tqchem.internal_coordinates¶

Classes¶

`InternalCoordinates`	Collection of internal coordinates for components of a system.
`MolecularGrid`	Grid representation of the conformers of a system

Functions¶

`linearize`(→ list[Any])	Converts dictionary values (Iterables) into a one-dimensional list
`indices_to_components`(indices, component_ranges)	Assign list of indices to the variables of the components
`internal_to_xyz`(→ tqchem.molgraph.MolecularSystem)	Transform internal coordinates to xyz coordinates.
`xyz_to_internal`(→ InternalCoordinates)	Transform xyz coordinates to internal coordinates.

Module Contents¶

class tqchem.internal_coordinates.InternalCoordinates¶

Bases: dict

Collection of internal coordinates for components of a system.

Dictionary mapping tuples of atom indices to a representation of internal coordinates, i.e. BATFrames or PuckeringFrames.

For conformer search we do not want to alter all coordinates, so Internal coordinates can be filtered for relevant ones (filter_subset) and there are coordinates that we don’t want to alter, but we need to make sure that they are correctly set (constant_coordinates)

update(coords: dict) → None¶: Update internal coordinates with (subset of) internal coordinates

combine(coords: dict) → None¶: Combine internal coordinates with (subset of) internal coordinates

variable_coordinates(molecule: tqchem.molgraph.MolecularSystem, atom_order: list[int]) → InternalCoordinates¶

Get subset of coordinates which are relevant/varied during conformer search

atom_order is a list of atom ids in the graph and determines the order in which the variables will be listed in the subset

constant_coordinates(molecule: tqchem.molgraph.MolecularSystem) → InternalCoordinates¶

Get subset of coordinates which need to stay constant during conformer search

This entails for example improper dihedrals for bonds going into and out of a ring, as well as bond lengths and bond angles

make_grid(**kwargs) → None¶: Make a discrete grid for each coordinate of each component.

evaluate_grid(indices: dict[tuple[int, Ellipsis], list[int]]) → InternalCoordinates¶

Evaluate indices on the grids and update the internal coordinates with the new values

indices: dict[tuple[int, …], list[int]: Maps atom indices of the components to a list of indices for each coordinate in the component

grid_range() → dict[tuple[int, Ellipsis], list[range]]¶: Return grid ranges for each component

class tqchem.internal_coordinates.MolecularGrid(molecule: tqchem.molgraph.MolecularSystem, shift_by_reference: bool = False, **bond_grids)¶

Grid representation of the conformers of a system

molecule¶

Graph representation of the molcule and interface to ase to modify the atom positions

Type:: Molecular System

variables¶

Subset of the InternalCoordinates of the system (mainly Dihedrals and puckering coordinates) which are represented on the grid, to perform Conformer Search.

Type:: InternalCoordinates

constant_coordinates¶

Subset of InternalCoordinates (Bonds, Angles, improper Dihedrals used for the connection of Rings) which should not change during the Conformer Search, but need to be set to make sure they remain the same.

Type:: InternalCoordinates

__call__:: Return new molecule based on the gridpoints received on input

shape:: Return range of indices for each element of the Molecular Grid

n_variables:: Return number of variable elements in the Molecular Grid

variable_atom_indices:: Return list of the variable elements in the Molecular Grid

closest_gridpoint:: Get grid point closest to the geometry/molecule system provided on input

molecule: _typeshed.Incomplete¶

variables: _typeshed.Incomplete¶

constant_coordinates: _typeshed.Incomplete¶

__call__(superidx: list[int]) → tqchem.molgraph.MolecularSystem¶

Construct new molecular system based on the incoming indices

Indices are delinearized to match the structure of the internal coordinates. The variables are updated (e.g. with new dihedral values), combined with the constants, and converted to a new MolecularSystem with xyz coordinates.

Parameters:: superidx (list[int]) – List of indices, one for each variable coordinate

shape() → list[int]¶

n_variables()¶

variable_atom_indices() → list[str]¶: Convenient way to get string representation of the variables of the grid

closest_gridpoint(molecule: tqchem.molgraph.MolecularSystem) → list[int]¶: Return the gridpoint most similar to the provided molecule

tqchem.internal_coordinates.linearize(dictionary: dict[Any, Iterable]) → list[Any]¶

Converts dictionary values (Iterables) into a one-dimensional list

Used to convert a dictionary relating components to a list of ranges for the component’s variables to a list which only contains the ranges

Example: Three components with 2, 1 and 0 dihedrals

>>> dictionary = {
        (0, 1, 2, 3, 4, 5): [range(0, 12), range(0, 10)],
        (6, 7, 8, 9): [range(0, 8)],
        (10): [],
    }
>>> linearize(dictionary)
[range(0, 12), range(0, 10), range(0, 8)]

tqchem.internal_coordinates.indices_to_components(indices: list[int], component_ranges: dict[tuple[int], list[range]])¶

Assign list of indices to the variables of the components

component_ranges is a dict mapping each component to a list containing as many ranges as there are variables in the component. This function returns an equivalent dict, but the ranges are replaced with the indices.

tqchem.internal_coordinates.internal_to_xyz(molecule: tqchem.molgraph.MolecularSystem, coordinates: InternalCoordinates) → tqchem.molgraph.MolecularSystem¶

Transform internal coordinates to xyz coordinates.

Internal Coordinates can consist of multiple components (BAT, puckering, BAT, …)

tqchem.internal_coordinates.xyz_to_internal(molecule: tqchem.molgraph.MolecularSystem) → InternalCoordinates¶

Transform xyz coordinates to internal coordinates.

Internal Coordinates can consist of multiple components (BAT, puckering, BAT, …)