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 run_corr(args):
print "reading trajectory"
traj = md.load(args.input_traj, top=args.pdb_file)
if args.feature_type == "positions":
print "aligning frames"
backbone = traj.topology.select_atom_indices("minimal")
traj.superpose(traj, atom_indices=backbone)
print "computing displacements"
alpha_carbons = traj.topology.select_atom_indices("alpha")
traj = traj.atom_slice(alpha_carbons)
features = np.sqrt(
np.sum((traj.xyz - np.mean(traj.xyz, axis=0))**2, axis=2))
elif args.feature_type == "dihedrals":
_, phi_angles = md.compute_phi(traj, periodic=False)
_, psi_angles = md.compute_psi(traj, periodic=False)
features = np.vstack([phi_angles, psi_angles])
elif args.feature_type == "transformed-dihedrals":
_, phi_angles = md.compute_phi(traj, periodic=False)
_, psi_angles = md.compute_psi(traj, periodic=False)
phi_sin = np.sin(phi_angles)
phi_cos = np.cos(phi_angles)
psi_sin = np.sin(psi_angles)
psi_cos = np.cos(psi_angles)
features = np.vstack([phi_sin, phi_cos, psi_sin, psi_cos])
elif args.feature_type == "transformed-chi-dihedrals":
_, chi_angles = md.compute_chi1(traj, periodic=False)
chi_sin = np.sin(chi_angles)
chi_cos = np.cos(chi_angles)
features = np.vstack([chi_sin, chi_cos])
print features.shape
print "Computing correlation matrix"
corr = np.corrcoef(features, rowvar=False)
print "Plotting correlation matrix"
if args.plot_type == "heatmap":
plt.pcolor(corr, vmin=-1.0, vmax=1.0)
plt.colorbar()
plt.tight_layout()
elif args.plot_type == "distribution":
import seaborn as sns
sns.distplot(np.ravel(corr), kde=False)
plt.xlabel("Correlation", fontsize=16)
plt.ylabel("Occurrences", fontsize=16)
plt.savefig(args.figure_fl, DPI=300)
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)
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)
def extract_features(args):
print "reading trajectory"
traj = md.load(args.input_traj,
top=args.pdb_file)
if args.select_residues:
selections = []
ranges = args.select_residues.split(",")
for range_ in args.select_residues.split(","):
if "-" in range_:
left, right = map(int, range_.split("-"))
selections.append("(residue %s to %s)" % (left, right))
else:
singleton = int(range_)
selections.append("(residue %s)" % singleton)
selection_str = " or ".join(selections)
selected_atoms = traj.topology.select(selection_str)
traj = traj.atom_slice(selected_atoms)
if args.feature_type == "positions":
print "aligning frames"
traj.superpose(traj)
features = traj.xyz.reshape(traj.n_frames,
traj.n_atoms * 3)
elif args.feature_type == "transformed-dihedrals":
print "computing dihedrals"
_, phi_angles = md.compute_phi(traj,
periodic=False)
_, psi_angles = md.compute_psi(traj,
periodic=False)
phi_sin = np.sin(phi_angles)
phi_cos = np.cos(phi_angles)
psi_sin = np.sin(psi_angles)
psi_cos = np.cos(psi_angles)
features = np.hstack([phi_sin,
phi_cos,
psi_sin,
psi_cos])
elif args.feature_type == "transformed-dihedrals-chi":
print "computing dihedrals"
_, phi_angles = md.compute_phi(traj,
periodic=False)
_, psi_angles = md.compute_psi(traj,
periodic=False)
_, chi_angles = md.compute_chi1(traj,
periodic=False)
phi_sin = np.sin(phi_angles)
phi_cos = np.cos(phi_angles)
psi_sin = np.sin(psi_angles)
psi_cos = np.cos(psi_angles)
chi_sin = np.sin(chi_angles)
chi_cos = np.cos(chi_angles)
features = np.hstack([phi_sin,
phi_cos,
psi_sin,
psi_cos,
chi_sin,
chi_cos])
elif args.feature_type == "residue-residue-distances":
print "computing residue-residue distances"
features, _ = md.compute_contacts(traj,
scheme="ca",
periodic=False)
elif args.feature_type == "inverse-residue-residue-distances":
print "computing inverse residue-residue distances"
features, _ = md.compute_contacts(traj,
scheme="ca",
periodic=False)
features = np.reciprocal(features)
else:
raise Exception, "Unknown feature type '%s'", args.features
return features, args.feature_type
frame = len(phi[1])
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]
def compare_dihedral_distributions(args):
msm = joblib.load(args.msm_model_file)
print "reading trajectory"
traj = md.load(args.input_traj,
top=args.pdb_file)
print "computing dihedrals"
if args.angle_type == "phi-psi":
_, phi_angles = md.compute_phi(traj,
periodic=False)
_, psi_angles = md.compute_psi(traj,
periodic=False)
# first residue has no phi angle
# last residue has no psi angle
# so we only have pairs for residues 1 to n - 2
angles = np.stack([phi_angles[:, :-1],
psi_angles[:, 1:]],
axis=2)
# 1-based indexing
resids = range(2, traj.n_residues)
elif args.angle_type == "chi":
atom_indices, chi_angles = md.compute_chi1(traj,
periodic=False)
angles = chi_angles.reshape(chi_angles.shape[0],
chi_angles.shape[1],
-1)
# not all residues have chi dihedrals
top = traj.topology
# convert to 1-based indexing
resids = [top.atom(atoms[0]).residue.index + 1 for atoms in atom_indices]
for state_1 in xrange(msm.n_states - 1):
state_1_frames = [idx for idx, state in enumerate(msm.labels) \
if state == state_1]
state_1_angles = angles[state_1_frames, :, :]
for state_2 in xrange(state_1 + 1, msm.n_states):
if msm.sym_counts[state_1, state_2] > 0:
print "Testing State %s vs State %s" % (state_1, state_2)
state_2_frames = [idx for idx, state in enumerate(msm.labels) \
if state == state_2]
state_2_angles = angles[state_2_frames, :, :]
pvalues = test_residue_dihedral_distributions(state_1_angles,
state_2_angles,
args.n_bins)
if len(pvalues) != len(resids):
raise Exception("Number of residue ids (%s) and p-values (%s) mismatched" % (len(resids), len(pvalues)))
residue_pvalues = zip(resids,
pvalues)
flname = os.path.join(args.output_dir,
"state_dihedral_tests_%s_%s_%s.tsv" % (args.angle_type,
state_1,
state_2))
with open(flname, "w") as fl:
for resid, pvalue in residue_pvalues:
fl.write("%s\t%s\n" % (resid, pvalue))