Medical-research-skills pubchem-database-skill

Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.

install

source · Clone the upstream repo

git clone https://github.com/aipoch/medical-research-skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/aipoch/medical-research-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/scientific-skills/Evidence Insight/pubchem-database-skill" ~/.claude/skills/aipoch-medical-research-skills-pubchem-database-skill && rm -rf "$T"

manifest: scientific-skills/Evidence Insight/pubchem-database-skill/SKILL.md

source content

Source: https://github.com/aipoch/medical-research-skills

When to Use

You need to search for chemical compounds by name, CID, SMILES, InChI, or molecular formula.
You want to retrieve physicochemical properties (e.g., molecular weight, LogP, TPSA, H-bond donors/acceptors).
You need to perform structure-based searches, such as similarity or substructure queries.
You want to obtain bioactivity data (e.g., assay summaries, target information) for a given compound.
You are building an automated cheminformatics or drug discovery workflow that requires programmatic access to PubChem.

Key Features

Flexible compound search by name, CID, SMILES, InChI, or formula.
Property retrieval via PubChem PUG-REST and PubChemPy (e.g., MW, LogP, Canonical SMILES).
Structure search:
- Similarity search
- Substructure search
Bioactivity retrieval linked to PubChem BioAssay records.
Rate-limit aware implementation (respects PubChem’s limit of max 5 requests/sec).
Python function interface for seamless integration into scientific pipelines.

Dependencies

Install the required Python packages:

uv pip install pubchempy requests

```
pubchempy
```
(version: not pinned)
```
requests
```
(version: not pinned)

Example Usage

Primary module:

```
scripts/pubchem_ops.py
```

1) Get compound properties

python -c "from scripts.pubchem_ops import get_properties; print(get_properties(query_value='Aspirin', query_type='name'))"

Or in Python:

from scripts.pubchem_ops import get_properties

result = get_properties(query_value="Aspirin", query_type="name")
print(result)

2) Structure search (similarity)

python -c "from scripts.pubchem_ops import structure_search; print(structure_search(query_value='CC(=O)OC1=CC=CC=C1C(=O)O', search_type='similarity'))"

Or in Python:

from scripts.pubchem_ops import structure_search

smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"
result = structure_search(query_value=smiles, search_type="similarity")
print(result)

3) Get bioactivity data

python -c "from scripts.pubchem_ops import get_bioactivity; print(get_bioactivity(cid=2244))"

Or in Python:

from scripts.pubchem_ops import get_bioactivity

result = get_bioactivity(cid=2244)
print(result)

Implementation Details

Primary script:
```
scripts/pubchem_ops.py
```
Data sources / endpoints:
- Compound & properties:
```
pubchem.ncbi.nlm.nih.gov/rest/pug
```
- Bioactivity: PubChem BioAssay endpoints
- Python wrapper:
```
PubChemPy
```
Supported operations:
- ```
get_properties
```
  : retrieve physicochemical properties by name/CID/SMILES/InChI/formula.
- ```
structure_search
```
  : perform similarity or substructure search.
- ```
get_bioactivity
```
  : retrieve assay and bioactivity-related data by CID.

Input constraints:

```
query_type
```
must match supported types (e.g.,
```
name
```
,
```
cid
```
,
```
smiles
```
,
```
inchi
```
,
```
formula
```
).
```
search_type
```
must be
```
similarity
```
or
```
substructure
```
.

Error handling:
- Returns structured error or
```
None
```
  if compound is not found.
- Handles PubChem rate limits (≤ 5 requests/sec).
Troubleshooting considerations:
- Ensure network access to
```
pubchem.ncbi.nlm.nih.gov
```
  .
- Verify query format (e.g., valid SMILES or InChI) if results are empty.
Additional reference:
- API documentation pointers:
```
references/api_reference.md
```