def ComputeDihedralsFromTrajectory(Trajectory):
"""
Compute dihedrals directly from trajectory files.
"""
traj = {}
traj['XYZList'] = Trajectory['XYZList']/1.0 #convert XYZList to float type
indices = dihedral.get_indices(Trajectory,'phi/psi')
dihedrals = dihedral.compute_dihedrals(traj,indices,'phi/psi')
return dihedrals
def extract_dihedral(project, close, stride, types=None, indices=None, far=None):
if indices is None:
indices = dihedralcalc.get_indices(project.empty_traj(), types)
# get trajectories for A, B, C
A,B,C = triplets(project, close, stride, far)
metric = metrics.Dihedral(indices=indices)
A = metric.prepare_trajectory(A)
B = metric.prepare_trajectory(B)
C = metric.prepare_trajectory(C)
return A-B, A-C
def prepare_trajectory(self, trajectory):
"""Prepare the dihedral angle representation of a trajectory, suitable
for distance calculations.
Parameters
----------
trajectory : msmbuilder.Trajectory
An MSMBuilder trajectory to prepare
Returns
-------
projected_angles : ndarray
A 2D array of dimension len(trajectory) x (2*number of dihedral
angles per frame), such that in each row, the first half of the entries
contain the cosine of the dihedral angles and the later dihedral angles
contain the sine of the dihedral angles. This transform is necessary so
that distance calculations preserve the periodic symmetry.
"""
traj_length = len(trajectory['XYZList'])
if self.angles=='user':
indices = self.read_dihedral_indices(self.userfilename)
else:
if self.indices is None:
indices = _dihedralcalc.get_indices(trajectory, self.angles)
else:
indices = self.indices
dihedrals = _dihedralcalc.compute_dihedrals(trajectory, indices, degrees=False)
# these dihedrals go between -pi and pi but obviously because of the
# periodicity, when we take distances we want the distance between -179
# and +179 to be very close, so we need to do a little transform
num_dihedrals = dihedrals.shape[1]
transformed = np.empty((traj_length, 2 * num_dihedrals))
transformed[:, 0:num_dihedrals] = np.cos(dihedrals)
transformed[:, num_dihedrals:2*num_dihedrals] = np.sin(dihedrals)
return np.double(transformed)
def prepare_trajectory(self, trajectory):
"""Prepare the dihedral angle representation of a trajectory, suitable
for distance calculations.
Parameters
----------
trajectory : msmbuilder.Trajectory
An MSMBuilder trajectory to prepare
Returns
-------
projected_angles : ndarray
A 2D array of dimension len(trajectory) x (2*number of dihedral
angles per frame), such that in each row, the first half of the entries
contain the cosine of the dihedral angles and the later dihedral angles
contain the sine of the dihedral angles. This transform is necessary so
that distance calculations preserve the periodic symmetry.
"""
traj_length = len(trajectory['XYZList'])
if self.indices is None:
indices = _dihedralcalc.get_indices(trajectory, self.angles)
else:
indices = self.indices
dihedrals = _dihedralcalc.compute_dihedrals(trajectory,
indices,
degrees=False)
# these dihedrals go between -pi and pi but obviously because of the
# periodicity, when we take distances we want the distance between -179
# and +179 to be very close, so we need to do a little transform
num_dihedrals = dihedrals.shape[1]
transformed = np.empty((traj_length, 2 * num_dihedrals))
transformed[:, 0:num_dihedrals] = np.cos(dihedrals)
transformed[:, num_dihedrals:2 * num_dihedrals] = np.sin(dihedrals)
return np.double(transformed)
import numpy as np
from msmbuilder import Trajectory
from msmbuilder.geometry import dihedral
ff_list = ["amber96","amber99","amber99sbnmr-ildn","oplsaa","charmm27"]
for ff in ff_list:
print(ff)
directory = "/home/kyleb/dat/lvbp/%s/" % ff
R = Trajectory.load_from_xtc([directory + "/production/trajout.xtc"],directory + "/final.pdb")
ind = dihedral.get_indices(R)
di = dihedral.compute_dihedrals(R,ind).T
phi = di[0]
psi = di[3]
data = np.array([phi,psi])
np.savez_compressed(directory + "/rama.npz", data)
"""
ff = "amber99"
R = Trajectory.load_from_xtc(["/home/kyleb/dat/lvbp/GA-%s/md/trajout.xtc"%ff],"/home/kyleb/dat/lvbp/GA-%s/equil/native.pdb"%ff)
ind = dihedral.get_indices(R)
di = dihedral.compute_dihedrals(R,ind)
io.saveh("/home/kyleb/dat/lvbp/GA-%s/rama.h5"%ff,di)
"""
