io

isicle.io._check_mol(mol, string_struct)[source]

Check if mol failed to generate. If so, throw error.

Parameters:

mol (:obj:`~rdkit.Chem.rdchem.Mol’) – RDKit representation of molecule structure.
string_struct (str) – Input used to initialize Mol object.

isicle.io._check_mol_obj(mol_obj)[source]

isicle.io._load_line_notation(path, func=None, force=False, string=False)[source]

Load line notation representation (InChI, SMILES) from file.

Parameters:

path (str) – Path to file
force (bool) – Indicate whether to force load input, ignoring errors.

Returns:

Molecule representation.

Return type:

Geometry

isicle.io._load_mol_from_file(path, func=None)[source]

Load RDKit mol representation from file (pdb, mol, mol2).

Parameters:

path (str) – Path to supported file.
func (onj)
basename (str)

Returns:

Molecule representation.

Return type:

Geometry

isicle.io._load_text(path: str)[source]

Load text from file.

Parameters:: path (str) – Path to text file.
Returns:: Lines from given text file.
Return type:: list

isicle.io.load(path, **kwargs)[source]

Reads in molecule information of the following supported file types: .smi, .inchi, .xyz, .mol, .mol2, .pkl, .pdb. Direct loaders can also be used, see load_* functions for more information.

Parameters:

path (str) – Path to file with molecule information.
kwargs – Keyword arguments passed to format-specific loaders.

Returns:

Molecule representation.

Return type:

Geometry or XYZGeometry

isicle.io.load_inchi(path, force=False)[source]

Load InChI from file.

Parameters:

path (str) – Path to file.
force (bool) – Indicate whether to force load input, ignoring errors.

Returns:

Molecule representation.

Return type:

Geometry

isicle.io.load_joblib(path)[source]

Load joblib file.

Parameters:: path (str) – Path to pickle.
Returns:: Previously pickled object instance.
Return type:: data

isicle.io.load_mol(path)[source]

Load mol from file.

Parameters:: path (str) – Path to mol file.
Returns:: Molecule representation.
Return type:: Geometry

isicle.io.load_mol2(path: str)[source]

Load mol2 from file.

Parameters:: path (str) – Path to mol2 file.
Returns:: Molecule representation.
Return type:: Geometry

isicle.io.load_mol_obj(mol_obj)[source]

Load RDKit mol object into geometry instance

Parameters:: mol_obj (mol) – RDKit mol object
Returns:: Molecule representation.
Return type:: Geometry

isicle.io.load_pdb(path)[source]

Load PDB from file.

Parameters:: path (str) – Path to PDB file.
Returns:: Molecule representation.
Return type:: Geometry

isicle.io.load_pickle(path)[source]

Load pickled file.

Parameters:: path (str) – Path to pickle.
Returns:: Previously pickled object instance.
Return type:: data

isicle.io.load_smiles(path, force=False)[source]

Load SMILES from file.

Parameters:

path (str) – Path to file.
force (bool) – Indicate whether to force load input, ignoring errors.

Returns:

Molecule representation.

Return type:

Geometry

isicle.io.load_xyz(path)[source]

Load XYZ from file.

Parameters:: path (str) – Path to XYZ file.
Returns:: Molecule representation.
Return type:: Geometry

isicle.io.save(path, data)[source]

Save molecule, format detected by path extension.

Parameters:

path (str) – Path to save file. Supported extensions include .pkl, .mfj, .xyz, .mol, .pdb, .inchi, .smi.
data (obj) – Object instance. Must be Geometry for .xyz and .mfj.

isicle.io.save_csv(path, dataframe)[source]

Save pandas.DataFrame as csv file.

Parameters:

path (str) – Path to output file.
dataframe (pandas.DataFrame) – Dataframe of results

isicle.io.save_inchi(path, geom)[source]

Save molecule geometry as InChI file.

Parameters:

path (str) – Path to output file.
geom (Geometry) – Molecule representation.

isicle.io.save_joblib(path, data)[source]

Save object as joblib file.

Parameters:

path (str) – Path to output file.
data (object) – Aribtrary object instance.

isicle.io.save_mfj(path, geom)[source]

Save molecule geometry as MFJ file. Must have energy and charge information.

Parameters:

path (str) – Path to output file.
geom (Geometry) – or XYZGeometry Molecule representation.

isicle.io.save_mol(path, geom)[source]

Save molecule geometry as MOL file.

Parameters:

path (str) – Path to output file.
geom (Geometry) – Molecule representation.

isicle.io.save_pdb(path, geom)[source]

Save molecule geometry as PDB file.

Parameters:

path (str) – Path to output file.
geom (Geometry) – Molecule representation.

isicle.io.save_pickle(path, data)[source]

Save object as pickle file.

Parameters:

path (str) – Path to output file.
data (object) – Aribtrary object instance.

isicle.io.save_smiles(path, geom)[source]

Save molecule geometry as SMILES file.

Parameters:

path (str) – Path to output file.
geom (Geometry) – Molecule representation.

isicle.io.save_xyz(path, geom)[source]

Save molecule geometry as XYZ file.

Parameters:

path (str) – Path to output file.
geom (Geometry) – or XYZGeometry Molecule representation.