shnitsel.geo.nonred

Functions

get_smiles_order_ignoring_h(mol)

Returns the order in which atoms would appear in the canonical SMILES of

flag_nonredundant(mol[, include_h])

Compute a non-redundant set of bonds, angles, and dihedrals

Module Contents

get_smiles_order_ignoring_h(mol)

Returns the order in which atoms would appear in the canonical SMILES of mol, ignoring hydrogens

Parameters:

mol (rdkit.Chem.Mol) – An rdkit.Chem.Mol object

Returns:

  • A list of integers representing indices of the original mol object (as opposed

  • to the integers assigned to the copy stripped of hydrogens)

Return type:

list[int]

flag_nonredundant(mol, include_h=True)

Compute a non-redundant set of bonds, angles, and dihedrals sufficient to uniquely determine the atoms of the input, given a fixed centre and whole-molecular orientation.

Parameters:

  • mol (rdkit.Chem.rdchem.Mol) – Molecule under study.

  • include_h (bool) – Whether to include internal coordinates for hydrogen atoms

Returns:

{

‘bonds’: […], ‘angles’: […], ‘dihedrals’: […]

}

Return type:

dict