vermouth.geometry module

Geometric operations.

vermouth.geometry.angle(vector_ba, vector_bc)

Calculate the angle in radians between two vectors.

The function assumes the following situation:

  B
 / \
A   C

It returns the angle between BA and BC.

vermouth.geometry.dihedral(coordinates)

Calculate the dihedral angle in radians.

Parameters:

coordinates (numpy.ndarray) – The coordinates of 4 points defining the dihedral angle. Each row corresponds to a point, and each column to a dimension.

Returns:

The calculated angle between -pi and +pi.

Return type:

float

vermouth.geometry.dihedral_phase(coordinates)

Calculate a dihedral angle in radians with a -pi phase correction.

Parameters:

coordinates (numpy.ndarray) – The coordinates of 4 points defining the dihedral angle. Each row corresponds to a point, and each column to a dimension.

Returns:

The calculated angle between -pi and +pi.

Return type:

float

See also

dihedral

Calculate a dihedral angle.

vermouth.geometry.distance_matrix(coordinates_a, coordinates_b)

Compute a distance matrix between two set of points.

Notes

This function does not account for periodic boundary conditions.

Parameters:

• coordinates_a (numpy.ndarray) – Coordinates of the points in the selections. Each row must correspond to a point and each column to a dimension.

• coordinates_b (numpy.ndarray) – Coordinates of the points in the selections. Each row must correspond to a point and each column to a dimension.

Returns:

Rows correspond to the points from coordinates_a, columns correspond from coordinates_b.

Return type:

numpy.ndarray