7.1. Compound I/O
Compound_io.py: Functions to load MINE databases from and dump compounds into common cheminformatics formats
- minedatabase.compound_io.export_inchi_rxns(mine_db: MINE, target: str, rxn_ids: Optional[List[str]] = None) None
Export reactions from a MINE db to a .tsv file.
- Parameters
- mine_dbMINE
Name of MongoDB to export reactions from.
- targetstr
Path to folder to save .tsv export file in.
- rxn_idsUnion[List[str], None], optional
Only export reactions with these ids, by default None.
- minedatabase.compound_io.export_kbase(mine_db: MINE, target: str) None
Exports MINE compound and reaction data as tab-separated values files amenable to use in ModelSEED.
- Parameters
- mine_dbMINE
The database to export.
- targetstr
Directory in which to place the files.
- minedatabase.compound_io.export_mol(mine_db: MINE, target: str, name_field: str = '_id') None
Exports compounds from the database as a MDL molfiles
- Parameters
- mine_dbMINE
MINE object that contains the database.
- targetstr
Directory in which to place the files.
- name_fieldstr, optional
FIeld to provide names for the mol files. Must be unique and universal. By default, “_id”.
- minedatabase.compound_io.export_sdf(mine_db: MINE, dir_path: str, max_compounds: Optional[int] = None) None
Exports compounds from the database as an MDL SDF file.
- Parameters
- mine_dbMINE
MINE object that contains the database.
- dir_pathstr
Directory for files.
- max_compoundsint, optional
Maximum number of compounds per file, by default None.
- minedatabase.compound_io.export_smiles(mine_db: MINE, dir_path: str, max_compounds: Optional[int] = None) None
Exports compounds from the database as a SMILES file.
- Parameters
- mine_dbMINE
MINE object that contains the database.
- dir_pathstr
Directory for files.
- max_compoundsint, optional
Maximum number of compounds per file, by default None.
- minedatabase.compound_io.export_tsv(mine_db: MINE, target: str, compound_fields: Tuple[str] = ('_id', 'Names', 'Model_SEED', 'Formula', 'Charge', 'Inchi'), reaction_fields: Tuple[str] = ('_id', 'SMILES_rxn', 'C_id_rxn')) None
Exports MINE compound and reaction data as tab-separated values files amenable to use in ModelSEED.
- Parameters
- mine_dbMINE
The database to export.
- targetstr
Directory, in which to place the files.
- compound_fieldsTuple[str], optional
Fields to export in the compound table, by default (‘_id’, ‘Names’, ‘Model_SEED’, ‘Formula’, ‘Charge’, ‘Inchi’).
- reaction_fieldsTuple[str], optional
Fields to export in the reaction table, by default (‘_id’, ‘SMILES_rxn’, ‘C_id_rxn’).
- minedatabase.compound_io.import_mol_dir(mine_db: MINE, target: str, name_field: str = 'Name', overwrite: bool = False) None
Imports a directory of molfiles as a MINE database.
- Parameters
- mine_dbMINE
The database to export.
- targetstr
Directory in which to place the files.
- name_fieldstr, optional
Field for the compound name, by default “Name”.
- overwritebool, optional
Replace old compounds with new ones if a collision happens, by default False.