rdtools.torsion#

Torsion related functions.

rdtools.torsion.determine_smallest_atom_index_in_torsion(atom1: Atom, atom2: Atom) → int#

Determine the smallest atom index connected to atom1 but not atom2.

Returns a heavy atom if available, otherwise a hydrogen atom. Useful for deterministically determining the indices of four atom in a torsion. This function assumes there ARE additional atoms connected to atom1, and that atom2 is not a hydrogen atom.

Parameters:

  • atom1 (Chem.Atom) – The atom who’s neighbors will be searched.

  • atom2 (Chem.Atom) – An atom connected to atom1 to exclude (a pivotal atom).

Returns:

int – The smallest atom index (1-indexed) connected to atom1 which is not atom2.

Raises:

ValueError – If no neighbors are found or if atom2 is a hydrogen atom.

rdtools.torsion.find_internal_torsions(mol: Mol, exclude_methyl: bool = False) → list[list[int]]#

Find the internal torsions from RDkit molecule.

Parameters:

  • mol (Chem.Mol) – RDKit molecule.

  • exclude_methyl (bool) – Whether exclude the torsions with methyl groups.

Returns:

list[list[int]] – A list of internal torsions.

rdtools.torsion.find_ring_torsions(mol: Mol) → list[list[int]]#

Find the ring from RDkit molecule.

Parameters:

mol (Chem.Mol) – RDKit molecule.

Returns:

list[list[int]] – A list of ring torsions.

rdtools.torsion.get_torsion_tops(mol: Mol, torsion: Sequence[int], allow_non_bonding_pivots: bool = False) → tuple[list[int], list[int]]#

Generate tops for the given torsion.

Top atoms are defined as atoms on one side of the torsion. The mol should be in one-piece when using this function, otherwise, the results will be misleading.

Parameters:

  • mol (Chem.Mol) – The molecule to get the torsion tops from.

  • torsion (Sequence[int]) – The atom indices of the pivot atoms (length of 2) or a length-4 atom index sequence with the 2nd and 3rd are the pivot of the torsion.

  • allow_non_bonding_pivots (bool, optional) – Allow pivots. Defaults to False. There are cases like CC#CC or X…H…Y, where a user may want to define a torsion with a nonbonding pivots.

Returns:

tuple[list[int], list[int]] – Two frags, one of the top of the torsion, and the other top of the torsion.

Raises:

ValueError – If the torsion is invalid.

rdtools.torsion.get_torsional_modes(mol: Mol, exclude_methyl: bool = False, include_ring: bool = True) → list[list[int]]#

Get the torsional modes from RDkit molecule.

Parameters:

  • mol (Chem.Mol) – RDKit molecule.

  • exclude_methyl (bool) – Whether exclude the torsions with methyl groups. defaults to False.

  • include_ring (bool) – Whether include the ring torsions. Defaults to True.

Returns:

list[list[int]] – A list of torsional modes.