Loading deepchem/utils/geometry_utils.py +56 −0 Original line number Diff line number Diff line Loading @@ -3,6 +3,7 @@ Geometric utility functions for 3D geometry. """ import logging import numpy as np from scipy.spatial.distance import cdist logger = logging.getLogger(__name__) Loading Loading @@ -110,3 +111,58 @@ def is_angle_within_cutoff(vector_i, vector_j, angle_cutoff): """ angle = angle_between(vector_i, vector_j) * 180. / np.pi return (angle > (180 - angle_cutoff) and angle < (180. + angle_cutoff)) def compute_centroid(coordinates): """Compute the (x,y,z) centroid of provided coordinates Parameters ---------- coordinates: np.ndarray Shape `(N, 3)`, where `N` is the number of atoms. """ centroid = np.mean(coordinates, axis=0) return (centroid) def subtract_centroid(xyz, centroid): """Subtracts centroid from each coordinate. Subtracts the centroid, a numpy array of dim 3, from all coordinates of all atoms in the molecule Note that this update is made in place to the array it's applied to. Parameters ---------- xyz: numpy array Of shape `(N, 3)` centroid: numpy array Of shape `(3,)` """ xyz -= np.transpose(centroid) return (xyz) def compute_pairwise_distances(first_xyz, second_xyz): """Computes pairwise distances between two molecules. Takes an input (m, 3) and (n, 3) numpy arrays of 3D coords of two molecules respectively, and outputs an m x n numpy array of pairwise distances in Angstroms between the first and second molecule. entry (i,j) is dist between the i"th atom of first molecule and the j"th atom of second molecule. Parameters ---------- first_xyz: np.ndarray Of shape (m, 3) seocnd_xyz: np.ndarray Of shape (n, 3) Returns ------- np.ndarray of shape (m, n) """ pairwise_distances = cdist(first_xyz, second_xyz, metric='euclidean') return pairwise_distances Loading
deepchem/utils/geometry_utils.py +56 −0 Original line number Diff line number Diff line Loading @@ -3,6 +3,7 @@ Geometric utility functions for 3D geometry. """ import logging import numpy as np from scipy.spatial.distance import cdist logger = logging.getLogger(__name__) Loading Loading @@ -110,3 +111,58 @@ def is_angle_within_cutoff(vector_i, vector_j, angle_cutoff): """ angle = angle_between(vector_i, vector_j) * 180. / np.pi return (angle > (180 - angle_cutoff) and angle < (180. + angle_cutoff)) def compute_centroid(coordinates): """Compute the (x,y,z) centroid of provided coordinates Parameters ---------- coordinates: np.ndarray Shape `(N, 3)`, where `N` is the number of atoms. """ centroid = np.mean(coordinates, axis=0) return (centroid) def subtract_centroid(xyz, centroid): """Subtracts centroid from each coordinate. Subtracts the centroid, a numpy array of dim 3, from all coordinates of all atoms in the molecule Note that this update is made in place to the array it's applied to. Parameters ---------- xyz: numpy array Of shape `(N, 3)` centroid: numpy array Of shape `(3,)` """ xyz -= np.transpose(centroid) return (xyz) def compute_pairwise_distances(first_xyz, second_xyz): """Computes pairwise distances between two molecules. Takes an input (m, 3) and (n, 3) numpy arrays of 3D coords of two molecules respectively, and outputs an m x n numpy array of pairwise distances in Angstroms between the first and second molecule. entry (i,j) is dist between the i"th atom of first molecule and the j"th atom of second molecule. Parameters ---------- first_xyz: np.ndarray Of shape (m, 3) seocnd_xyz: np.ndarray Of shape (n, 3) Returns ------- np.ndarray of shape (m, n) """ pairwise_distances = cdist(first_xyz, second_xyz, metric='euclidean') return pairwise_distances
