neurosnap.database.ccd module

Chemical Component Dictionary metadata helpers.

class neurosnap.database.ccd.CCD(code, name, smiles)

Bases: object

Minimal Chemical Component Dictionary entry.

code

CCD identifier, typically 1-5 characters.

name

Human-readable component name.

smiles

SMILES string for the component (technically canonicalized but the canonicalization algorithm used by wwPDB is inconsistent with that of RDkit).

code: str

name: str

smiles: str

smiles_canonical()

Return the RDKit-canonicalized SMILES string for this CCD entry.

Return type:

str

to_mol()

Return an RDKit molecule parsed from the canonical SMILES string.

Return type:

Mol

Returns:

RDKit molecule for the CCD entry.

Raises:

ValueError – If the stored canonical SMILES cannot be parsed.

neurosnap.database.ccd.get_ccd(code, *, cache_path='~/.cache/neurosnap/ccd_entries.json', overwrite=False, max_age_days=7, timeout=30)

Return a CCD entry by its component code.

Return type:

Optional[CCD]

neurosnap.database.ccd.get_ccd_entries(*, cache_path='~/.cache/neurosnap/ccd_entries.json', overwrite=False, max_age_days=7, timeout=30)

Fetch and cache CCD metadata entries.

The CCD payload is cached locally and refreshed when the cached payload exceeds max_age_days based on its embedded created_at timestamp.

Parameters:

• cache_path (str) – Local cache file path for the raw JSON payload.

• overwrite (bool) – If True, force a fresh download.

• max_age_days (int) – Maximum accepted payload age in days.

• timeout (int) – HTTP timeout in seconds for the download request.

Return type:

Dict[str, CCD]

Returns:

Dictionary mapping CCD code to CCD.