MetaLig API
- class DARTassembler.src.metalig.db.BaseDB(db)[source]
Bases:
object- to_dict(desc='Convert DB to dict')[source]
Converts all molecules in the database to a dictionary format.
- Parameters:
desc – str: Description for the progress bar.
- Returns:
A dictionary where keys are molecule identifiers and values are dictionaries representing the molecules.
- save_to_file(path, desc=None, json_lines=True)[source]
Saves the database to a .json or .jsonlines file.
- Parameters:
path – Path to the output file where the database will be saved.
desc – Description for the progress bar. If None, no progress bar will be shown.
json_lines – If True, saves the database as jsonlines. If False, saves the database as a single json file.
- Returns:
None
- class DARTassembler.src.metalig.db.LigandDB(db)[source]
Bases:
BaseDB- classmethod from_json(path='metalig', n_max=None, show_progress=True)[source]
Loads a ligand database from a .jsonlines file.
- Parameters:
path – Path to the .jsonlines file of the ligand database. Alternatively, the string ‘metalig’ can be used to load the default ligand database.
n_max – Maximum number of ligands to load. If None, all ligands will be loaded.
show_progress – If True, a progress bar will be shown.
- Returns:
A LigandDB object
- get_df(max_entries=5)[source]
Returns a DataFrame with important ligand information for all ligands in the database, such as charge, stoichiometry, archetype, and more.
- Parameters:
max_entries – Maximum number of entries for long lists in the DataFrame, such as the list of CSD codes in which this ligand is present.
- Returns:
A DataFrame with ligand information, with the index being unique_name.
- save_to_csv(outpath, max_entries=5)[source]
Saves a csv file with important ligand information for all ligands in the database, such as charge, stoichiometry, archetype, and more.
- Parameters:
outpath – Path to the output csv file.
max_entries – Maximum number of entries for long lists in the DataFrame, such as the list of CSD codes in which this ligand is present.
- Returns:
A DataFrame with ligand information.
- save_to_concat_xyz(outpath, with_metal=True, comment=None)[source]
Save a concatenated xyz file with all ligands in the database.
- Parameters:
outpath – Path to the output xyz file.
with_metal – If True, the output structure of each ligand will contain a metal center at the original position for better visualization. If False, only the ligand structure itself will be saved.
comment – A comment to be added to each xyz structure. If None, a default comment will be used.
- Returns:
A concatenated xyz string with all ligands in the database.
- get_concat_xyz_string(with_metal=True, comment=None)[source]
Get a concatenated xyz string with all ligands in the database.
- Parameters:
with_metal – If True, the output structure of each ligand will contain a metal center at the original position for better visualization. If False, only the ligand structure itself will be saved.
comment – A comment to be added to each xyz structure. If None, a default comment will be used.
- Returns:
A concatenated xyz string with all ligands in the database.