Manim Chemistry Molecules¶
- class manim_chemistry.manim_chemistry_molecule.mc_molecule.MCMolecule(atoms: List[MCAtom] | None = None, bonds: List[MCBond] | None = None, name: str | None = None)[source]¶
Abstraction of a molecule made of: - MCAtoms. - MCBonds. - Molecule name. - Extra properties (To be defined)
- add_atoms_from_atoms_dict(atoms_dict: Dict)[source]¶
Uses the atoms dict returned by a parser to add the atoms to the molecule.
- Args:
atoms_dict (Dict): Atoms dict from a parser. See BaseParser.
- add_bonds_from_bonds_dict(bonds_dict: Dict)[source]¶
Uses the bonds dict returned by a parser to add the bonds to the molecule.
- Args:
bonds_dict (Dict): Bonds dict from a parser. See Base Parser.
- static construct_from_data_dict(atoms_data_dict: dict, bonds_data_dict: dict, ignore_hydrogens: bool = True, ignore_all_hydrogens: bool = False)[source]¶
Given data with the format provided by a parser, constructs a MCMolecule, the corresponding MCAtoms and MCBonds and stablishes the connections between MCAtoms and bonds.
- Args:
atoms_data_dict (dict): Atoms data bonds_data_dict (dict): Bonds data
- static construct_from_file(filepath, ignore_hydrogens: bool = True, ignore_all_hydrogens: bool = False)[source]¶
Returns an MCMolecule given a file path.
- Args:
filepath: File path
- static construct_from_string(string: str, format: str = 'json', ignore_hydrogens: bool = True, ignore_all_hydrogens: bool = False)[source]¶
Reads a string and returns a molecule. Supported formats are: - mol - sdf - asnt - json - xml
Uses json format by default.