qstack.c2mio

Converter from cell2mol Cell objects to PySCF Mole.

qstack.c2mio.get_cell(fpath, workdir='.')[source]

Load a unit cell from a .cell or .cif file.

If a .cif file is provided, the function checks for a corresponding .cell file in the working directory. If it exists, it loads the .cell file; otherwise, it calls cell2mol to process the .cif file to generate the unit cell.

Parameters:

  • fpath (str) – Path to the input file (.cell or .cif).

  • workdir (str) – Directory to read / write .cell file and logs if a .cif file is provided. Defaults to ‘.’.

Returns:

Unit cell object.

Return type:

cell2mol.unitcell

Raises:

NotImplementedError – If the file extension is not .cell or .cif.

qstack.c2mio.get_cell2mol_xyz(mol)[source]

Extract XYZ coordinates, charge, and spin from a cell2mol object.

Parameters:

mol – cell2mol molecule or ligand object.

Returns:

A tuple containing: - xyz (str): XYZ coordinate string. - charge (int): Total charge of the molecule. - spin (int): Number of unpaired electrons of the molecule (multiplicity - 1) for molecules and None for ligands.

Return type:

tuple

qstack.c2mio.get_ligand(cell, mol_idx=0, lig_idx=0, basis='minao', ecp=None)[source]

Convert a ligand in a cell2mol unit cell object to a pyscf Mole object.

Parameters:

  • cell – cell2mol unit cell object.

  • mol_idx (int) – Index of the molecule in the cell. Defaults to 0.

  • lig_idx (int) – Index of the ligand in the molecule. Defaults to 0.

  • basis (str or dict) – Basis set. Defaults to ‘minao’.

  • ecp (str) – Effective core potential. Defaults to None.

Returns:

pyscf Mole object for the ligand.

Return type:

pyscf.gto.Mole

qstack.c2mio.get_mol(cell, mol_idx=0, basis='minao', ecp=None)[source]

Convert a molecule in a cell2mol unit cell object to a pyscf Mole object.

Parameters:

  • cell – cell2mol unit cell object.

  • mol_idx (int) – Index of the molecule in the cell. Defaults to 0.

  • basis (str or dict) – Basis set. Defaults to ‘minao’.

  • ecp (str) – Effective core potential. Defaults to None.

Returns:

pyscf Mole object for the molecule.

Return type:

pyscf.gto.Mole