FPSim2.io package¶
Subpackages¶
Submodules¶
FPSim2.io.chem module¶
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FPSim2.io.chem.get_bounds_range(query: numpy.ndarray, threshold: Optional[float], a: Optional[float], b: Optional[float], ranges: list, search_type: str) → Union[Tuple[int, int], Tuple]¶
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FPSim2.io.chem.get_fp_length(fp_type: str, fp_params: Dict[str, Any]) → int¶ Returns the FP length given the name of the FP function and it’s parameters.
- Parameters
fp_type (str) – Name of the function used to generate the fingerprints.
fp_params (dict) – Parameters used to generate the fingerprints.
- Returns
fp_length – fp length of the fingerprint.
- Return type
int
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FPSim2.io.chem.get_mol_supplier(io_source: Any) → Optional[Callable[[…], Iterable[Tuple[int, rdkit.Chem.rdchem.Mol]]]]¶ Returns a mol supplier depending on the object type and file extension.
- Parameters
mols_source (str or iterable) – .smi or .sdf filename or iterable.
fps_sort (bool) – Whether if the FPs should be sorted or not.
- Returns
function that will read the molecules from the input.
- Return type
callable
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FPSim2.io.chem.it_mol_supplier(iterable: Iterable, gen_ids: bool, **kwargs) → Iterable[Tuple[int, rdkit.Chem.rdchem.Mol]]¶ Generator function that reads from iterables.
- Parameters
iterable (iterable) – Python iterable storing molecules.
gen_ids (bool) – generate ids or not.
- Yields
tuple – int id and rdkit mol.
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FPSim2.io.chem.load_molecule(mol_string: str) → rdkit.Chem.rdchem.Mol¶ Reads SMILES, molblock or InChI and returns a RDKit mol.
- Parameters
mol_string (str) – SMILES, molblock or InChI.
- Returns
mol – RDKit molecule.
- Return type
ROMol
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FPSim2.io.chem.rdmol_to_efp(rdmol: rdkit.Chem.rdchem.Mol, fp_func: str, fp_params: Dict[str, Any]) → List[int]¶
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FPSim2.io.chem.sdf_mol_supplier(filename: str, gen_ids: bool, **kwargs) → Iterable[Tuple[int, rdkit.Chem.rdchem.Mol]]¶ Generator function that reads from a .sdf file.
- Parameters
filename (str) – .sdf filename.
gen_ids (bool) – generate ids or not.
- Yields
tuple – int id and rdkit mol.
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FPSim2.io.chem.smi_mol_supplier(filename: str, gen_ids: bool, **kwargs) → Iterable[Tuple[int, rdkit.Chem.rdchem.Mol]]¶ Generator function that reads from a .smi file.
- Parameters
filename (str) – .smi file name.
gen_ids (bool) – generate ids or not.
- Yields
tuple – int id and rdkit mol.