def test_angle_pbc_0():
# Check that angles are calculated correctly accross periodic boxes
random = np.random.RandomState(0)
boxLengths = [1,2,3]
N = 1000
X = np.cumsum(0.1 * random.randn(N*3, 3), axis=0).reshape(N, 3, 3)
center = X.mean(axis=1).reshape(N, 1, 3)
cell = np.floor(center / boxLengths)
X_cell = X - (cell * boxLengths)
assert not np.all(X == X_cell)
t0 = md.Trajectory(xyz=X, topology=None)
t1 = md.Trajectory(xyz=X_cell, topology=None)
t1.unitcell_vectors = np.tile(np.diag(boxLengths), [len(X), 1, 1])
r0 = md.compute_angles(t0, [[0,1,2]], opt=False).reshape(-1)
r1 = md.compute_angles(t1, [[0,1,2]], opt=False).reshape(-1)
r2 = md.compute_angles(t0, [[0,1,2]], opt=True).reshape(-1)
r3 = md.compute_angles(t1, [[0,1,2]], opt=True).reshape(-1)
np.testing.assert_array_almost_equal(r0, r1, decimal=4)
np.testing.assert_array_almost_equal(r2, r3, decimal=4)
np.testing.assert_array_almost_equal(r0, r3, decimal=4)
def test_generator():
N_FRAMES = 2
N_ATOMS = 5
xyz = np.asarray(np.random.randn(N_FRAMES, N_ATOMS, 3), dtype=np.float32)
ptraj = md.Trajectory(xyz=xyz, topology=None)
triplets = np.array(list(itertools.combinations(range(N_ATOMS), 3)), dtype=np.int32)
triplets2 = itertools.combinations(range(N_ATOMS), 3)
a = md.compute_angles(ptraj, triplets)
b = md.compute_angles(ptraj, triplets2)
eq(a, b)
def water_nbr_orientations(self, traj, water, nbrs):
"""Calculates orientations of the neighboring water molecules of a given water molecule. The orientation is
defined as the miniumum of four possible Donor-H-Acceptor angles.
Parameters
----------
traj : md.trajectory
MDTraj trajectory object for which hydrogen bonds are to be calculates.
water : int
The index of water oxygen atom
nbrs : np.ndarray, int, shape=(N^{ww}_nbr, )
Indices of the water oxygen or solute atoms in the first solvation shell of the water molecule.
Returns
-------
wat_orientations : np.ndarray
Array of angles between the given and each one of its neighbors
"""
angle_triplets = []
for wat_nbr in nbrs:
angle_triplets.extend([[water, wat_nbr, wat_nbr + 1],
[water, wat_nbr, wat_nbr + 2],
[wat_nbr, water, water + 1],
[wat_nbr, water, water + 2]])
angle_triplets = np.asarray(angle_triplets)
angles = md.compute_angles(traj, angle_triplets)
angles[np.isnan(angles)] = 0.0
wat_orientations = [
np.rad2deg(np.min(angles[0, i * 4:(i * 4) + 4]))
for i in range(nbrs.shape[0])
]
return wat_orientations
def extract_Q_indxd(frame, neighbors, idx_A, species_indx):
"""
Handy for calculating the Q order parameter for
a specific species in the simulation (e.g. for
HOD vs H2O oxygens.
NOTE: species_indx is 1-indexed
neighbors contains 0-indexed location in idx_A
idx_A contains 0-indexed global index of the oxygen atoms
"""
triplet_list = []
neighbors = idx_A[neighbors]
target_Os = species_indx - 1
for i in range(len(neighbors)):
tagged = idx_A[i]
# Only want to calculate Qs for the target Os
if tagged in target_Os:
neighs = [O for O in neighbors[i] if not O == tagged]
for j in range(3):
for k in range(j+1,4):
trio = (neighs[j], tagged, neighs[k])
triplet_list.append(trio)
triplet_list = np.array(triplet_list, dtype=int)
angle_in_rad = md.compute_angles(frame, triplet_list, opt=True).reshape(-1, 6)
sum_elements = np.sum(np.square(np.cos(angle_in_rad) + 1./3.), axis=1)
Qs = (1. - 3./8. * sum_elements).reshape(-1, len(species_indx))
return Qs
def water_nbr_orientations(self, traj, water, nbrs):
"""Calculates hydrogen bonds made by a water molecule with its first shell
water and solute neighbors.
Parameters
----------
traj : md.trajectory
MDTraj trajectory object for which hydrogen bonds are to be calculates.
water : int
The index of water oxygen atom
nbrs : np.ndarray, int, shape=(N^{ww}_nbr, )
Indices of the water oxygen or solute atoms in the first solvation shell of the water molecule.
water_water : bool
Boolean for whether water-water or solute-water hbonds are desired
Returns
-------
hbonds : np.ndarray
Array of hydrogen bonds where each hydrogen bond is represented by an array of indices
of three participating atoms [Donor, H, Acceptor]
"""
angle_triplets = []
for wat_nbr in nbrs:
angle_triplets.extend(
[[water, wat_nbr, wat_nbr + 1], [water, wat_nbr, wat_nbr + 2], [wat_nbr, water, water + 1],
[wat_nbr, water, water + 2]])
angle_triplets = np.asarray(angle_triplets)
angles = md.compute_angles(traj, angle_triplets)
angles[np.isnan(angles)] = 0.0
wat_orientations = [np.rad2deg(np.min(angles[0, i*4:(i*4)+4])) for i in range(nbrs.shape[0])]
return wat_orientations
def test_no_indices():
for fn in ['2EQQ.pdb', '1bpi.pdb']:
for opt in [True, False]:
t = md.load(get_fn(fn))
assert md.compute_distances(t, np.zeros((0,2), dtype=int), opt=opt).shape == (t.n_frames, 0)
assert md.compute_angles(t, np.zeros((0,3), dtype=int), opt=opt).shape == (t.n_frames, 0)
assert md.compute_dihedrals(t, np.zeros((0,4), dtype=int), opt=opt).shape == (t.n_frames, 0)
def test_angle_nan():
t = md.Trajectory(topology=None, xyz=np.array([
[0, 0, 0.2],
[0, 0, 0.3],
[0, 0, 0.0]
]))
angles = md.compute_angles(t, [[0, 1, 2]], opt=True)
np.testing.assert_array_almost_equal(angles, [[0]])
def hbond(traj,donor,acceptor,hydrogen,angle):
#function that returns whether a hydrogen bond exists between a given set of
#candidates for the donor, the acceptor, and the hydrogen
#assumes that the donor-acceptor distance is already within the correct limit
#so simply checks the angle
#angle should be in radians
dhang = md.compute_angles(traj,np.array([[donor,hydrogen,acceptor]]))
return (dhang[0,0] > angle)
def transform(self, traj):
rad = mdtraj.compute_angles(traj, self.angle_indexes, self.periodic)
if self.cossin:
rad = np.dstack((np.cos(rad), np.sin(rad)))
rad = rad.reshape(rad.shape[0], rad.shape[1] * rad.shape[2])
if self.deg and not self.cossin:
return np.rad2deg(rad)
else:
return rad
def compute_angles(self, angle_indices):
"""
:param angle_indices: Each row gives the indices of three atoms which together make an angle (np.ndarray, shape=(num_angles, 3), dtype=int)
:return: The angles are in radians (np.ndarray, shape=[n_frames, n_angles], dtype=float)
"""
return md.compute_angles(self.traj, angle_indices)
def calc_angles(self, triplets, range=None):
quantity = md.compute_angles(self.traj, triplets)
hist, edges = np.histogram(quantity,
density=True,
range=range,
bins=200)
bins = (edges[1:] + edges[:-1]) * 0.5
hist /= np.sin(bins)
hist /= np.sum(hist) * (bins[1] - bins[0])
return bins, hist
def transform(self, traj):
rad = mdtraj.compute_angles(traj, self.angle_indexes, self.periodic)
if self.cossin:
rad = np.dstack((np.cos(rad), np.sin(rad)))
rad = rad.reshape(functools.reduce(lambda x, y: x * y,
rad.shape), )
if self.deg and not self.cossin:
return np.rad2deg(rad)
else:
return rad
def _add_sbm_angles(self, Model):
structure = Model.mapping
if hasattr(Model, "ref_traj"):
ka = self._default_parameters["ka"]
code = self._default_potentials["angle"]
for atm1, atm2, atm3 in structure._angles:
idxs = np.array([[atm1.index, atm2.index, atm3.index]])
theta0 = md.compute_angles(Model.ref_traj, idxs)[0][0]
self._add_angle(code, atm1, atm2, atm3, ka, theta0)
else:
util.missing_reference_warning()
def partial_transform(self, traj):
ca = [a.index for a in traj.top.atoms if a.name == 'CA']
if len(ca) < 5:
return np.zeros((len(traj), 0), dtype=np.float32)
angle_indices = np.array(
[(ca[i - 2], ca[i], ca[i + 2]) for i in range(2, len(ca) - 2)])
result = md.compute_angles(traj, angle_indices)
if self.cos:
return np.cos(result)
assert result.shape == (traj.n_frames, traj.n_residues - 4)
return result
def partial_transform(self, traj):
ca = [a.index for a in traj.top.atoms if a.name == 'CA']
if len(ca) < 5:
return np.zeros((len(traj), 0), dtype=np.float32)
angle_indices = np.array(
[(ca[i - 2], ca[i], ca[i + 2]) for i in range(2, len(ca) - 2)])
result = md.compute_angles(traj, angle_indices)
if self.cos:
return np.cos(result)
assert result.shape == (traj.n_frames, traj.n_residues - 4)
return result
def dangling(frame, dictionary, sign, dist, distOSN, idx, idxOSN, normals):
pair_ox = np.asarray(list(itertools.product(idx, idxOSN)))
# remove pairs of same index
pair_ox = pair_ox[np.std(pair_ox, axis=1) != 0]
dist_ox = md.compute_distances(frame, pair_ox).reshape(idx.size, -1)
h1o = np.c_[idx, idx + 1]
h2o = np.c_[idx, idx + 2]
# compute H-O vectors
vec_h1o = md.compute_displacements(frame, h1o).reshape(-1, 3)
vec_h2o = md.compute_displacements(frame, h2o).reshape(-1, 3)
cosine_h1o = np.einsum('ij,ij->i', vec_h1o, normals) / np.linalg.norm(
vec_h1o, axis=1)
cosine_h2o = np.einsum('ij,ij->i', vec_h2o, normals) / np.linalg.norm(
vec_h2o, axis=1)
angle_h1o = np.arccos(np.clip(cosine_h1o, -1, 1)) / np.pi * 180
angle_h2o = np.arccos(np.clip(cosine_h2o, -1, 1)) / np.pi * 180
h1ox = np.c_[np.asarray(pair_ox)[:, 0] + 1,
np.asarray(pair_ox)[:, 0],
np.asarray(pair_ox)[:, 1]]
h2ox = np.c_[np.asarray(pair_ox)[:, 0] + 2,
np.asarray(pair_ox)[:, 0],
np.asarray(pair_ox)[:, 1]]
# compute H-O...O angles
angle_h1ox = md.compute_angles(frame, h1ox).reshape(idx.size,
-1) / np.pi * 180
angle_h2ox = md.compute_angles(frame, h2ox).reshape(idx.size,
-1) / np.pi * 180
# selection of dangling OH based on R-beta definition (DOI: 10.1021/acs.jctc.7b00566)
Rc = dist_ox <= .35
beta1 = angle_h1ox <= 50
beta2 = angle_h2ox <= 50
angles_ho = np.append(angle_h1o[np.sum(beta1 * Rc, axis=1) == 0],
angle_h2o[np.sum(beta2 * Rc, axis=1) == 0])
dictionary['ndang'] = np.append(dictionary['ndang'], angles_ho.size)
dictionary['all'] = np.append(dictionary['all'], idx.size)
hist, _ = np.histogram(angles_ho, bins=np.arange(0, 181, 2), density=False)
dictionary['theta'] += hist
def gln_array(*args):
if len(args) == 4:
dihedral = np.array([[args[0], args[1], args[2], args[3]]])
gln_dihedral_array = md.compute_dihedrals(traj, dihedral)
return gln_dihedral_array
elif len(args) == 3:
angle = np.array([[args[0], args[1], args[2]]])
gln_angle_array = md.compute_angles(traj, angle)
return gln_angle_array
else:
print(
'The amount of arguments (number of atoms) is not compatible with the selected light state'
)
def angf(traj, residues, tol=15, ref=88):
tol = float(tol)
ref = float(ref)
minimum = np.amin(residues)
maximum = np.amax(residues)
ca = traj.topology.select('name CA and protein and resid %i to %i' %
(minimum, maximum))
indices = np.zeros([ca.shape[0] - 2, 3])
for i in range(indices.shape[0]):
indices[i] = ca[i:i + 3]
angles = md.compute_angles(traj, indices)
angles = angles / (2 * math.pi) * 360
angf = np.zeros(angles.shape)
angf[:, :] = 1 / (1 + (angles[:, :] - ref)**2 / tol**2)
return angf
def calc_coord(traj, idxs):
vals = np.zeros(traj.n_frames)
idxs = np.array(idxs)
NM_IN_ANG = 10.0
RAD_IN_DEG = 180.0/np.pi
if len(idxs) == 2:
vals = md.compute_distances(traj, idxs.reshape(1, -1))
vals *= NM_IN_ANG
elif len(idxs) == 3:
vals = md.compute_angles(traj, idxs.reshape(1, -1))
vals *= RAD_IN_DEG
elif len(idxs) == 4:
vals = md.compute_dihedrals(traj, idxs.reshape(1, -1))
vals *= RAD_IN_DEG
return vals[:, 0]
def calculate_hydrogen_bonds(self, traj, water, nbrs, water_water=True):
"""Calculates hydrogen bonds made by a water molecule with its first shell
water and solute neighbors.
Parameters
----------
traj : md.trajectory
MDTraj trajectory object for which hydrogen bonds are to be calculates.
water : int
The index of water oxygen atom
nbrs : np.ndarray
Indices of the water oxygen or solute atoms in the first solvation shell of the water molecule.
water_water : bool
Boolean for whether water-water or solute-water hbonds are desired
Returns
-------
hbonds : np.ndarray
Array of hydrogen bonds where each hydrogen bond is represented by an array of indices
of three participating atoms [Donor, H, Acceptor]
"""
hbond_data = []
angle_triplets = []
if water_water:
for wat_nbr in nbrs:
angle_triplets.extend([[water, wat_nbr, wat_nbr + 1],
[water, wat_nbr, wat_nbr + 2],
[wat_nbr, water, water + 1],
[wat_nbr, water, water + 2]])
else:
for solute_nbr in nbrs:
if self.prot_hb_types[solute_nbr] == 1 or self.prot_hb_types[
solute_nbr] == 3:
angle_triplets.extend([[solute_nbr, water, water + 1],
[solute_nbr, water, water + 2]])
if self.prot_hb_types[solute_nbr] == 2 or self.prot_hb_types[
solute_nbr] == 3:
for don_H_pair in self.don_H_pair_dict[solute_nbr]:
angle_triplets.extend(
[[water, solute_nbr, don_H_pair[1]]])
angle_triplets = np.asarray(angle_triplets)
angles = md.compute_angles(traj, angle_triplets)
angles[np.isnan(angles)] = 0.0
hbonds = angle_triplets[np.where(angles[0, :] <= ANGLE_CUTOFF_RAD)]
return hbonds
def test_KappaFeaturizer_describe_features():
feat = KappaAngleFeaturizer()
rnd_traj = np.random.randint(len(trajectories))
features = feat.transform([trajectories[rnd_traj]])
df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))
for f in range(25):
f_index = np.random.choice(len(df))
atom_inds = df.iloc[f_index].atominds
feature_value = md.compute_angles(trajectories[rnd_traj], [atom_inds])
if feat.cos:
func = getattr(np, '%s' % df.iloc[f_index].otherinfo)
feature_value = func(feature_value)
assert (features[0][:, f_index] == feature_value.flatten()).all()
def test_KappaFeaturizer_describe_features():
feat = KappaAngleFeaturizer()
rnd_traj = np.random.randint(len(trajectories))
features = feat.transform([trajectories[rnd_traj]])
df = pd.DataFrame(feat.describe_features(trajectories[rnd_traj]))
for f in range(25):
f_index = np.random.choice(len(df))
atom_inds = df.iloc[f_index].atominds
feature_value = md.compute_angles(trajectories[rnd_traj], [atom_inds])
if feat.cos:
func = getattr(np, '%s' % df.iloc[f_index].otherinfo)
feature_value = func(feature_value)
assert (features[0][:, f_index] == feature_value.flatten()).all()
def extract_Q(frame, neighbors, idx_A):
triplet_list = []
neighbors = idx_A[neighbors]
for i in range(len(neighbors)):
tagged = idx_A[i]
neighs = [O for O in neighbors[i] if not O == tagged]
for j in range(3):
for k in range(j+1,4):
trio = (neighs[j], tagged, neighs[k])
triplet_list.append(trio)
triplet_list = np.array(triplet_list, dtype=int)
angle_in_rad = md.compute_angles(frame, triplet_list, opt=True).reshape(-1, 6)
sum_elements = np.sum(np.square(np.cos(angle_in_rad) + 1./3.), axis=1)
Qs = (1. - 3./8. * sum_elements).reshape(-1, len(idx_A))
return Qs
def calculate_hydrogen_bonds2(self, traj, water, water_nbrs, solute_nbrs):
"""Calculates hydrogen bonds made by a water molecule with its first shell
water and solute neighbors.
Parameters
----------
traj : md.trajectory
MDTraj trajectory object for which hydrogen bonds are to be calculates.
water : int
The index of water oxygen atom
water_nbrs : np.ndarray, int, shape=(N^{ww}_nbr, )
Indices of the water oxygen atoms in the first solvation shell of the water molecule.
solute_nbrs : np.ndarray, int, shape=(N^{sw}_nbr, )
Indices of thesolute atoms in the first solvation shell of the water molecule.
Returns
-------
(hbonds_ww, hbonds_sw) : tuple
A tuple consisting of two np.ndarray objects for water-water and solute-water
hydrogen bonds. A hydrogen bond is represented by an array of indices
of three atom particpating in the hydrogen bond, [Donor, H, Acceptor]
"""
hbond_data = []
angle_triplets = []
for wat_nbr in water_nbrs:
angle_triplets.extend(
[[water, wat_nbr, wat_nbr + 1], [water, wat_nbr, wat_nbr + 2], [wat_nbr, water, water + 1],
[wat_nbr, water, water + 2]])
for solute_nbr in solute_nbrs:
if self.prot_hb_types[solute_nbr] == 1 or self.prot_hb_types[solute_nbr] == 3:
angle_triplets.extend([[solute_nbr, water, water + 1], [solute_nbr, water, water + 2]])
if self.prot_hb_types[solute_nbr] == 2 or self.prot_hb_types[solute_nbr] == 3:
for don_H_pair in self.don_H_pair_dict[solute_nbr]:
angle_triplets.extend([[water, solute_nbr, don_H_pair[1]]])
angle_triplets = np.asarray(angle_triplets)
angles = md.compute_angles(traj, np.asarray(angle_triplets))
angles[np.isnan(angles)] = 0.0
angles_ww = angles[0, 0:water_nbrs.shape[0] * 4]
angles_sw = angles[0, water_nbrs.shape[0] * 4:]
angle_triplets_ww = angle_triplets[:water_nbrs.shape[0] * 4]
angle_triplets_sw = angle_triplets[water_nbrs.shape[0] * 4:]
hbonds_ww = angle_triplets_ww[np.where(angles_ww <= ANGLE_CUTOFF_RAD)]
hbonds_sw = angle_triplets_sw[np.where(angles_sw <= ANGLE_CUTOFF_RAD)]
return (hbonds_ww, hbonds_sw)
def get_angles(self, angle_index):
"""calculate angles between three atoms for a trajectory
Parameters
----------
angle_index: list, shape=[n, 3]
the atom indices for angle calculations
Returns
-------
angles: ndarray, shape=[N, M]
angles, N is number of frames, M is the number
of the angles per frame
"""
angles = mt.compute_angles(self.traj, angle_indices=angle_index)
return angles
def get_internal_coordinates(top, coordinate_type, pca_traj, atom_indices):
'get the different types of internal coordinates as per user selections'
calpha_idx = top.select_atom_indices(atom_indices)
if coordinate_type == 'distance':
print('Pair wise atomic distance selected\n ')
atom_pairs = list(combinations(calpha_idx,
2)) # all unique pairs of elements
pairwise_distances = md.geometry.compute_distances(
pca_traj, atom_pairs)
int_cord = pairwise_distances
if coordinate_type == 'phi':
print('phi torsions selected\n')
atom_pairs = list(combinations(calpha_idx, 3))
angle = md.compute_phi(pca_traj)
int_cord = angle[
1] ## apparently compute_phi returns tupple of atoms indices and phi angles, index 1 has phi angles
if coordinate_type == 'psi':
print('psi torsions selected\n')
atom_pairs = list(combinations(calpha_idx, 3))
angle = md.compute_psi(pca_traj)
int_cord = angle[
1] ## apparently compute_psi returns tupple of atoms indices and psi angles, index 1 has psi angles
if coordinate_type == 'angle':
print('1-3 angle selected between N,CA and C')
nrow = len(top.select(
"name CA")) # to get the number of amino acid ignoring ligand etc.
ncol = 3
# make a matrix of N,CA, C index, each row index making bond
B = np.ones((nrow, ncol))
B[:, 0] = top.select('backbone and name N')
B[:, 1] = top.select('backbone and name CA')
B[:, 2] = top.select('backbone and name C')
# compute angle between N,CA, C
angle = md.compute_angles(pca_traj, B)
int_cord = angle
return int_cord
def tetra_struct_Q(frame, neighbors):
print('Computing tetrahedrality...')
Qs = []
for cluster in neighbors:
doub_sum = 0.
for i in range(3):
for j in range(i+1,4):
trio = (cluster[1][i], cluster[0], cluster[1][j])
ang_in_rad = md.compute_angles(frame, [trio])[0][0]
doub_sum += (math.cos(ang_in_rad) + 1./3.)**2
Q = 1. - (3./8.) * doub_sum
Qs.append(Q)
print('Done.')
print('')
return Qs
def test_equality_with_cgnet_angles():
# Make sure CA distances caluclated internally are consistent with mdtraj.
# This test appears here because it requires an mdtraj dependency.
molecule = CGMolecule(names=names, resseq=resseq, resmap=resmap)
traj = molecule.make_trajectory(data)
# Grab the CA inds only to get the backbone angles and compute them
# with mdtraj
CA_inds = [i for i, name in enumerate(names) if name == 'CA']
backbone_angles = [(CA_inds[i], CA_inds[i + 1], CA_inds[i + 2])
for i in range(len(CA_inds) - 2)]
mdtraj_angles = md.compute_angles(traj, backbone_angles)
# Get the GeometryFeature for just the
geom_feature = GeometryFeature(feature_tuples=backbone_angles)
out = geom_feature.forward(data_tensor)
cgnet_angles = geom_feature.angles
np.testing.assert_allclose(mdtraj_angles, cgnet_angles, rtol=1e-4)
def calc_angle_energy(self, traj, sum=True):
"""Energy for angle interactions
Parameters
----------
traj : mdtraj.Trajectory
sum : bool (opt.)
If sum=True return the total energy.
"""
theta = md.compute_angles(traj, self._angle_idxs)
if sum:
Eangle = np.zeros(traj.n_frames, float)
else:
Eangle = np.zeros((traj.n_frames, self.n_angles), float)
for i in range(self.n_angles):
if sum:
Eangle += self._angles[i].V(theta[:,i])
else:
Eangle[:,i] = self._angles[i].V(theta[:,i])
return Eangle
chunk_size = 100
indexes = np.array([np.arange(len(apairs)) for _ in range(chunk_size)])
index_all = np.array([], dtype=int)
ha_all = np.array([], dtype=float)
da_all = np.array([], dtype=float)
# variable to sum up total frames
tt = 0
for chunk_index, traj in enumerate(
md.iterload(filename, chunk=chunk_size, top='begin.gro')):
print('Reading chunk %d of %d frames' % (chunk_index, chunk_size))
tt += len(traj)
dists = md.compute_distances(traj, apairs[:, [0, 2]])
ha_dists = md.compute_distances(traj, apairs[:, [1, 2]])
angles = md.compute_angles(traj, apairs)
# Using this way we could also obtain the info for the distance distribution
#remaining = angles[np.where(dists <= cutoff)]
#final = remaining[np.where(remaining > acri)]
locs = np.where(angles > acri)
da = dists[locs]
ha = ha_dists[locs]
ind_temp = indexes[locs]
locs = np.where(da <= cutoff)
da_all = np.append(da_all, da[locs])
ha_all = np.append(ha_all, ha[locs])
index_all = np.append(index_all, ind_temp[locs])
## Compare the sequence pair indexes to determine each frame.
## Most cases should be fine, but there could be cases that the starting index
## of next frame is higher than the ending index of previous frame.
#for i in range(3):
# temp.append(topology.select_pairs(topology.select("name %s" %donor_name[i]), topology.select("name =~ 'F.*'")))
#pdb.set_trace()
dists = md.compute_distances(traj, pairs)
dist_all = []
hdist_all = []
print(time.time() - start)
for i, frame in enumerate(traj):
if i % 10 == 0:
print(i)
remaining = []
for j, item in enumerate(dists[i]):
if item <= cutoff:
remaining.append(j)
temp = apairs[remaining, :]
angles = md.compute_angles(frame, temp)[0]
final = []
ind = []
for j, item in enumerate(angles):
if item >= acri:
ind.append(remaining[j])
for item in ind:
outfile.write('%d ' % item)
outfile.write('\n')
dist_all.extend(dists[i][ind])
hdist_all.extend(md.compute_distances(frame, apairs[ind, :][:, [1, 2]])[0])
print('Average distance:', np.mean(dist_all))
print('Hydrogen bonds per frame:', len(dist_all) / float(len(traj)))
print(time.time() - start)
outfile.close()
np.savetxt('hbond_da_dist_acn.txt', dist_all)
for i in range(ndimers):
#pdbin=inputstr[intcode]+str(i)+'.pdb'
#traj=md.load(pdbin,top=pdbin)
#topology=traj.topology
xyzin = inputstr[intcode] + str(i) + '.xyz'
traj = md.load_xyz(xyzin, top="sample_Urea_Chol.pdb")
#if intcode==2:
#be careful. if chol cl order swapped(due to residue index), need to change calculation
# if 'Cl' in str(topology.atom(0)): #first atom is Cl -> chol cl swapped
# list_distc1=np.array([mother_list_dist[4]])
# list_angle=np.array([mother_list_angle[4]])
# list_dih1=np.array([mother_list_dih1[4]])
sub_distc1 = (md.compute_distances(traj, list_distc1)).flatten()[0]
sub_distc2 = 10000000
sub_ang1 = (md.compute_angles(traj, list_angle)).flatten()[0]
if intcode == 1 or intcode == 3 or intcode == 5:
sub_distc2 = (md.compute_distances(traj, list_distc2)).flatten()[0]
#if intcode==0:
#elif intcode==1:
#chHuN distance: choose closer one
#elif intcode==2:
#be careful. if chol cl order swapped(due to residue index), need to change calculation
#elif intcode==3:
#chHuN distance: choose closer one
sub_dist1 = np.minimum(sub_distc1, sub_distc2)
main_dih = (md.compute_dihedrals(traj, list_dih1)).flatten()[0]
maindist = (md.compute_distances(traj, list_maindist)).flatten()[0]
#sub_dih2=(md.compute_dihedrals(traj,list_dih2)).flatten()[0]
#main_dih,sub_dih2,sub_ang1=main_dih*180.0/math.pi,sub_dih2*180.0/math.pi,sub_ang1*180.0/math.pi
main_dih, sub_ang1 = main_dih * 180.0 / math.pi, sub_ang1 * 180.0 / math.pi
cs83 = topo.select('resSeq 83 and name SG')
cs87 = topo.select('resSeq 87 and name SG')
cs93 = topo.select('resSeq 93 and name SG')
cc83 = topo.select('resSeq 83 and name CB')
cc87 = topo.select('resSeq 87 and name CB')
cc93 = topo.select('resSeq 93 and name CB')
# cysteines for ZN248
cs185 = topo.select('resSeq 185 and name SG')
cs232 = topo.select('resSeq 232 and name SG')
cs234 = topo.select('resSeq 234 and name SG')
cs239 = topo.select('resSeq 239 and name SG')
cc185 = topo.select('resSeq 185 and name CB')
cc232 = topo.select('resSeq 232 and name CB')
cc234 = topo.select('resSeq 234 and name CB')
cc239 = topo.select('resSeq 239 and name CB')
# make arrays of trios
list246 = [[int(zn246), int(cs53), int(cc53)], [int(zn246), int(cs55), int(cc55)], [int(zn246), int(cs70), int(cc70)], [int(zn246), int(cs74), int(cc74)]]
list247 = [[int(zn247), int(cs70), int(cc70)], [int(zn247), int(cs83), int(cc83)], [int(zn247), int(cs87), int(cc87)], [int(zn247), int(cs93), int(cc93)]]
list248 = [[int(zn248), int(cs185), int(cc185)], [int(zn248), int(cs232), int(cc232)], [int(zn248), int(cs234), int(cc234)], [int(zn248), int(cs239), int(cc239)]]
array246 = np.asarray(list246)
array247 = np.asarray(list247)
array248 = np.asarray(list248)
# calc angles
angles246 = md.compute_angles(traj, array246)
angles247 = md.compute_angles(traj, array247)
angles248 = md.compute_angles(traj, array248)
# save results
np.savetxt('angles246.txt', angles246)
np.savetxt('angles247.txt', angles247)
np.savetxt('angles248.txt', angles248)
def angles(traj, indices=None):
x = []
y = md.compute_angles(traj, angle_indices=indices, periodic=True)
x.extend([np.sin(y), np.cos(y)])
return np.hstack(x)
def map(self, traj):
rad = mdtraj.compute_angles(traj, self.angle_indexes)
if self.deg:
return np.rad2deg(rad)
else:
return rad
def main():
#Part to load coordinate file
topfile = sys.argv[1]
trjfile = sys.argv[2]
outfile = open(sys.argv[3], 'w')
aname1 = input("atom names for donors? ex) OW \n")
aname2 = input("atom names for hydrogens? ex) HW1 HW2 \n")
aname3 = input("atom names for acceptors? ex) UO \n")
rrange = input(
"minimum, maximum D-A distance in angstroms? ex) 1.00 5.00 \n")
rsplit = rrange.split()
rmin, rmax = float(rsplit[0]) * angtonm, float(rsplit[1]) * angtonm
rbin = float(input("r bin size in angstrom? ex) 0.02 \n")) * angtonm
abin = float(input("cosine(theta) bin size? ex) 0.02 \n"))
rnbin, anbin = int((rmax - rmin) / rbin), int(2 / abin)
hbrcut = float(
input(
"cutoff distance(D-A) for hydrogen bond in angstroms? ex) 3.5 ? \n"
)) * angtonm
#In the donor-H -- acceptor triplet, D - A RDF r_min should be considered.
hbacut = float(
input(
"cutoff angle in degree width from 180, for hydrogen bond? ex) 30 \n"
))
hbamin, hbamax = (180.0 - hbacut) * degtorad, (
180.0 + hbacut) * degtorad #in radian.
tskip = int(
input("Once in how many frames do you want to take? ex) 10 \n"))
teq = int(
input(
"How many initial frames do you want to cut as equilibration? ex) 5000 \n"
))
start_time = timeit.default_timer()
#input 1 : load surf traj. (big file)
traj = md.load(trjfile, top=topfile)
traj = traj[teq::tskip]
topology = traj.topology
nstep = traj.n_frames
nmon = topology.n_residues
if nstep >= 100: #if there're many frames..
nfrag = 200
else:
nfrag = 1
elapsed = timeit.default_timer() - start_time
print('finished trajectory loading {}'.format(elapsed))
print(nstep, nmon)
#prepare 2dbins for hydrogen-acceptor distance and H-bond angle
#sdbin,count=numpy.zeros(nstep),numpy.zeros(nstep) #bin & stat weight of dr^2(t) ave
#make atom indices list (before filtering too far pairs)
#should avoid intramolecular atomic pair
asplit1, asplit2, asplit3 = aname1.split(), aname2.split(), aname3.split()
text1, text2, text3 = '', '', ''
for word in asplit1:
text1 += 'name ' + word + ' or '
for word in asplit2:
text2 += 'name ' + word + ' or '
for word in asplit3:
text3 += 'name ' + word + ' or '
text1, text2, text3 = text1[:-4], text2[:-4], text3[:-4]
seld = topology.select(text1)
selh = topology.select(text2)
sela = topology.select(text3)
n_atomd, n_atomh, n_atoma = len(seld), len(selh), len(sela)
print(n_atomd, n_atomh, n_atoma)
dhpairs = []
for j in topology.bonds:
if j[0].index in selh and j[1].index in seld:
dhpairs.append([j[1].index, j[0].index])
elif j[0].index in seld and j[1].index in selh:
dhpairs.append([j[0].index, j[1].index])
fulllist_angles = []
for row in dhpairs:
for i in sela:
if topology.atom(row[1]).residue != topology.atom(i).residue:
extrow = row.copy()
extrow.append(i)
fulllist_angles.append(extrow)
#list_dist=numpy.array(list_dist)
fulllist_angles = numpy.array(fulllist_angles)
n_angles_full = len(fulllist_angles)
print("dhpairs # = {}, full list # angles = {} ".format(
len(dhpairs), n_angles_full))
hbtot = 0
for ifrag in range(
nfrag): #loop of fragmental calculation, to save memory.
blength = int(nstep / nfrag)
bstart, bend = ifrag * blength, (ifrag + 1) * blength
fragtraj = traj[bstart:bend]
#calculate distances between donors and acceptors, angle
dist = (md.compute_distances(fragtraj,
fulllist_angles[:, [0, 2]])).flatten()
#index_thres=numpy.where(full_dist<=rmax)[0]
#dist=numpy.array(full_dist[index_thres])
#print(dist)
#list_angles=fulllist_angles[index_thres,:]
## calculate angles and distances
angl = (md.compute_angles(fragtraj, fulllist_angles)).flatten()
#n_angles=len(list_angles)
#print(" list # distances(within threshold) = {}".format(len(dist)))
#print(" list # angles = {}".format(n_angles))
i_thresd, i_thresa = numpy.where(dist <= hbrcut), numpy.where(
numpy.logical_and(hbamin <= angl, angl <= hbamax))
hbtot += len(numpy.intersect1d(i_thresd[0], i_thresa[0]))
# recalculate NaN values of angles
import copy
for nan_item in numpy.argwhere(numpy.isnan(angl)).reshape(-1):
i_frame = int(nan_item / n_angles_full)
i_angle = nan_item % n_angles_full
#print(" Nan at {} th frame and {} th angle".format(i_frame,i_angle))
#print(" <-- {} th atoms".format(list_angles[i_angle]))
i_abc = fulllist_angles[i_angle]
a = traj.xyz[i_frame][i_abc[0]]
b = traj.xyz[i_frame][i_abc[1]]
c = traj.xyz[i_frame][i_abc[2]]
print(" <-- position: \n {} \n {} \n {}".format(a, b, c))
ba = a - b
bc = c - b
cosine_angle = numpy.dot(
ba, bc) / (numpy.linalg.norm(ba) * numpy.linalg.norm(bc))
print(" distance= {}".format(numpy.linalg.norm(bc)))
angle = numpy.arccos(cosine_angle)
print(" get correct value from NaN, {} (rad) {} (deg)".format(
angle, angle * 180.0 / numpy.pi))
angl[nan_item] = copy.copy(angle)
cosangl = numpy.cos(angl)
#print(cosangl)
#printing section - should regard gnuplot pm3d-compatible format.
#hold x. increment y. when a full cycle of y range ends, make an empty line.
#histogram
counts_2d, edge_r, edge_cosa = numpy.histogram2d(dist,
cosangl,
bins=[rnbin, anbin],
range=[[rmin, rmax],
[-1.0, 1.0]])
#volume in each radial shell
vol = numpy.power(edge_r[1:], 3) - numpy.power(edge_r[:-1], 3)
vol *= 4 / 3.0 * numpy.pi
# Average number density
box_vol = numpy.average(fragtraj.unitcell_volumes)
density = n_angles_full / box_vol
rdf_2d = (counts_2d * anbin / nstep) / (density * vol[:, None])
if ifrag == 0:
totrdf_2d = numpy.copy(rdf_2d)
else:
totrdf_2d += rdf_2d
elapsed = timeit.default_timer() - start_time
print('finished fragment {} time {}'.format(ifrag, elapsed))
for i in range(rnbin):
for j in range(anbin):
xval, yval = (rmin + rbin * i) / angtonm, -1.0 + abin * j
outfile.write('{:11.4f} {:11.4f} {:11.4f}\n'.format(
xval, yval, totrdf_2d[i][j]))
outfile.write('\n')
#average number of H-bonds normalization : when D-H -- A exist, number of A atoms satisfies criterion, per one D-H.
#therefore, (Total count in the whole trajectory)/((# of frames)*(total# of D-H pairs in 1 system))
hbavg = hbtot / (nstep * len(dhpairs))
print(
'Detected H-bond rcut {:8.3f} A angcut {:8.3f} deg totcount {} avg {:11.4f}'
.format(hbrcut / angtonm, hbacut, hbtot, hbavg))
elapsed = timeit.default_timer() - start_time
print('finished job {}'.format(elapsed))
#numpy.savetxt(outfile,numpy.transpose(rdf_2d), \
#header='x = distance [{},{}], y= cos angle [{},{}]' \
#.format(rmin,rmax,-1.0,1.0),fmt='%f',comments='# ')
#numpy.save(outfile,numpy.transpose(rdf_2d))
#print(rdf_2d)
outfile.close()
print_frequency=print_frequency,
output_data=output_data)
else:
replica_energies, replica_positions, replica_states = read_replica_exchange_data(
system=cgmodel.system,
topology=cgmodel.topology,
temperature_list=temperature_list,
output_data=output_data,
print_frequency=print_frequency)
bond_angles = []
make_replica_pdb_files(cgmodel.topology, replica_positions)
for replica_index in range(len(replica_positions)):
trajectory = md.load(str("replica_" + str(replica_index + 1) + ".pdb"))
for angle in angle_list:
traj_angles = md.compute_angles(trajectory, [angle])
for sample in traj_angles:
bond_angles.append(sample)
bond_angles = np.array([float(angle) for angle in bond_angles])
n_bond_angle_bins = 100
bond_angle_bin_counts = np.zeros((n_bond_angle_bins + 1), dtype=int)
min_bond_angle = bond_angles[np.argmin(bond_angles)]
max_bond_angle = bond_angles[np.argmax(bond_angles)]
bond_angle_step = (max_bond_angle - min_bond_angle) / (n_bond_angle_bins +
1)
bond_angle_ranges = [[
min_bond_angle + bond_angle_step * i,
min_bond_angle + bond_angle_step * (i + 1)
] for i in range(n_bond_angle_bins + 1)]