def test_angles(self):
from MDAnalysis.lib.distances import calc_angles
# Shift atom coordinates a few box lengths in random directions and see if we still get same results
a2 = (self.a + self.box * (-1, 0, 0)).astype(
np.float32) # seem to get converted to float64 otherwise
b2 = (self.b + self.box * (1, 0, 1)).astype(np.float32)
c2 = (self.c + self.box * (-2, 5, -7)).astype(np.float32)
ref = calc_angles(self.a, self.b, self.c, backend=self.backend)
test1 = calc_angles(a2,
self.b,
self.c,
box=self.box,
backend=self.backend)
test2 = calc_angles(self.a,
b2,
self.c,
box=self.box,
backend=self.backend)
test3 = calc_angles(self.a,
self.b,
c2,
box=self.box,
backend=self.backend)
test4 = calc_angles(a2, b2, c2, box=self.box, backend=self.backend)
for val in [test1, test2, test3, test4]:
assert_almost_equal(
ref,
val,
self.prec,
err_msg="Min image in angle calculation failed")
def test_angles(self):
from MDAnalysis.lib.distances import calc_angles
# Shift atom coordinates a few box lengths in random directions and see if we still get same results
a2 = (self.a + self.box * (-1, 0, 0)).astype(np.float32) # seem to get converted to float64 otherwise
b2 = (self.b + self.box * (1, 0, 1)).astype(np.float32)
c2 = (self.c + self.box * (-2, 5, -7)).astype(np.float32)
ref = calc_angles(self.a, self.b, self.c, backend=self.backend)
test1 = calc_angles(a2, self.b, self.c, box=self.box, backend=self.backend)
test2 = calc_angles(self.a, b2, self.c, box=self.box, backend=self.backend)
test3 = calc_angles(self.a, self.b, c2, box=self.box, backend=self.backend)
test4 = calc_angles(a2, b2, c2, box=self.box, backend=self.backend)
for val in [test1, test2, test3, test4]:
assert_almost_equal(ref, val, self.prec, err_msg="Min image in angle calculation failed")
def _single_frame(self, ts, atomgroups):
u = atomgroups[0].universe
box = ts.dimensions
# Update donor-hydrogen pairs if necessary
if self.update_selections:
acceptors = u.select_atoms(self.acceptors_sel)
donors, hydrogens = self._get_dh_pairs(u)
else:
acceptors = u.atoms[self._acceptors_ids]
donors = u.atoms[self._donors_ids]
hydrogens = u.atoms[self._hydrogens_ids]
# find D and A within cutoff distance of one another
# min_cutoff = 1.0 as an atom cannot form a hydrogen bond with itself
d_a_indices, d_a_distances = capped_distance(
donors.positions,
acceptors.positions,
max_cutoff=self.d_a_cutoff,
min_cutoff=1.0,
box=box,
return_distances=True,
)
# Remove D-A pairs more than d_a_cutoff away from one another
tmp_donors = donors[d_a_indices.T[0]]
tmp_hydrogens = hydrogens[d_a_indices.T[0]]
tmp_acceptors = acceptors[d_a_indices.T[1]]
# Find D-H-A angles greater than d_h_a_angle_cutoff
d_h_a_angles = np.rad2deg(
calc_angles(
tmp_donors.positions,
tmp_hydrogens.positions,
tmp_acceptors.positions,
box=box
)
)
hbond_indices = np.where(d_h_a_angles > self.d_h_a_angle)[0]
# Retrieve atoms, distances and angles of hydrogen bonds
hbond_donors = tmp_donors[hbond_indices]
hbond_hydrogens = tmp_hydrogens[hbond_indices]
hbond_acceptors = tmp_acceptors[hbond_indices]
hbond_distances = d_a_distances[hbond_indices]
hbond_angles = d_h_a_angles[hbond_indices]
# Store data on hydrogen bonds found at this frame
hbonds = [[], [], [], [], [], []]
hbonds[0].extend(np.full_like(hbond_donors, ts.frame))
hbonds[1].extend(hbond_donors.ids)
hbonds[2].extend(hbond_hydrogens.ids)
hbonds[3].extend(hbond_acceptors.ids)
hbonds[4].extend(hbond_distances)
hbonds[5].extend(hbond_angles)
return np.asarray(hbonds).T
def test_right_type_angles(self):
assert_equal(self.agroup.angles(),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions))
assert_equal(self.agroup.angles(pbc=True),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions,
box=self.u.dimensions))
assert_equal(self.agroup.values(),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions))
assert_equal(self.agroup.values(pbc=True),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions,
box=self.u.dimensions))
def test_right_type_angles(self, agroup, PSFDCD):
assert_equal(agroup.angles(),
calc_angles(agroup.atom1.positions,
agroup.atom2.positions,
agroup.atom3.positions))
assert_equal(agroup.angles(pbc=True),
calc_angles(agroup.atom1.positions,
agroup.atom2.positions,
agroup.atom3.positions,
box=PSFDCD.dimensions))
assert_equal(agroup.values(),
calc_angles(agroup.atom1.positions,
agroup.atom2.positions,
agroup.atom3.positions))
assert_equal(agroup.values(pbc=True),
calc_angles(agroup.atom1.positions,
agroup.atom2.positions,
agroup.atom3.positions,
box=PSFDCD.dimensions))
def test_right_type_angles(self, agroup, PSFDCD):
assert_equal(
agroup.angles(),
calc_angles(agroup.atom1.positions, agroup.atom2.positions,
agroup.atom3.positions))
assert_equal(
agroup.angles(pbc=True),
calc_angles(agroup.atom1.positions,
agroup.atom2.positions,
agroup.atom3.positions,
box=PSFDCD.dimensions))
assert_equal(
agroup.values(),
calc_angles(agroup.atom1.positions, agroup.atom2.positions,
agroup.atom3.positions))
assert_equal(
agroup.values(pbc=True),
calc_angles(agroup.atom1.positions,
agroup.atom2.positions,
agroup.atom3.positions,
box=PSFDCD.dimensions))
def test_right_type_angles(self):
assert_equal(
self.agroup.angles(),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions))
assert_equal(
self.agroup.angles(pbc=True),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions,
box=self.u.dimensions))
assert_equal(
self.agroup.values(),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions))
assert_equal(
self.agroup.values(pbc=True),
calc_angles(self.agroup.atom1.positions,
self.agroup.atom2.positions,
self.agroup.atom3.positions,
box=self.u.dimensions))
def _single_frame(self):
box = self._ts.dimensions
# Update donor-hydrogen pairs if necessary
if self.update_selections:
self._donors, self._hydrogens = self._get_dh_pairs()
# find D and A within cutoff distance of one another
# min_cutoff = 1.0 as an atom cannot form a hydrogen bond with itself
d_a_indices, d_a_distances = capped_distance(
self._donors.positions,
self._acceptors.positions,
max_cutoff=self.d_a_cutoff,
min_cutoff=1.0,
box=box,
return_distances=True,
)
# Remove D-A pairs more than d_a_cutoff away from one another
tmp_donors = self._donors[d_a_indices.T[0]]
tmp_hydrogens = self._hydrogens[d_a_indices.T[0]]
tmp_acceptors = self._acceptors[d_a_indices.T[1]]
# Find D-H-A angles greater than d_h_a_angle_cutoff
d_h_a_angles = np.rad2deg(
calc_angles(
tmp_donors.positions,
tmp_hydrogens.positions,
tmp_acceptors.positions,
box=box
)
)
hbond_indices = np.where(d_h_a_angles > self.d_h_a_angle)[0]
# Retrieve atoms, distances and angles of hydrogen bonds
hbond_donors = tmp_donors[hbond_indices]
hbond_hydrogens = tmp_hydrogens[hbond_indices]
hbond_acceptors = tmp_acceptors[hbond_indices]
hbond_distances = d_a_distances[hbond_indices]
hbond_angles = d_h_a_angles[hbond_indices]
# Store data on hydrogen bonds found at this frame
self.hbonds[0].extend(np.full_like(hbond_donors, self._ts.frame))
self.hbonds[1].extend(hbond_donors.indices)
self.hbonds[2].extend(hbond_hydrogens.indices)
self.hbonds[3].extend(hbond_acceptors.indices)
self.hbonds[4].extend(hbond_distances)
self.hbonds[5].extend(hbond_angles)
def getInterAtomicAnglesForInpGeom(inpCell, angleIndices, degrees=True):
""" Gets a list of requested angles between atoms for inpCell taking PBCs into account.
Args:
inpCell: (plato_pylib UnitCell object)
angleIndices: (iter of len-3 iters) Each element contains [idxA,idxB,idxC] which means calculate the angle between idA,idxB,idxC for indices in inpCell.cartCoords
degrees: (Bool) If True then return angles in degrees; else use radians
Returns
outAngles: (iter of floats) Length is the same as len(angleIndices); each is an angle calculated for a value in angleIndices
"""
#1) Check indices not empty; if empty just return empty list
if len(angleIndices) == 0:
return list()
cartCoords = inpCell.cartCoords
#Convert to format needed for mdAnalysis function
numbAngles = len(angleIndices)
cartCoordsA = np.array([
np.array(cartCoords[angleIndices[idx][0]][:3])
for idx in range(numbAngles)
])
cartCoordsB = np.array([
np.array(cartCoords[angleIndices[idx][1]][:3])
for idx in range(numbAngles)
])
cartCoordsC = np.array([
np.array(cartCoords[angleIndices[idx][2]][:3])
for idx in range(numbAngles)
])
#Calculate using md analysis
dims = mdAnalysisInter.getMDAnalysisDimsFromUCellObj(inpCell)
outAnglesRadians = distLib.calc_angles(cartCoordsA,
cartCoordsB,
cartCoordsC,
box=dims)
outAnglesRadians = [x for x in outAnglesRadians]
#Convert output to the form i want
if degrees:
outAngles = [math.degrees(x) for x in outAnglesRadians]
else:
outAngles = outAnglesRadians
return outAngles
def ang_measure(sel1, sel2, sel3):
"""
This functions measures the angle between 3 specified atoms and returns the value between 0 and 360 degrees.
The input selections have to be single atoms.
"""
from numpy import rad2deg
for sel in (sel1, sel2, sel3):
if len(sel) != 1:
raise NotSingleAtomSelectionError
return ((float(
rad2deg(
mdadist.calc_angles(sel1.positions,
sel2.positions,
sel3.positions,
backend='OpenMP')))) + 360) % 360
def aops(oxy, ts):
#oxy = u.select_atoms('type 3')
ts1 = center_in_box(oxy, wrap=True)(ts)
oxy.atoms.wrap()
dists = sp.spatial.distance.squareform(sda(oxy.positions,
oxy.dimensions))
# in format (x-pos, aop)
AOPs = np.ones((len(oxy), 2))
all_inds = []
num_each = []
for i in range(len(oxy)):
nearby = np.where(dists[i] <= 3.5)[0]
nearby = nearby[nearby != i]
if nearby.size > 1:
AOPs[i, 0] = oxy[i].position[0]
inds = np.array(list(combinations(nearby, 2)))
combs = inds.shape[0]
xyz_inds = np.insert(inds, 1, np.full(combs, i), axis=1)
all_inds.append(xyz_inds)
num_each.append(combs)
elif nearby.size == 1:
num_each.append(0)
AOPs[i, 0] = oxy[i].position[0]
AOPs[i, 1] = 0.1 # it has one neighbor, so just say it's liquid
else:
num_each.append(0)
AOPs[i, 0] = np.nan
all_pos = oxy.positions[np.concatenate(all_inds)]
angles = calc_angles(all_pos[:, 0, :], all_pos[:, 1, :],
all_pos[:, 2, :], box=oxy.dimensions)
i = 0
# go through the angles and calculate AOP
for j, num in enumerate(num_each):
AOPs[j, 1] = aop(angles[i:i+num])
i += num
# remove the ones that were too far away to begin with
# AOPs = AOPs[~np.isnan(AOPs).any(axis=1)]
# left, right = np.min(oxy.positions[:, 0]), np.max(oxy.positions[:, 0])
# AOP_means = stats.binned_statistic(AOPs[:, 0], AOPs[:, 1], bins=8)
return AOPs
def calcSingleAngleBetweenCoords_minImageConv(inpCell, coordA, coordB, coordC):
""" Gets the angle (ABC) between three co-ordinates in inpCell using the minimum image convention; thus, this will use the closest possible A,B,C versions
Args:
inpCell: (plato_pylib UnitCell object) We use this to get the lattice vectors needed to account for PBCs
coordA: (len 3 iter) Co-ordinates of first atom
coordB: (len 3 iter) Co-ordinates of second atom
coordC: (len 3 iter) Co-ordinates of third atom
Returns
angle: (float) The angle (in degrees) between the co-ordinates after taking PBCs into account
"""
dims = mdAnalysisInter.getMDAnalysisDimsFromUCellObj(inpCell)
args = [
np.array([coordA[:3]]),
np.array([coordB[:3]]),
np.array([coordC[:3]])
]
angles = distLib.calc_angles(*args, box=dims)
assert len(angles) == 1
return math.degrees(angles[0])
def run(self, start=None, stop=None, step=None, verbose=None, debug=None):
"""Analyze trajectory and produce timeseries.
Stores the water bridge data per frame as
:attr:`WaterBridgeAnalysis.timeseries` (see there for output
format).
Parameters
----------
start : int (optional)
starting frame-index for analysis, ``None`` is the first one, 0.
`start` and `stop` are 0-based frame indices and are used to slice
the trajectory (if supported) [``None``]
stop : int (optional)
last trajectory frame for analysis, ``None`` is the last one
[``None``]
step : int (optional)
read every `step` between `start` (included) and `stop` (excluded),
``None`` selects 1. [``None``]
verbose : bool (optional)
toggle progress meter output
:class:`~MDAnalysis.lib.log.ProgressMeter` [``True``]
debug : bool (optional)
enable detailed logging of debugging information; this can create
*very big* log files so it is disabled (``False``) by default;
setting `debug` toggles the debug status for
:class:`WaterBridgeAnalysis`, namely the value of
:attr:`WaterBridgeAnalysis.debug`.
See Also
--------
:meth:`WaterBridgeAnalysis.generate_table` :
processing the data into a different format.
"""
self._setup_frames(self.u.trajectory, start, stop, step)
logger.info("WBridge analysis: starting")
logger.debug("WBridge analysis: donors %r", self.donors)
logger.debug("WBridge analysis: acceptors %r", self.acceptors)
logger.debug("WBridge analysis: water bridge %r", self.water_selection)
if debug is not None and debug != self.debug:
self.debug = debug
logger.debug("Toggling debug to %r", self.debug)
if not self.debug:
logger.debug("WBridge analysis: For full step-by-step debugging output use debug=True")
self._timeseries = []
self.timesteps = []
self._water_network = []
if verbose is None:
verbose = self._verbose
pm = ProgressMeter(self.n_frames,
format="WBridge frame {current_step:5d}: {step:5d}/{numsteps} [{percentage:5.1f}%]\r",
verbose=verbose)
logger.info("Starting analysis (frame index start=%d stop=%d, step=%d)",
self.start, self.stop, self.step)
for progress, ts in enumerate(self.u.trajectory[self.start:self.stop:self.step]):
# all bonds for this timestep
# dict of tuples (atom.index, atom.index) for quick check if
# we already have the bond (to avoid duplicates)
frame = ts.frame
timestep = ts.time
self.timesteps.append(timestep)
pm.echo(progress, current_step=frame)
self.logger_debug("Analyzing frame %(frame)d, timestep %(timestep)f ps", vars())
if self.update_selection1:
self._update_selection_1()
if self.update_selection2:
self._update_selection_2()
if self.update_water_selection:
self._update_water_selection()
s1_frame_results_dict = defaultdict(list)
if (self.selection1_type in ('donor', 'both') and
self._water_acceptors):
self.logger_debug("Selection 1 Donors <-> Water Acceptors")
ns_acceptors = AtomNeighborSearch(self._water_acceptors)
for i, donor_h_set in self._s1_donors_h.items():
d = self._s1_donors[i]
for h in donor_h_set:
res = ns_acceptors.search(h, self.distance)
for a in res:
donor_atom = h if self.distance_type != 'heavy' else d
dist = distances.calc_bonds(donor_atom.position,
a.position)
if dist <= self.distance:
angle = distances.calc_angles(d.position, h.position,
a.position)
angle = np.rad2deg(angle)
if angle >= self.angle:
self.logger_debug(
"S1-D: {0!s} <-> W-A: {1!s} {2:f} A, {3:f} DEG"\
.format(h.index, a.index, dist, angle))
s1_frame_results_dict[(a.resname, a.resid)].append(
(h.index, a.index,
(h.resname, h.resid, h.name),
(a.resname, a.resid, a.name),
dist, angle))
if (self.selection1_type in ('acceptor', 'both') and
self._s1_acceptors):
self.logger_debug("Selection 1 Acceptors <-> Water Donors")
ns_acceptors = AtomNeighborSearch(self._s1_acceptors)
for i, donor_h_set in self._water_donors_h.items():
d = self._water_donors[i]
for h in donor_h_set:
res = ns_acceptors.search(h, self.distance)
for a in res:
donor_atom = h if self.distance_type != 'heavy' else d
dist = distances.calc_bonds(donor_atom.position,
a.position)
if dist <= self.distance:
angle = distances.calc_angles(d.position, h.position,
a.position)
angle = np.rad2deg(angle)
if angle >= self.angle:
self.logger_debug(
"S1-A: {0!s} <-> W-D: {1!s} {2:f} A, {3:f} DEG"\
.format(a.index, h.index, dist, angle))
s1_frame_results_dict[(h.resname, h.resid)].append(
(h.index, a.index,
(h.resname, h.resid, h.name),
(a.resname, a.resid, a.name),
dist, angle))
# Narrow down the water selection
selection_resn_id = list(s1_frame_results_dict.keys())
if not selection_resn_id:
self._timeseries.append([])
continue
selection_resn_id = ['(resname {} and resid {})'.format(
resname, resid) for resname, resid in selection_resn_id]
water_bridges = self._water.select_atoms(' or '.join(selection_resn_id))
self.logger_debug("Size of water bridge selection: {0} atoms".format(len(water_bridges)))
if not water_bridges:
logger.warning("No water forming hydrogen bonding with selection 1.")
water_bridges_donors = water_bridges.select_atoms(
'name {0}'.format(' '.join(self.donors)))
water_bridges_donors_h = {}
for i, d in enumerate(water_bridges_donors):
tmp = self._get_bonded_hydrogens(d)
if tmp:
water_bridges_donors_h[i] = tmp
self.logger_debug("water bridge donors: {0}".format(len(water_bridges_donors)))
self.logger_debug("water bridge donor hydrogens: {0}".format(len(water_bridges_donors_h)))
water_bridges_acceptors = water_bridges.select_atoms(
'name {0}'.format(' '.join(self.acceptors)))
self.logger_debug("water bridge: {0}".format(len(water_bridges_acceptors)))
# Finding the hydrogen bonds between water bridge and selection 2
s2_frame_results_dict = defaultdict(list)
if self._s2_acceptors:
self.logger_debug("Water bridge Donors <-> Selection 2 Acceptors")
ns_acceptors = AtomNeighborSearch(self._s2_acceptors)
for i, donor_h_set in water_bridges_donors_h.items():
d = water_bridges_donors[i]
for h in donor_h_set:
res = ns_acceptors.search(h, self.distance)
for a in res:
donor_atom = h if self.distance_type != 'heavy' else d
dist = distances.calc_bonds(donor_atom.position,
a.position)
if dist <= self.distance:
angle = distances.calc_angles(d.position, h.position,
a.position)
angle = np.rad2deg(angle)
if angle >= self.angle:
self.logger_debug(
"WB-D: {0!s} <-> S2-A: {1!s} {2:f} A, {3:f} DEG"\
.format(h.index, a.index, dist, angle))
s2_frame_results_dict[(h.resname, h.resid)].append(
(h.index, a.index,
(h.resname, h.resid, h.name),
(a.resname, a.resid, a.name),
dist, angle))
if water_bridges_acceptors:
self.logger_debug("Selection 2 Donors <-> Selection 2 Acceptors")
ns_acceptors = AtomNeighborSearch(water_bridges_acceptors)
for i, donor_h_set in self._s2_donors_h.items():
d = self._s2_donors[i]
for h in donor_h_set:
res = ns_acceptors.search(h, self.distance)
for a in res:
donor_atom = h if self.distance_type != 'heavy' else d
dist = distances.calc_bonds(donor_atom.position,
a.position)
if dist <= self.distance:
angle = distances.calc_angles(d.position, h.position,
a.position)
angle = np.rad2deg(angle)
if angle >= self.angle:
self.logger_debug(
"WB-A: {0!s} <-> S2-D: {1!s} {2:f} A, {3:f} DEG"\
.format(a.index, h.index, dist, angle))
s2_frame_results_dict[(a.resname, a.resid)].append(
(h.index, a.index,
(h.resname, h.resid, h.name),
(a.resname, a.resid, a.name),
dist, angle))
# Generate the water network
water_network = {}
for key in s2_frame_results_dict:
s1_frame_results = set(s1_frame_results_dict[key])
s2_frame_results = set(s2_frame_results_dict[key])
if len(s1_frame_results.union(s2_frame_results)) > 1:
# Thus if selection 1 and selection 2 are the same and both
# only form a single hydrogen bond with a water, this entry
# won't be included.
water_network[key] = [s1_frame_results,
s2_frame_results.difference(s1_frame_results)]
# Generate frame_results
frame_results = []
for s1_frame_results, s2_frame_results in water_network.values():
frame_results.extend(list(s1_frame_results))
frame_results.extend(list(s2_frame_results))
self._timeseries.append(frame_results)
self._water_network.append(water_network)
logger.info("WBridge analysis: complete; timeseries %s.timeseries",
self.__class__.__name__)
def _single_run(self, start, stop):
"""Perform a single pass of the trajectory"""
self.u.trajectory[start]
# Calculate partners at t=0
box = self.u.dimensions if self.pbc else None
# 2d array of all distances
d = distance_array(self.h.positions, self.a.positions, box=box)
if self.exclusions:
# set to above dist crit to exclude
d[self.exclusions] = self.d_crit + 1.0
# find which partners satisfy distance criteria
hidx, aidx = np.where(d < self.d_crit)
a = calc_angles(self.d.positions[hidx],
self.h.positions[hidx],
self.a.positions[aidx],
box=box)
# from amongst those, who also satisfiess angle crit
idx2 = np.where(a > self.a_crit)
hidx = hidx[idx2]
aidx = aidx[idx2]
nbonds = len(hidx) # number of hbonds at t=0
results = np.zeros_like(np.arange(start, stop, self._skip),
dtype=np.float32)
if self.time_cut:
# counter for time criteria
count = np.zeros(nbonds, dtype=np.float64)
for i, ts in enumerate(self.u.trajectory[start:stop:self._skip]):
box = self.u.dimensions if self.pbc else None
d = calc_bonds(self.h.positions[hidx],
self.a.positions[aidx],
box=box)
a = calc_angles(self.d.positions[hidx],
self.h.positions[hidx],
self.a.positions[aidx],
box=box)
winners = (d < self.d_crit) & (a > self.a_crit)
results[i] = winners.sum()
if self.bond_type is 'continuous':
# Remove losers for continuous definition
hidx = hidx[np.where(winners)]
aidx = aidx[np.where(winners)]
elif self.bond_type is 'intermittent':
if self.time_cut:
# Add to counter of where losers are
count[~winners] += self._skip * self.u.trajectory.dt
count[winners] = 0 # Reset timer for winners
# Remove if you've lost too many times
# New arrays contain everything but removals
hidx = hidx[count < self.time_cut]
aidx = aidx[count < self.time_cut]
count = count[count < self.time_cut]
else:
pass
if len(hidx) == 0: # Once everyone has lost, the fun stops
break
results /= nbonds
return results
def main():
"""Run main procedure."""
# TODO(schneiderfelipe): accept multiple files
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("traj_files", nargs="+")
args = parser.parse_args()
gnorms = []
energies = []
all_atomnos = []
all_atomcoords = []
for traj_file in args.traj_files:
atomnos, comments, atomcoords = read_xyz(traj_file)
all_atomnos.extend(atomnos)
all_atomcoords.extend(atomcoords)
for comment in comments:
fields = comment.split()
gnorms.append(float(fields[3]))
energies.append(float(fields[1]))
energies = np.array(energies)
energies -= energies.min()
energies *= hartree * N_A / (kilo * calorie)
u = mda.Universe.empty(n_atoms=len(all_atomnos[0]), trajectory=True)
u.add_TopologyAttr("type", [element[i] for i in all_atomnos[0]])
u.load_new(all_atomcoords, order="fac")
print(u)
selection = None
print("(enter 'q' for exit, 'h' for help)")
while True:
code = input("select> ").strip().split()
if code[0] == "q":
break
elif code[0] == "h":
for key in commands:
print(f"{key:15s}: {commands[key]}")
elif code[0] == "e":
fig, ax = plt.subplots(2)
ax[0].plot(energies)
ax[0].set_xlabel("frame")
ax[0].set_ylabel("energy (kcal/mol)")
ax[1].plot(gnorms)
ax[1].set_xlabel("frame")
ax[1].set_ylabel("grad. norm (Eh/a0)")
plt.show()
elif code[0] == "s":
print(selection)
if selection is not None:
print(selection_text)
elif code[0] == "pca":
if selection is None:
print("empty selection, doing nothing")
continue
p = pca.PCA(u, select=selection_text)
p.run()
n_pcs = np.where(p.cumulated_variance > 0.95)[0][0]
print(n_pcs)
print(p.cumulated_variance[0:n_pcs])
pca_space = p.transform(selection, n_components=n_pcs)
print(pca_space)
print(pca.cosine_content(pca_space, 0))
elif code[0] == "p":
if selection is None:
print("empty selection, doing nothing")
continue
n = len(selection)
if n == 2:
data_label = "bond length (Å)"
elif n == 3:
data_label = "bond angle (°)"
elif n == 4:
data_label = "dihedral angle (°)"
else:
print("too few or too many indices")
continue
data = []
for i, (e, ts) in enumerate(zip(energies, u.trajectory)):
if n == 2:
d = distances.calc_bonds(
selection[0].position, selection[1].position
)
elif n == 3:
d = np.degrees(
distances.calc_angles(
selection[0].position,
selection[1].position,
selection[2].position,
)
)
elif n == 4:
d = np.degrees(
distances.calc_dihedrals(
selection[0].position,
selection[1].position,
selection[2].position,
selection[3].position,
)
)
data.append(d)
if i % 100 == 0 or i == len(u.trajectory) - 1:
print(
f"frame = {ts.frame:4d}: e = {e:5.1f} kcal/mol, {data_label.split('(')[0][:-1]} = {d:7.3f} {data_label[-2]}"
)
data = np.array(data)
fig, ax = plt.subplots(1, 2)
ax[0].plot(data)
ax[0].set_xlabel("frame")
ax[0].set_ylabel(data_label)
ax[1].plot(energies, data, "o", label="data points")
ax[1].set_xlabel("energy (kcal/mol)")
ax[1].set_ylabel(data_label)
if n == 2:
dx = 0.1
elif n == 3:
dx = 10.0
elif n == 4:
dx = 10.0
res = stats.binned_statistic(
data, energies, "min", min(25, (data.max() - data.min()) / dx)
)
# print(res.statistic)
mask = np.isnan(res.statistic)
res.statistic[mask] = np.interp(
np.flatnonzero(mask), np.flatnonzero(~mask), res.statistic[~mask]
)
# print(res.statistic)
# ax[1].hlines(res.statistic, res.bin_edges[:-1], res.bin_edges[1:], colors='g', lw=2, label='binned min. energies')
ax[1].barh(
(res.bin_edges[:-1] + res.bin_edges[1:]) / 2,
res.statistic,
align="center",
height=res.bin_edges[1:] - res.bin_edges[:-1],
alpha=0.25,
label="binned min. energies",
)
ax[1].legend()
plt.show()
else:
try:
selection_text = " ".join(code)
selection = u.select_atoms(selection_text)
except mda.exceptions.SelectionError as e:
print(e)
print("bye")
def _single_run(self, start, stop):
"""Perform a single pass of the trajectory"""
self.u.trajectory[start]
# Calculate partners at t=0
box = self.u.dimensions if self.pbc else None
# 2d array of all distances
d = distance_array(self.h.positions, self.a.positions, box=box)
if self.exclusions:
# set to above dist crit to exclude
d[self.exclusions] = self.d_crit + 1.0
# find which partners satisfy distance criteria
hidx, aidx = numpy.where(d < self.d_crit)
a = calc_angles(self.d.positions[hidx], self.h.positions[hidx],
self.a.positions[aidx], box=box)
# from amongst those, who also satisfiess angle crit
idx2 = numpy.where(a > self.a_crit)
hidx = hidx[idx2]
aidx = aidx[idx2]
nbonds = len(hidx) # number of hbonds at t=0
results = numpy.zeros_like(numpy.arange(start, stop, self._skip),
dtype=numpy.float32)
if self.time_cut:
# counter for time criteria
count = numpy.zeros(nbonds, dtype=numpy.float64)
for i, ts in enumerate(self.u.trajectory[start:stop:self._skip]):
box = self.u.dimensions if self.pbc else None
d = calc_bonds(self.h.positions[hidx], self.a.positions[aidx],
box=box)
a = calc_angles(self.d.positions[hidx], self.h.positions[hidx],
self.a.positions[aidx], box=box)
winners = (d < self.d_crit) & (a > self.a_crit)
results[i] = winners.sum()
if self.bond_type is 'continuous':
# Remove losers for continuous definition
hidx = hidx[numpy.where(winners)]
aidx = aidx[numpy.where(winners)]
elif self.bond_type is 'intermittent':
if self.time_cut:
# Add to counter of where losers are
count[~ winners] += self._skip * self.u.trajectory.dt
count[winners] = 0 # Reset timer for winners
# Remove if you've lost too many times
# New arrays contain everything but removals
hidx = hidx[count < self.time_cut]
aidx = aidx[count < self.time_cut]
count = count[count < self.time_cut]
else:
pass
if len(hidx) == 0: # Once everyone has lost, the fun stops
break
results /= nbonds
return results
def _single_frame(self):
angle = calc_angles(self.ag1.positions,
self.ag2.positions,
self.ag3.positions,
box=self.ag1.dimensions)
self.result.append(angle)