def test_shape_when_none():
t = md.load(get_fn('frame0.h5'))
np.hstack((md.compute_phi(t)[1],
md.compute_psi(t)[1],
md.compute_chi1(t)[1],
md.compute_chi2(t)[1],
md.compute_chi3(t)[1],
md.compute_chi1(t)[1],
md.compute_omega(t)[1]))
def test_shape_when_none():
t = md.load(get_fn('frame0.h5'))
np.hstack((md.compute_phi(t)[1],
md.compute_psi(t)[1],
md.compute_chi1(t)[1],
md.compute_chi2(t)[1],
md.compute_chi3(t)[1],
md.compute_chi1(t)[1],
md.compute_omega(t)[1]))
def dataset_chi(traj):
dataset = []
indices, angles1 = md.compute_chi1(traj)
indices, angles2 = md.compute_chi2(traj)
indices, angles3 = md.compute_chi3(traj)
#indices,angles4 = md.compute_chi4(traj)
#print(angles1)
#print(type(angles1))
#print(len(angles1))
angles = np.concatenate((angles1, angles2, angles3), axis=1)
dataset.append(angles)
print("Done constructing dataset using chi angles")
return dataset
def __init__(self, mdtraj_trajectory):
WrappedPose.__init__(self)
if md is None:
print(
"MDTrajPoseWrapper requires the mdtraj library to be installed"
)
raise ImportError
assert isinstance(mdtraj_trajectory, md.Trajectory)
assert mdtraj_trajectory.n_frames == 1
self.trajectory = mdtraj_trajectory
# RADIANS:
self.phi_atoms, self.phis = md.compute_phi(self.trajectory)
self.psi_atoms, self.psis = md.compute_psi(self.trajectory)
self.chis = [None, None, None, None,
None] # Adding zero element just to make indexing easier
self.chi_atoms = [None, None, None, None, None]
self.chi_atoms[1], self.chis[1] = md.compute_chi1(self.trajectory)
self.chi_atoms[2], self.chis[2] = md.compute_chi2(self.trajectory)
self.chi_atoms[3], self.chis[3] = md.compute_chi3(self.trajectory)
self.chi_atoms[4], self.chis[4] = md.compute_chi4(self.trajectory)
# define a featurizer
feat = coor.featurizer(topology)
# define basis functions: heavy-atom contact distances, heavy atom coordinates, all torsions
print('define basis functions: heavy-atom contact distances, heavy atom coordinates, all torsions, inverse distances')
print('\n')
sys.stdout.flush()
featurizer = coor.featurizer(topology)
featurizer.add_residue_mindist(residue_pairs='all', scheme='closest-heavy')
featurizer.add_all()
featurizer.add_backbone_torsions(cossin=True)
featurizer.add_chi1_torsions(cossin=True)
indx = md.compute_chi2(traj)[0]
featurizer.add_dihedrals(indx, cossin=True)
indx = md.compute_chi3(traj)[0]
featurizer.add_dihedrals(indx, cossin=True)
indx = md.compute_chi4(traj)[0]
featurizer.add_dihedrals(indx, cossin=True)
indx = md.compute_omega(traj)[0]
featurizer.add_dihedrals(indx, cossin=True)
indx = md.compute_contacts(traj,contacts='all',scheme='closest-heavy')[1]
featurizer.add_custom_func(one_over_d, np.shape(indx)[0])
print(featurizer.describe())
print(featurizer.dimension())
sys.stdout.flush()
# use featurizer to read in trajectories
inp = coor.source([trajfile], featurizer, chunk_size=10000, stride=nskip)
def traj_dihedral_classes(trajin, dihedral_classes):
#
dihedrals_temp = None
dihedral_ids_temp = None
for dihedral_class in dihedral_classes:
#
#print("Loading {:s} angles...".format(dihedral_class))
if re.match("phi", dihedral_class):
#
phi_atoms, phi = md.compute_phi(trajin)
if dihedrals_temp is None:
#
dihedrals_temp = np.cos(phi)
dihedral_ids_temp = extract_res_info(trajin.top, phi_atoms,
"phi")
#
else:
#
dihedrals_temp = np.append(dihedrals_temp, np.cos(phi), axis=1)
dihedral_ids_temp = np.append(dihedral_ids_temp,
extract_res_info(
trajin.top, phi_atoms,
"phi"),
axis=0)
#
#
if re.match("psi", dihedral_class):
#
psi_atoms, psi = md.compute_psi(trajin)
if dihedrals_temp is None:
#
dihedrals_temp = np.sin(psi)
dihedral_ids_temp = extract_res_info(trajin.top, psi_atoms,
"psi")
#
else:
#
dihedrals_temp = np.append(dihedrals_temp, np.sin(psi), axis=1)
dihedral_ids_temp = np.append(dihedral_ids_temp,
extract_res_info(
trajin.top, psi_atoms,
"psi"),
axis=0)
#
#
if re.match("chi1", dihedral_class):
#
chi1_atoms, chi1 = md.compute_chi1(trajin)
if dihedrals_temp is None:
#
dihedrals_temp = np.sin(chi1)
dihedral_ids_temp = extract_res_info(trajin.top, chi1_atoms,
"chi1")
#
else:
#
dihedrals_temp = np.append(dihedrals_temp,
np.sin(chi1),
axis=1)
dihedral_ids_temp = np.append(dihedral_ids_temp,
extract_res_info(
trajin.top, chi1_atoms,
"chi1"),
axis=0)
#
#
if re.match("chi2", dihedral_class):
#
chi2_atoms, chi2 = md.compute_chi2(trajin)
if dihedrals_temp is None:
#
dihedrals_temp = np.sin(chi2)
dihedral_ids_temp = extract_res_info(trajin.top, chi2_atoms,
"chi2")
#
else:
#
dihedrals_temp = np.append(dihedrals_temp,
np.sin(chi2),
axis=1)
dihedral_ids_temp = np.append(dihedral_ids_temp,
extract_res_info(
trajin.top, chi2_atoms,
"chi2"),
axis=0)
#
#
if re.match("chi3", dihedral_class):
#
chi3_atoms, chi3 = md.compute_chi3(trajin)
if dihedrals_temp is None:
#
dihedrals_temp = np.sin(chi3)
dihedral_ids_temp = extract_res_info(trajin.top, chi3_atoms,
"chi3")
#
else:
#
dihedrals_temp = np.append(dihedrals_temp,
np.sin(chi3),
axis=1)
dihedral_ids_temp = np.append(dihedral_ids_temp,
extract_res_info(
trajin.top, chi3_atoms,
"chi3"),
axis=0)
#
#
if re.match("chi4", dihedral_class):
#
chi4_atoms, chi4 = md.compute_chi4(trajin)
if dihedrals_temp is None:
#
dihedrals_temp = np.sin(chi4)
dihedral_ids_temp = extract_res_info(trajin.top, chi4_atoms,
"chi4")
#
else:
#
dihedrals_temp = np.append(dihedrals_temp,
np.sin(chi4),
axis=1)
dihedral_ids_temp = np.append(dihedral_ids_temp,
extract_res_info(
trajin.top, chi4_atoms,
"chi4"),
axis=0)
#
#
if dihedral_class is None:
#
raise Exception(
"Feature format \"{:s}\" is invalid in a dihedral class measurement context."
.format(dihedral_class))
#
#
return (dihedrals_temp, dihedral_ids_temp)
files = open(main_files, 'w')
char = ''
for frame_cur in range(0, frame):
for index in range(0, angle_mount):
phi_cur = phi[1][frame_cur][index]
psi_cur = psi[1][frame_cur][index]
char = '%10.6lf %10.6lf %s' % (phi_cur, psi_cur, char)
char = '%s \n' % (char)
files.write(char)
char = ''
files.close()
files = open(side_files, 'w')
chi1 = md.compute_chi1(traj)
chi2 = md.compute_chi2(traj)
chi3 = md.compute_chi3(traj)
chi4 = md.compute_chi4(traj)
for frame_cur in range(0, frame):
for index in range(0, len(chi1[0])):
chi_cur = chi1[1][frame_cur][index]
char = '%10.6lf %s' % (chi_cur, char)
for index in range(0, len(chi2[0])):
chi_cur = chi2[1][frame_cur][index]
char = '%10.6lf %s' % (chi_cur, char)
for index in range(0, len(chi3[0])):
chi_cur = chi3[1][frame_cur][index]
char = '%10.6lf %s' % (chi_cur, char)
for index in range(0, len(chi4[0])):
chi_cur = chi4[1][frame_cur][index]
char = '%10.6lf %s' % (chi_cur, char)
char = '%s \n' % (char)
