Molecular Io

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkNone observedNo outbound calls in the source
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass.

Audit 0.4.1 · source sha c8c1fc3a2b13 · 19 Oct 2026Report an issue or request a re-scan

• PublisherGPTomics GitHub organizationOwner of the repository this skill is read from
• Source folderGPTomics/bioSkills/chemoinformatics/molecular-ioThe exact folder we audited
• LicenceMITAs the repository states it
• Commit pinned for this verdictc8c1fc3a2b13A new audit runs when the source changes
• Repository statusArchivedLast push 65 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: 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,…

---
name: bio-molecular-io
description: 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.
tool_type: python
primary_tool: RDKit
---

## 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 |
|--------|-----|--------|---------|----------|------------|
| SMILES | 2D | Atom chirality `@/@@`; double-bond `/` and `\` | Atom-local formal charges | Compact, web-friendly, fast parse | Loses absolute coordinates; aromatic perception ambiguous across toolkits; tautomers not canonical |
| InChI | 2D | `/b`, `/t`, `/m`, `/s` stereo sublayers | `/q` charge and `/p` added/removed-proton sublayers; `/p` is not a pH model | Canonical by construction; cross-toolkit identity | Standard InChI normalizes mobile-H forms; limited organometallic stereo; large molecules may require special handling |
| SDF V2000 | 2D/3D | Wedge bonds | M CHG line | Industry default; metadata via tags | 999-atom limit; cannot encode multi-component reactions; query atoms ambiguous |
| SDF V3000 | 2D/3D | Wedge + stereo flag | Inline charge | No atom limit; query support; rich properties | Some software (legacy) cannot read; verbose |
| MOL2 (Tripos) | 3D | Common records rely on 3D coordinates and toolkit perception; no portable explicit stereo field | Per-atom partial | SYBYL atom types preserved for docking | Atom-type dialects diverge (SYBYL vs Corina); RDKit MOL2 parser brittle |
| PDB | 3D | None | None standard | Universal protein format | No bond orders; aromatic perception lost; ligand names truncated to 3 chars |
| PDBQT | 3D | None | Gasteiger / AD4 | AutoDock-ready; torsion tree encoded | Specific to docking; no aromaticity layer |
| BinaryCIF (MMTF retired) | 3D | Encoded | Encoded | BinaryCIF (`.bcif`) is the current compact structural format; RCSB stopped serving MMTF files on July 2, 2024 and recommends BinaryCIF (RCSB PDB 2024) | Not all toolkits parse; binary format |
| CDX/CDXML | 2D | Drawing | Drawing | ChemDraw native | Not a structural format; converts unreliably |
| InChIKey | Hash | Stereo layer | n/a | Database key, fast lookup | Collision probability depends on key block and collection size; cannot recover structure |

## Aromaticity Perception (most common silent error)

Different toolkits perceive aromaticity differently. The same SMILES round-tripped between toolkits may produce different canonical strings and different fingerprints.

| Model | Toolkit | Rule | Symptom of mismatch |
|-------|---------|------|---------------------|
| Daylight | OpenEye, Daylight | 4n+2 π on planar ring | Furan, thiophene aromatic |
| RDKit default | RDKit | Daylight-like with extensions for fused / N-containing | Compatible with Daylight for drug-like molecules |
| MDL | Available in several toolkits, including RDKit as `AROMATICITY_MDL` | Five-membered rings are not aromatic unless part of a fused aromatic system; only C/N and one-electron donors qualify; exocyclic double bonds exclude an atom | Five-membered heteroaromatics and exocyclic-bond systems may differ from the default RDKit model |
| OpenEye | OEAroModel | Several modes | Charged thiophene non-aromatic in MDL but aromatic in OpenEye |

**Fix:** Always re-canonicalize via the toolkit doing analysis. If aromaticity must be reassigned explicitly in RDKit, use a concrete model, for example `Chem.SetAromaticity(mol, Chem.AromaticityModel.AROMATICITY_RDKIT)`, after the molecule is in an appropriate sanitized or kekulized state.

## Stereochemistry Layers

Stereo loss is the second most common silent error. Each format encodes stereo differently:

- SMILES: `@/@@` for tetrahedral, `/` and `\` for cis/trans double bonds
- InChI: `/b` for double-bond stereo, `/t` for tetrahedral stereo, and `/m` plus `/s` for inversion/overall stereo type
- SDF: wedge/hash bond + parity 0/1/2; cis/trans encoded via bond direction
- MOL2: common Tripos records provide 3D coordinates but no portable wedge or explicit stereo field; verify toolkit perception by round trip

**Round-trip tests:** If `Chem.MolToSmiles(Chem.MolFromSmiles(smi), isomericSmiles=True)` does not preserve the represented stereochemistry, inspect whether the source contained stereo markers and whether any step called `Chem.RemoveStereochemistry()` or discarded stereochemical coordinates/bond directions. Sanitization alone does not intentionally remove valid stereochemistry. If `MolFromMolFile` returns a molecule missing wedge bonds, inspect the source's coordinates, bond directions, and parity encoding.

## Reading SMILES with Stereo Preservation

**Goal:** Pars

Excerpt, first 6,000 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

pip install rdkit
pip install openbabel-wheel  # For additional format support

git clone https://github.com/GPTomics/bioSkills
git -C bioSkills checkout c8c1fc3a2b13

Works in

1. 2026-10-19
   ✓SAFE B 89 / 100

   first audit · source c8c1fc3a2b13

Questions about Molecular Io

• github.com/GPTomics/bioSkills/tree/main/chemoinformatics/molecul — the audited source at commit c8c1fc3a2b13 and every finding aboveObserved · 19 Oct 2026

Spotted something wrong? Report a correction · Methodology