molecular-io

Name: molecular-io
Author: GPTomics

1.1kstars185forks

How to install molecular-io?

gptomics/bioskills/molecular-io

$npx -y skills add GPTomics/bioSkills --skill molecular-io

Installs into the current project.

Summary

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

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SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: RDKit 2024.09+, Open Babel 3.1.1+, ChEMBL structure_pipeline 1.2+.
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7	- CLI: `obabel -V`; `obabel -L formats`
8
9	If code throws ImportError, AttributeError, or TypeError, introspect the installed
10	package and adapt the example to match the actual API rather than retrying.
11
12	# Molecular I/O
13
14	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.
15
16	For full standardization (canonicalization, salt stripping, tautomer enumeration) see `chemoinformatics/molecular-standardization`. For generating 3D conformers from parsed 2D molecules, see `chemoinformatics/conformer-generation`.
17
18	## Format Taxonomy
19
20	\| Format \| Dim \| Stereo \| Charges \| Strength \| Fails when \|
21	\|--------\|-----\|--------\|---------\|----------\|------------\|
22	\| 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 \|
23	\| 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 \|
24	\| 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 \|
25	\| SDF V3000 \| 2D/3D \| Wedge + stereo flag \| Inline charge \| No atom limit; query support; rich properties \| Some software (legacy) cannot read; verbose \|
26	\| 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 \|
27	\| PDB \| 3D \| None \| None standard \| Universal protein format \| No bond orders; aromatic perception lost; ligand names truncated to 3 chars \|
28	\| PDBQT \| 3D \| None \| Gasteiger / AD4 \| AutoDock-ready; torsion tree encoded \| Specific to docking; no aromaticity layer \|
29	\| 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 \|
30	\| CDX/CDXML \| 2D \| Drawing \| Drawing \| ChemDraw native \| Not a structural format; converts unreliably \|
31	\| InChIKey \| Hash \| Stereo layer \| n/a \| Database key, fast lookup \| Collision probability depends on key block and collection size; cannot recover structure \|
32
33	## Aromaticity Perception (most common silent error)
34
35	Different toolkits perceive aromaticity differently. The same SMILES round-tripped between toolkits may produce different canonical strings and different fingerprints.
36
37	\| Model \| Toolkit \| Rule \| Symptom of mismatch \|
38	\|-------\|---------\|------\|---------------------\|
39	\| Daylight \| OpenEye, Daylight \| 4n+2 π on planar ring \| Furan, thiophene aromatic \|
40	\| RDKit default \| RDKit \| Daylight-like with extensions for fused / N-containing \| Compatible with Daylight for drug-like molecules \|
41	\| 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 \|
42	\| OpenEye \| OEAroModel \| Several modes \| Charged thiophene non-aromatic in MDL but aromatic in OpenEye \|
43
44	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.
45
46	## Stereochemistry Layers
47
48	Stereo loss is the second most common silent error. Each format encodes ster

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molecular-io

1.1kstars185forks

View on GitHub

How to install molecular-io?

gptomics/bioskills/molecular-io

$npx -y skills add GPTomics/bioSkills --skill molecular-io

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: RDKit 2024.09+, Open Babel 3.1.1+, ChEMBL structure_pipeline 1.2+.
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7	- CLI: `obabel -V`; `obabel -L formats`
8
9	If code throws ImportError, AttributeError, or TypeError, introspect the installed
10	package and adapt the example to match the actual API rather than retrying.
11
12	# Molecular I/O
13
14	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.
15
16	For full standardization (canonicalization, salt stripping, tautomer enumeration) see `chemoinformatics/molecular-standardization`. For generating 3D conformers from parsed 2D molecules, see `chemoinformatics/conformer-generation`.
17
18	## Format Taxonomy
19
20	\| Format \| Dim \| Stereo \| Charges \| Strength \| Fails when \|
21	\|--------\|-----\|--------\|---------\|----------\|------------\|
22	\| 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 \|
23	\| 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 \|
24	\| 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 \|
25	\| SDF V3000 \| 2D/3D \| Wedge + stereo flag \| Inline charge \| No atom limit; query support; rich properties \| Some software (legacy) cannot read; verbose \|
26	\| 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 \|
27	\| PDB \| 3D \| None \| None standard \| Universal protein format \| No bond orders; aromatic perception lost; ligand names truncated to 3 chars \|
28	\| PDBQT \| 3D \| None \| Gasteiger / AD4 \| AutoDock-ready; torsion tree encoded \| Specific to docking; no aromaticity layer \|
29	\| 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 \|
30	\| CDX/CDXML \| 2D \| Drawing \| Drawing \| ChemDraw native \| Not a structural format; converts unreliably \|
31	\| InChIKey \| Hash \| Stereo layer \| n/a \| Database key, fast lookup \| Collision probability depends on key block and collection size; cannot recover structure \|
32
33	## Aromaticity Perception (most common silent error)
34
35	Different toolkits perceive aromaticity differently. The same SMILES round-tripped between toolkits may produce different canonical strings and different fingerprints.
36
37	\| Model \| Toolkit \| Rule \| Symptom of mismatch \|
38	\|-------\|---------\|------\|---------------------\|
39	\| Daylight \| OpenEye, Daylight \| 4n+2 π on planar ring \| Furan, thiophene aromatic \|
40	\| RDKit default \| RDKit \| Daylight-like with extensions for fused / N-containing \| Compatible with Daylight for drug-like molecules \|
41	\| 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 \|
42	\| OpenEye \| OEAroModel \| Several modes \| Charged thiophene non-aromatic in MDL but aromatic in OpenEye \|
43
44	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.
45
46	## Stereochemistry Layers
47
48	Stereo loss is the second most common silent error. Each format encodes ster

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