bio-molecular-io skillA
bio-molecular-io is agent-read markdown (skill) from pku-yuangroup/openai4s: Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking..
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+, Open Babel 3.1.1+, ChEMBL structure_pipeline 1.2+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `obabel -V`; `obabel -L formats` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Molecular I/O Parse, write, and convert molecular file formats. Most downstream errors trace back to silent I/O issues: incorrect aromaticity perception, lost stereochemistry, mishandled charges, dropped stereo bonds, or non-canonical tautomers. This skill enumerates each format's failure modes and prescribes the correct toolchain for each scenario. For full standardization (canonicalization, salt stripping, tautomer enumeration) see `chemoinformatics/molecular-standardization`. For generating 3D conformers from parsed 2D molecules, see `chemoinformatics/conformer-generation`. ## Format Taxonomy | Format | Dim | Stereo | Charges | Strength | Fails when | …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-molecular-io@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-molecular-io@sha256:819be9fa3a611743Pin 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_qee3xksorcwqxrc4)
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Versions
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (15778 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qee3xksorcwqxrc4 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-molecular-io GET https://markdownregistry.com/api/v1/blob/819be9fa3a611743ac46bbcc7b2536c77d16ad8fde4263c2e7cc8251ff11b1ef
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