def helanal_trajectory(universe,
selection="name CA",
start=None,
end=None,
begin=None,
finish=None,
matrix_filename="bending_matrix.dat",
origin_pdbfile="origin.pdb",
summary_filename="summary.txt",
screw_filename="screw.xvg",
tilt_filename="local_tilt.xvg",
fitted_tilt_filename="fit_tilt.xvg",
bend_filename="local_bend.xvg",
twist_filename="unit_twist.xvg",
prefix="helanal_",
ref_axis=None,
quiet=False):
"""Perform HELANAL_ helix analysis on all frames in *universe*.
.. Note::
Only a single helix is analyzed. Use the selection to specify the
helix, e.g. with "name CA and resid 1:20" or use start=1, stop=20.
:Arguments:
*universe*
:class:`~MDAnalysis.core.AtomGroup.Universe`
:Keywords:
*selection*
selection string that selects Calpha atoms [``"name CA"``]
*start*
start residue resid
*end*
end residue resid
*begin*
start analysing for time (ps) >= *begin*; ``None`` starts from the
beginning [``None``]
*finish*
stop analysis for time (ps) =< *finish*; ``None`` goes to the
end of the trajectory [``None``]
*matrix_filename*
Output file- bending matrix [``"bending_matrix.dat"``]
*origin_pdbfile*
Output file- origin pdb file [``"origin.pdb"``]
*summary_filename*
Output file- all of the basic data [``"summary.txt"``]
*screw_filename*
Output file- local tilts of individual residues from 2 to n-1
[``"screw.xvg"``]
*tilt_filename*
Output file- tilt of line of best fit applied to origin axes
[``"local_tilt.xvg"``]
*bend_filename*
Output file- local bend angles between successive local helix axes
[``"local_bend.xvg"``]
*twist_filename*
Output file- local unit twist between successive helix turns
[``"unit_twist.xvg"``]
*prefix*
Prefix to add to all output file names; set to ``None`` to disable
[``"helanal__"``]
*ref_axis*
Calculate tilt angle relative to the axis; if ``None`` then ``[0,0,1]``
is chosen [``None``]
*quiet*
Suppress most diagnostic output.
:Raises:
FinishTimeException
If the specified finish time precedes the specified start time or
current time stamp of trajectory object.
.. versionchanged:: 0.13.0
New *quiet* keyword to silence frame progress output and most of the
output that used to be printed to stdout is now logged to the logger
*MDAnalysis.analysis.helanal* (at logelevel *INFO*).
"""
if ref_axis is None:
ref_axis = np.array([0., 0., 1.])
else:
# enable MDA API so that one can use a tuple of atoms or AtomGroup with
# two atoms
ref_axis = np.asarray(ref_axis)
if not (start is None and end is None):
if start is None:
start = universe.atoms[0].resid
if end is None:
end = universe.atoms[-1].resid
selection += " and resid {start:d}:{end:d}".format(**vars())
ca = universe.select_atoms(selection)
trajectory = universe.trajectory
if finish is not None:
if trajectory.ts.time > finish:
# you'd be starting with a finish time (in ps) that has already passed or not
# available
raise FinishTimeException(
'The input finish time ({finish} ps) precedes the current trajectory time of {traj_time} ps.'
.format(finish=finish, traj_time=trajectory.time))
if start is not None and end is not None:
logger.info("Analysing from residue %d to %d", start, end)
elif start is not None and end is None:
logger.info("Analysing from residue %d to the C termini", start)
elif start is None and end is not None:
logger.info("Analysing from the N termini to %d", end)
logger.info("Analysing %d/%d residues", ca.n_atoms,
universe.atoms.n_residues)
if prefix is not None:
prefix = str(prefix)
matrix_filename = prefix + matrix_filename
origin_pdbfile = prefix + origin_pdbfile
summary_filename = prefix + summary_filename
screw_filename = prefix + screw_filename
tilt_filename = prefix + tilt_filename
fitted_tilt_filename = prefix + fitted_tilt_filename
bend_filename = prefix + bend_filename
twist_filename = prefix + twist_filename
backup_file(matrix_filename)
backup_file(origin_pdbfile)
backup_file(summary_filename)
backup_file(screw_filename)
backup_file(tilt_filename)
backup_file(fitted_tilt_filename)
backup_file(bend_filename)
backup_file(twist_filename)
global_height = []
global_twist = []
global_rnou = []
global_bending = []
global_bending_matrix = []
global_tilt = []
global_fitted_tilts = []
global_screw = []
pm = ProgressMeter(trajectory.n_frames,
quiet=quiet,
format="Frame %(step)10d: %(time)20.1f ps\r")
for ts in trajectory:
pm.echo(ts.frame, time=ts.time)
frame = ts.frame
if begin is not None:
if trajectory.time < begin:
continue
if finish is not None:
if trajectory.time > finish:
break
ca_positions = ca.positions
twist, bending_angles, height, rnou, origins, local_helix_axes, local_screw_angles = \
main_loop(ca_positions, ref_axis=ref_axis)
origin_pdb(origins, origin_pdbfile)
#calculate local bending matrix( it is looking at all i, j combinations)
if len(global_bending_matrix) == 0:
global_bending_matrix = [[[] for item in local_helix_axes]
for item in local_helix_axes]
for i in range(len(local_helix_axes)):
for j in range(i + 1, len(local_helix_axes)):
angle = np.rad2deg(
np.arccos(np.dot(local_helix_axes[i],
local_helix_axes[j])))
global_bending_matrix[i][j].append(angle)
#global_bending_matrix[j][i].append(angle)
#global_bending_matrix[i][i].append(0.)
fit_vector, fit_tilt = vector_of_best_fit(origins)
global_height += height
global_twist += twist
global_rnou += rnou
#global_screw.append(local_screw_angles)
global_fitted_tilts.append(np.rad2deg(fit_tilt))
#print out rotations across the helix to a file
with open(twist_filename, "a") as twist_output:
print(frame, end='', file=twist_output)
for loc_twist in twist:
print(loc_twist, end='', file=twist_output)
print("", file=twist_output)
with open(bend_filename, "a") as bend_output:
print(frame, end='', file=bend_output)
for loc_bend in bending_angles:
print(loc_bend, end='', file=bend_output)
print("", file=bend_output)
with open(screw_filename, "a") as rot_output:
print(frame, end='', file=rot_output)
for rotation in local_screw_angles:
print(rotation, end='', file=rot_output)
print("", file=rot_output)
with open(tilt_filename, "a") as tilt_output:
print(frame, end='', file=tilt_output)
for tilt in local_helix_axes:
print(np.rad2deg(mdamath.angle(tilt, ref_axis)),
end='',
file=tilt_output)
print("", file=tilt_output)
with open(fitted_tilt_filename, "a") as tilt_output:
print(frame, np.rad2deg(fit_tilt), file=tilt_output)
if len(global_bending) == 0:
global_bending = [[] for item in bending_angles]
#global_tilt = [ [] for item in local_helix_axes ]
for store, tmp in zip(global_bending, bending_angles):
store.append(tmp)
#for store,tmp in zip(global_tilt,local_helix_axes): store.append(mdamath.angle(tmp,ref_axis))
twist_mean, twist_sd, twist_abdev = stats(global_twist)
height_mean, height_sd, height_abdev = stats(global_height)
rnou_mean, rnou_sd, rnou_abdev = stats(global_rnou)
ftilt_mean, ftilt_sd, ftilt_abdev = stats(global_fitted_tilts)
bending_statistics = [stats(item) for item in global_bending]
#tilt_statistics = [ stats(item) for item in global_tilt]
bending_statistics_matrix = [[stats(col) for col in row]
for row in global_bending_matrix]
with open(matrix_filename, 'w') as mat_output:
print("Mean", file=mat_output)
for row in bending_statistics_matrix:
for col in row:
formatted_angle = "{0:6.1f}".format(col[0])
print(formatted_angle, end='', file=mat_output)
print('', file=mat_output)
print('\nSD', file=mat_output)
for row in bending_statistics_matrix:
for col in row:
formatted_angle = "{0:6.1f}".format(col[1])
print(formatted_angle, end='', file=mat_output)
print('', file=mat_output)
print("\nABDEV", file=mat_output)
for row in bending_statistics_matrix:
for col in row:
formatted_angle = "{0:6.1f}".format(col[2])
print(formatted_angle, end='', file=mat_output)
print('', file=mat_output)
logger.info("Height: %g SD: %g ABDEV: %g (Angstroem)", height_mean,
height_sd, height_abdev)
logger.info("Twist: %g SD: %g ABDEV: %g", twist_mean, twist_sd,
twist_abdev)
logger.info("Residues/turn: %g SD: %g ABDEV: %g", rnou_mean, rnou_sd,
rnou_abdev)
logger.info("Fitted tilt: %g SD: %g ABDEV: %g", ftilt_mean, ftilt_sd,
ftilt_abdev)
logger.info("Local bending angles:")
residue_statistics = zip(*bending_statistics)
measure_names = ["Mean ", "SD ", "ABDEV"]
if start is None:
output = " ".join([
"{0:8d}".format(item)
for item in range(4,
len(residue_statistics[0]) + 4)
])
else:
output = " ".join([
"{0:8d}".format(item)
for item in range(start + 3,
len(residue_statistics[0]) + start + 3)
])
logger.info("ResID %s", output)
for measure, name in zip(residue_statistics, measure_names):
output = str(name) + " "
output += " ".join(["{0:8.1f}".format(residue) for residue in measure])
logger.info(output)
with open(summary_filename, 'w') as summary_output:
print("Height:",
height_mean,
"SD",
height_sd,
"ABDEV",
height_abdev,
'(nm)',
file=summary_output)
print("Twist:",
twist_mean,
"SD",
twist_sd,
"ABDEV",
twist_abdev,
file=summary_output)
print("Residues/turn:",
rnou_mean,
"SD",
rnou_sd,
"ABDEV",
rnou_abdev,
file=summary_output)
print("Local bending angles:", file=summary_output)
residue_statistics = list(zip(*bending_statistics))
measure_names = ["Mean ", "SD ", "ABDEV"]
print("ResID", end='', file=summary_output)
if start is None:
for item in range(4, len(residue_statistics[0]) + 4):
output = "{0:8d}".format(item)
print(output, end='', file=summary_output)
else:
for item in range(start + 3,
len(residue_statistics[0]) + start + 3):
output = "{0:8d}".format(item)
print(output, end='', file=summary_output)
print('', file=summary_output)
for measure, name in zip(residue_statistics, measure_names):
print(name, end='', file=summary_output)
for residue in measure:
output = "{0:8.1f}".format(residue)
print(output, end='', file=summary_output)
print('', file=summary_output)
def helanal_trajectory(universe, selection="name CA", start=None, end=None, begin=None, finish=None,
matrix_filename="bending_matrix.dat", origin_pdbfile="origin.pdb",
summary_filename="summary.txt", screw_filename="screw.xvg",
tilt_filename="local_tilt.xvg", fitted_tilt_filename="fit_tilt.xvg",
bend_filename="local_bend.xvg", twist_filename="unit_twist.xvg",
prefix="helanal_", ref_axis=None):
"""Perform HELANAL_ helix analysis on all frames in *universe*.
.. Note::
Only a single helix is analyzed. Use the selection to specify the
helix, e.g. with "name CA and resid 1:20" or use start=1, stop=20.
:Arguments:
*universe*
:class:`~MDAnalysis.core.AtomGroup.Universe`
:Keywords:
*selection*
selection string that selects Calpha atoms [``"name CA"``]
*start*
start residue
*end*
end residue
*begin*
start analysing for time (ps) >= *begin*; ``None`` starts from the
beginning [``None``]
*finish*
stop analysis for time (ps) =< *finish*; ``None`` goes to the
end of the trajectory [``None``]
*matrix_filename*
Output file- bending matrix [``"bending_matrix.dat"``]
*origin_pdbfile*
Output file- origin pdb file [``"origin.pdb"``]
*summary_filename*
Output file- all of the basic data [``"summary.txt"``]
*screw_filename*
Output file- local tilts of individual residues from 2 to n-1
[``"screw.xvg"``]
*tilt_filename*
Output file- tilt of line of best fit applied to origin axes
[``"local_tilt.xvg"``]
*bend_filename*
Output file- local bend angles between successive local helix axes
[``"local_bend.xvg"``]
*twist_filename*
Output file- local unit twist between successive helix turns
[``"unit_twist.xvg"``]
*prefix*
Prefix to add to all output file names; set to ``None`` to disable
[``"helanal__"``]
*ref_axis*
Calculate tilt angle relative to the axis; if ``None`` then ``[0,0,1]``
is chosen [``None``]
:Raises:
FinishTimeException
If the specified finish time precedes the specified start time or current time stamp of trajectory object.
"""
if ref_axis is None:
ref_axis = np.array([0., 0., 1.])
else:
# enable MDA API so that one can use a tuple of atoms or AtomGroup with
# two atoms
ref_axis = np.asarray(ref_axis)
if start is None and end is None:
pass
else:
if start is None:
start = universe.atoms[0].resid
if end is None:
end = universe.atoms[-1].resid
selection += " and resid %(start)d:%(end)d" % vars()
ca = universe.select_atoms(selection)
trajectory = universe.trajectory
if finish is not None:
if trajectory.ts.time > finish: # you'd be starting with a finish time (in ps) that has already passed or not
# available
raise FinishTimeException(
'The input finish time ({finish} ps) precedes the current trajectory time of {traj_time} ps.'.format(
finish=finish, traj_time=trajectory.time))
if start is not None and end is not None:
print "Analysing from residue", start, "to", end
elif start is not None and end is None:
print "Analysing from residue", start, "to the C termini"
elif start is None and end is not None:
print "Analysing from the N termini to", end
print "Analysing %d/%d residues" % (ca.n_atoms, universe.atoms.n_residues)
if not prefix is None:
prefix = str(prefix)
matrix_filename = prefix + matrix_filename
origin_pdbfile = prefix + origin_pdbfile
summary_filename = prefix + summary_filename
screw_filename = prefix + screw_filename
tilt_filename = prefix + tilt_filename
fitted_tilt_filename = prefix + fitted_tilt_filename
bend_filename = prefix + bend_filename
twist_filename = prefix + twist_filename
backup_file(matrix_filename)
backup_file(origin_pdbfile)
backup_file(summary_filename)
backup_file(screw_filename)
backup_file(tilt_filename)
backup_file(fitted_tilt_filename)
backup_file(bend_filename)
backup_file(twist_filename)
global_height = []
global_twist = []
global_rnou = []
global_bending = []
global_bending_matrix = []
global_tilt = []
global_fitted_tilts = []
global_screw = []
for ts in trajectory:
frame = ts.frame
if begin is not None:
if trajectory.time < begin:
continue
if finish is not None:
if trajectory.time > finish:
break
ca_positions = ca.coordinates()
twist, bending_angles, height, rnou, origins, local_helix_axes, local_screw_angles = \
main_loop(ca_positions, ref_axis=ref_axis)
origin_pdb(origins, origin_pdbfile)
#calculate local bending matrix( it is looking at all i, j combinations)
if len(global_bending_matrix) == 0:
global_bending_matrix = [[[] for item in local_helix_axes] for item in local_helix_axes]
for i in range(len(local_helix_axes)):
for j in range(i + 1, len(local_helix_axes)):
angle = np.rad2deg(np.arccos(vecscaler(local_helix_axes[i], local_helix_axes[j])))
global_bending_matrix[i][j].append(angle)
#global_bending_matrix[j][i].append(angle)
#global_bending_matrix[i][i].append(0.)
fit_vector, fit_tilt = vector_of_best_fit(origins)
global_height += height
global_twist += twist
global_rnou += rnou
#global_screw.append(local_screw_angles)
global_fitted_tilts.append(np.rad2deg(fit_tilt))
#print out rotations across the helix to a file
with open(twist_filename, "a") as twist_output:
print >> twist_output, frame,
for loc_twist in twist:
print >> twist_output, loc_twist,
print >> twist_output, ""
with open(bend_filename, "a") as bend_output:
print >> bend_output, frame,
for loc_bend in bending_angles:
print >> bend_output, loc_bend,
print >> bend_output, ""
with open(screw_filename, "a") as rot_output:
print >> rot_output, frame,
for rotation in local_screw_angles:
print >> rot_output, rotation,
print >> rot_output, ""
with open(tilt_filename, "a") as tilt_output:
print >> tilt_output, frame,
for tilt in local_helix_axes:
print >> tilt_output, np.rad2deg(vecangle(tilt, ref_axis)),
print >> tilt_output, ""
with open(fitted_tilt_filename, "a") as tilt_output:
print >> tilt_output, frame, np.rad2deg(fit_tilt)
if len(global_bending) == 0:
global_bending = [[] for item in bending_angles]
#global_tilt = [ [] for item in local_helix_axes ]
for store, tmp in zip(global_bending, bending_angles):
store.append(tmp)
#for store,tmp in zip(global_tilt,local_helix_axes): store.append(vecangle(tmp,ref_axis))
#simple ticker
formated_time = "%20.1f" % trajectory.time
frame += 1
formated_frame = "%10d" % frame
print '\r', formated_time, ' ps', formated_frame,
sys.stdout.flush()
print '\nComplete'
twist_mean, twist_sd, twist_abdev = stats(global_twist)
height_mean, height_sd, height_abdev = stats(global_height)
rnou_mean, rnou_sd, rnou_abdev = stats(global_rnou)
ftilt_mean, ftilt_sd, ftilt_abdev = stats(global_fitted_tilts)
bending_statistics = [stats(item) for item in global_bending]
#tilt_statistics = [ stats(item) for item in global_tilt]
bending_statistics_matrix = [[stats(col) for col in row] for row in global_bending_matrix]
with open(matrix_filename, 'w') as mat_output:
print >> mat_output, "Mean"
for row in bending_statistics_matrix:
for col in row:
formatted_angle = "%6.1f" % col[0]
print >> mat_output, formatted_angle,
print >> mat_output, ''
print >> mat_output, "\nSD"
for row in bending_statistics_matrix:
for col in row:
formatted_angle = "%6.1f" % col[1]
print >> mat_output, formatted_angle,
print >> mat_output, ''
print >> mat_output, "\nABDEV"
for row in bending_statistics_matrix:
for col in row:
formatted_angle = "%6.1f" % col[2]
print >> mat_output, formatted_angle,
print >> mat_output, ''
print "Height:", height_mean, "SD", height_sd, "ABDEV", height_abdev, '(Angstroem)'
print "Twist:", twist_mean, "SD", twist_sd, "ABDEV", twist_abdev
print "Residues/turn:", rnou_mean, "SD", rnou_sd, "ABDEV", rnou_abdev
print "Fitted tilt:", ftilt_mean, "SD", ftilt_sd, "ABDEV", ftilt_abdev
print "Local bending angles:"
residue_statistics = zip(*bending_statistics)
measure_names = ["Mean ", "SD ", "ABDEV"]
print "ResID",
if start is None:
for item in range(4, len(residue_statistics[0]) + 4):
output = "%8d" % item
print output,
else:
for item in range(start + 3, len(residue_statistics[0]) + start + 3):
output = "%8d" % item
print output,
print ""
for measure, name in zip(residue_statistics, measure_names):
print name,
for residue in measure:
output = "%8.1f" % residue
print output,
print ''
with open(summary_filename, 'w') as summary_output:
print >> summary_output, "Height:", height_mean, "SD", height_sd, "ABDEV", height_abdev, '(nm)'
print >> summary_output, "Twist:", twist_mean, "SD", twist_sd, "ABDEV", twist_abdev
print >> summary_output, "Residues/turn:", rnou_mean, "SD", rnou_sd, "ABDEV", rnou_abdev
print >> summary_output, "Local bending angles:"
residue_statistics = zip(*bending_statistics)
measure_names = ["Mean ", "SD ", "ABDEV"]
print >> summary_output, "ResID",
if start is None:
for item in range(4, len(residue_statistics[0]) + 4):
output = "%8d" % item
print >> summary_output, output,
else:
for item in range(start + 3, len(residue_statistics[0]) + start + 3):
output = "%8d" % item
print >> summary_output, output,
print >> summary_output, ""
for measure, name in zip(residue_statistics, measure_names):
print >> summary_output, name,
for residue in measure:
output = "%8.1f" % residue
print >> summary_output, output,
print >> summary_output, ''