stko.molecule_analysis.GeometryAnalyser

class stko.molecule_analysis.GeometryAnalyser

Bases: object

Tools for analysing the geometry of molecules.

Warning

This code is only present in the latest versions of stko that require Python 3.11!

Methods

calculate_angles	Calculate angles for all angles defined by molecule bonding.
calculate_bonds	Calculate bond lengths for all stk.Molecule.get_bonds().
calculate_torsions	Calculate all torsions defined by molecule bonding.
get_avg_centroid_distance	Get the average distance between the molecule and centroid.
get_max_diameter	Get the maximum diameter of the molecule (defined in stk).
get_metal_centroid_metal_angle	Get all metal-centroid-metal angles.
get_metal_distances	Get all metal atom pair distances.
get_min_atom_atom_distance	Get the minimum distance between atoms in molecule.
get_min_centroid_distance	Get the minimum distance between the molecule and centroid.
get_radius_gyration	Get the radius of gyration of the molecule.

calculate_angles(molecule)

Calculate angles for all angles defined by molecule bonding.

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

Dictionary of angles organised by element triplet.

Return type:

dict[tuple[str, str, str], list[float]]

calculate_bonds(molecule)

Calculate bond lengths for all stk.Molecule.get_bonds().

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

Dictionary of bonds organised by element pair.

Return type:

dict[tuple[str, str], list[float]]

calculate_torsions(molecule)

Calculate all torsions defined by molecule bonding.

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

Dictionary of torsions organised by elements.

Return type:

dict[tuple[str, …], list[float]]

get_avg_centroid_distance(molecule)

Get the average distance between the molecule and centroid.

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

The average and std. deviation of centroid to atom distances.

Return type:

tuple[float, float]

get_max_diameter(molecule)

Get the maximum diameter of the molecule (defined in stk).

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

The maximum diameter in Angstrom.

Return type:

float

get_metal_centroid_metal_angle(molecule, metal_atom_nos)

Get all metal-centroid-metal angles.

Parameters:

• molecule (Molecule) – The molecule to analyse.

• metal_atom_nos (tuple[int, ...]) – The atomic numbers to delete. Can be a tuple of one or any element on periodic table.

Returns:

The angles in degrees and associated metal atom ids.

Return type:

dict[tuple[int, int], float]

get_metal_distances(molecule, metal_atom_nos)

Get all metal atom pair distances.

Parameters:

• molecule (Molecule) – The molecule to analyse.

• metal_atom_nos (tuple[int, ...]) – The atomic numbers to delete. Can be a tuple of one or any element on periodic table.

Returns:

The distances and associated metal atom ids.

Return type:

dict[tuple[int, int], float]

get_min_atom_atom_distance(molecule)

Get the minimum distance between atoms in molecule.

This does not consider bonding.

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

The minimum distance.

Return type:

float

get_min_centroid_distance(molecule)

Get the minimum distance between the molecule and centroid.

This is nearly equivalent to a pore radius.

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

The minimum centroid to atom distance.

Return type:

float

get_radius_gyration(molecule)

Get the radius of gyration of the molecule.

Parameters:

molecule (Molecule) – The molecule to analyse.

Returns:

R_g in Angstrom.

Return type:

float