xenopict.declarative package

Submodules

• xenopict.declarative.types module
  • MarkSpec
    • MarkSpec.atoms
    • MarkSpec.model_config
    • MarkSpec.substructure_atoms
    • MarkSpec.substructure_bonds
    • MarkSpec.validate_mark_spec()
  • MoleculeSpec
    • MoleculeSpec.color
    • MoleculeSpec.halo
    • MoleculeSpec.id
    • MoleculeSpec.mark
    • MoleculeSpec.model_config
    • MoleculeSpec.smiles
  • XenopictSpec
    • XenopictSpec.align
    • XenopictSpec.color
    • XenopictSpec.halo
    • XenopictSpec.model_config
    • XenopictSpec.molecules

Module contents

Declarative API for xenopict.

This module provides a high-level interface for creating molecule visualizations using JSON-like specifications. It supports both single and multiple molecule visualizations with automatic alignment.

xenopict.declarative.parse(spec)

Parse a specification into a list of Xenopict objects.

This function serves as the main entry point for the declarative API. It accepts specifications in multiple formats and returns a list of Xenopict objects.

Parameters:

spec (Union[Dict[str, Any], XenopictSpec, str, Path]) – The specification for creating molecules. Can be one of: - A dict matching the XenopictSpec schema - A XenopictSpec instance - A JSON string matching the XenopictSpec schema - A Path to a JSON file containing a XenopictSpec

Return type:

List[Xenopict]

Returns:

List of Xenopict objects, one for each molecule in the specification

Raises:

ValueError – If the input is invalid or required fields are missing

Examples

>>> # From a dict
>>> spec = {
...     "molecules": {
...         "smiles": "CCO"
...     }
... }
>>> xenopicts = parse(spec)
>>> len(xenopicts)
1

>>> # From a JSON string with marking
>>> json_str = '''
... {
...     "molecules": [
...         {
...             "smiles": "CCO",
...             "mark": {
...                 "atoms": [0, 1]
...             }
...         },
...         {
...             "smiles": "CCCO",
...             "mark": {
...                 "substructure_atoms": [0, 1, 2]
...             }
...         }
...     ]
... }
... '''
>>> xenopicts = parse(json_str)
>>> len(xenopicts)
2

>>> # From a file path
>>> from pathlib import Path
>>> path = Path("molecules.json")  
>>> xenopicts = parse(path)