vermouth.geometry module¶
Geometric operations.

vermouth.geometry.
angle
(vector_ba, vector_bc)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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: