Spatial

Useful utilities involving field of points.

calculate_distance_two_points(point1, point2)

Calculates the distance between two points in a 3D coordinate system.

PARAMETER	DESCRIPTION
point1	coordinates of first point. [x, y, z] TYPE: Sequence[float]
point2	coordinates of second point. [x, y, z] TYPE: Sequence[float]

RETURNS	DESCRIPTION
float	Distance between point1 and point2.

get_centroid(fop_pocket)

Calculates the centroid or the center of mass for equal masses of a field of points.

PARAMETER	DESCRIPTION
fop_pocket	the field of points defining the pocket shape. TYPE: Sequence[Sequence[float]]

RETURNS	DESCRIPTION
Sequence[float]	Coordinates of the pocket centroid.

get_rmsd(R, R_ref)

Compute the Root Mean Square Deviation (RMSD) between two sets of atomic coordinates.

RMSD is a measure of the average distance between atoms of two superimposed sets of coordinates. This function calculates RMSD without any alignment or fitting of the structures, assuming that the input arrays are already aligned.

PARAMETER	DESCRIPTION
R	A 2D array of shape (N, 3) representing the atomic coordinates. Each row corresponds to the coordinates of one atom. TYPE: ndarray
R_ref	A 2D array of shape (N, 3) representing the reference atomic coordinates. Each row corresponds to the coordinates of one atom. TYPE: ndarray

RETURNS	DESCRIPTION
float	The RMSD value between the two sets of atomic coordinates. TYPE: float

RAISES	DESCRIPTION
ValueError	If the input arrays R and R_ref do not have the same shape.

Example

R = np.array([[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]) R_ref = np.array([[1.1, 2.1, 3.1], [4.1, 5.1, 6.1]]) get_rmsd(R, R_ref) 0.1