Source code for mdtraj.geometry.angle

##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
#         Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################


import numpy as np

from mdtraj.geometry import _geometry, distance
from mdtraj.utils import ensure_type

__all__ = ["compute_angles"]


[docs] def compute_angles(traj, angle_indices, periodic=True, opt=True): """Compute the bond angles between the supplied triplets of indices in each frame of a trajectory. Parameters ---------- traj : Trajectory An mdtraj trajectory. angle_indices : np.ndarray, shape=(num_angles, 3), dtype=int Each row gives the indices of three atoms which together make an angle. periodic : bool, default=True If `periodic` is True and the trajectory contains unitcell information, we will treat angles that cross periodic images using the minimum image convention. opt : bool, default=True Use an optimized native library to calculate distances. Our optimized SSE angle calculation implementation is 10-20x faster than the (itself optimized) numpy implementation. Returns ------- angles : np.ndarray, shape=[n_frames, n_angles], dtype=float The angles are in radians """ xyz = ensure_type( traj.xyz, dtype=np.float32, ndim=3, name="traj.xyz", shape=(None, None, 3), warn_on_cast=False, ) triplets = ensure_type( angle_indices, dtype=np.int32, ndim=2, name="angle_indices", shape=(None, 3), warn_on_cast=False, ) if not np.all(np.logical_and(triplets < traj.n_atoms, triplets >= 0)): raise ValueError("angle_indices must be between 0 and %d" % traj.n_atoms) if len(triplets) == 0: return np.zeros((len(xyz), 0), dtype=np.float32) out = np.zeros((xyz.shape[0], triplets.shape[0]), dtype=np.float32) if periodic is True and traj._have_unitcell: box = ensure_type( traj.unitcell_vectors, dtype=np.float32, ndim=3, name='unitcell_vectors', shape=(len(xyz), 3, 3), warn_on_cast=False, ) if opt: orthogonal = np.allclose(traj.unitcell_angles, 90) _geometry._angle_mic( xyz, triplets, box.transpose(0, 2, 1).copy(), out, orthogonal, ) return out else: _angle(traj, triplets, periodic, out) return out if opt: _geometry._angle(xyz, triplets, out) else: _angle(traj, triplets, periodic, out) return out
def _angle(traj, angle_indices, periodic, out): ix01 = angle_indices[:, [1, 0]] ix21 = angle_indices[:, [1, 2]] u_prime = distance.compute_displacements(traj, ix01, periodic=periodic, opt=False) v_prime = distance.compute_displacements(traj, ix21, periodic=periodic, opt=False) u_norm = np.sqrt((u_prime**2).sum(-1)) v_norm = np.sqrt((v_prime**2).sum(-1)) # adding a new axis makes sure that broasting rules kick in on the third # dimension u = u_prime / (u_norm[..., np.newaxis]) v = v_prime / (v_norm[..., np.newaxis]) # use np.clip() to guard against errors when angles approach 180 degrees: return np.arccos(np.clip((u * v).sum(-1), -1.0, 1.0), out=out)