bio-conformer-generation skillA
bio-conformer-generation is agent-read markdown (skill) from pku-yuangroup/openai4s: Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility Reference examples tested with: RDKit 2024.09+, xtb 6.7+, CREST 3.0+, OpenMM 8.1+ for follow-up MD. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `xtb --version`; `crest --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Conformer Generation Generate 3D conformer ensembles for molecules from 2D structures. The choice of method depends on molecule size, flexibility, and downstream use: ETKDG (Riniker & Landrum 2015) and its ETKDGv3 macrocycle update (Wang et al. 2020) are modern defaults for drug-like molecules, MMFF94/UFF provide fast energy minimization, and CREST + GFN2-xTB provide higher-cost semi-empirical sampling. A single conformer may be insufficient when the downstream result is conformation-sensitive; determine ensemble size by convergence of the downstream descriptor, alignment, or docking result. …
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How to install
mdr add pku-yuangroup/openai4s/bio-conformer-generation@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-conformer-generation@sha256:51a37945250a282ePin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_i7lesauiudniqoot)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_i7lesauiudniqoot GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-conformer-generation GET https://markdownregistry.com/api/v1/blob/51a37945250a282e83530fed59a3a5ea7ae2e82e35268c91b3494f162fd86065
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