installs into the current project.

Summary

Use this skill to compute Murcko scaffold summaries for a small local molecule set with RDKit. Prefer it for deterministic scaffold grouping and smoke-scale cheminformatics checks.

Files · 1

View on GitHub

SKILL.md

1	## Purpose
2	Analyze a small local TSV of SMILES strings with RDKit Murcko scaffolds and emit a compact JSON summary that can feed later smoke integration or scaffold triage workflows.
3
4	## When to use
5	- You need a local scaffold grouping summary for a small curated molecule set.
6	- You want canonical SMILES, Murcko scaffolds, generic scaffolds, and group counts from one deterministic run.
7
8	## When not to use
9	- You need large library clustering, matched molecular pair analysis, or SAR interpretation.
10	- You need remote compound lookup or medicinal-chemistry recommendations.
11
12	## Inputs
13	- A TSV file with columns `name` and `smiles`
14	- Optional JSON output path
15
16	## Outputs
17	- JSON with per-molecule canonical SMILES, Murcko scaffold, generic scaffold, scaffold groups, generic scaffold groups, and summary counts
18
19	## Requirements
20	- `slurm/envs/chem-tools/bin/python`
21	- RDKit available in that environment
22
23	## Procedure
24	1. Inspect `examples/molecules.tsv`.
25	2. Run `slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-scaffold-analysis-starter/scripts/run_rdkit_scaffold_analysis.py --input skills/drug-discovery-and-cheminformatics/rdkit-scaffold-analysis-starter/examples/molecules.tsv`.
26	3. Review `molecules`, `scaffold_groups`, and `summary`.
27
28	## Validation
29	- The bundled example returns at least one scaffold group with count `>= 2`.
30	- Invalid SMILES input returns a non-zero exit code with a clear error message.
31
32	## Failure modes and fixes
33	- Invalid SMILES: fix the offending row in the input TSV.
34	- Missing RDKit environment: rerun with `slurm/envs/chem-tools/bin/python`.
35	- Missing `name` or `smiles` columns: use a header row with exactly those field names.
36
37	## Safety and limits
38	- Local scaffold computation only.
39	- No medicinal-chemistry conclusions are implied by the grouping.
40
41	## Provenance
42	- RDKit docs: https://www.rdkit.org/docs/index.html
43	- RDKit Murcko scaffold API: https://www.rdkit.org/docs/source/rdkit.Chem.Scaffolds.MurckoScaffold.html
44	- RDKit repository: https://github.com/rdkit/rdkit
45
46	## Related skills
47	- `rdkit-molecular-descriptors`
48	- `rdkit-molecule-standardization`

People who liked this also viewed

6 picks

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