Category Transforms#

Transforms operating on Biotite’s CIFBlock and CIFCategory objects.

These transforms are used to extract information from the CIFBlock and return a dictionary containing processed information.

atomworks.io.transforms.categories.category_to_df(cif_block_or_category: CIFBlock | BinaryCIFBlock | CIFCategory | BinaryCIFCategory, category: str | None = None) → DataFrame | None[source]#

Convert CIF component to pandas DataFrame.

Accepts either (CIFBlock, category_name) or (CIFCategory) directly. Supports both text CIF and binary CIF (BinaryCIF) formats.

Parameters:

  • cif_block_or_category – CIFBlock, BinaryCIFBlock, or CIFCategory | BinaryCIFCategory

  • category – Category name when passing CIFBlock/BinaryCIFBlock, omit when passing CIFCategory

Returns:

DataFrame containing the category data, or None if category doesn’t exist (CIFBlock mode only)

atomworks.io.transforms.categories.category_to_dict(cif_block_or_category: CIFBlock | BinaryCIFBlock | CIFCategory | BinaryCIFCategory, category: str | None = None) → dict[str, ndarray][source]#

Convert CIF component to dict mapping column names to numpy arrays.

Accepts either (CIFBlock, category_name) or (CIFCategory) directly. Supports both text CIF and binary CIF (BinaryCIF) formats.

Parameters:

  • cif_block_or_category – CIFBlock, BinaryCIFBlock, or CIFCategory | BinaryCIFCategory

  • category – Category name when passing CIFBlock/BinaryCIFBlock, omit when passing CIFCategory

Returns:

Dict mapping column names to numpy arrays

atomworks.io.transforms.categories.extract_crystallization_details(crystal_dict: dict) → dict[str, list[float] | None][source]#

Extracts crystallization details from the crystallization dictionary.

Parameters:

crystal_dict – Dictionary for the exptl_crystal_grow CIF category.

Returns:

  • “pH”: A list of two floats [min_pH, max_pH], or None if unavailable.

Return type:

A dictionary with crystallization details. Currently includes

atomworks.io.transforms.categories.get_ligand_of_interest_info(cif_block: CIFBlock) → dict[source]#

Extract ligand of interest information from a CIF block.

Reference:

PDB101 Small Molecule Ligands Guide

atomworks.io.transforms.categories.get_metadata_from_category(cif_block: CIFBlock, fallback_id: str | None = None) → dict[source]#

Extract metadata from the CIF block. If the entry.id field is not present in the CIF block, the fallback_id is used instead (e.g., the filename of the CIF).

From RCSB CIF files, this function extracts:

  • ID (e.g., PDB ID)

  • Method (e.g., X-ray, NMR, etc.)

  • Deposition date (initial)

  • Release date (smallest revision date)

  • Resolution (e.g., 5.0, 3.0, etc.)

  • Chem comp type (elements of atomworks.constants.CHEM_COMP_TYPES)

For custom CIF files (e.g., distillation), this function extracts:

  • Extra metadata (all other categories)

Parameters:

  • cif_block (CIFBlock) – The CIF block to extract metadata from.

  • fallback_id (str) – A fallback ID to use if the entry.id field is not present in the CIF block.