def main(topology,
trajectories,
insort=False,
selection=None,
maintain=None,
top_output='_frame0.pdb',
traj_output='nosol.dcd',
**kwargs):
"""Execute main client logic."""
log.info(T('Removing solvent'))
trj = libmdt.load_traj(topology, trajectories, insort=insort)
if selection:
log.info(S('selecting {}', selection))
atom_sel = trj.top.select(selection)
trj.atom_slice(atom_sel, inplace=True)
trj.remove_solvent(inplace=True, exclude=maintain)
if top_output:
fout = libio.parse_top_output(top_output, traj_output)
trj[0].save(fout.str())
log.info(S('first frame topology saved: {}', fout))
log.info(T('saving trajectory'))
log.info(S('destination: {}', traj_output))
trj.save(traj_output)
log.info(S('saved'))
def main(
topology,
trajectories,
insort=False,
traj_output='imaged.dcd',
top_output=False,
protocol=1,
**kwargs
):
"""Execute main client logic."""
log.info(T('Attempting image molecules'))
log.info(T('loading input'))
traj = libmdt.load_traj(topology, trajectories, insort=insort)
protocols = {
1: libmdt.imagemol_protocol1,
2: libmdt.imagemol_protocol2,
}
reimaged = protocols[protocol](traj)
log.info(T('saving the output'))
reimaged.save(traj_output)
log.info(S('saved trajectory: {}', traj_output))
if top_output:
fout = libio.parse_top_output(top_output, traj_output)
reimaged[0].save(fout.str())
log.info(S('saved frame 0 to: {}', fout.resolve()))
return
def imagemol_protocol1(traj):
"""Attempt to image molecules acting on the whole traj."""
log.info(T('running reimage protocol #1'))
log.info(S('finding molecules'))
mols = traj.top.find_molecules()
log.info(S('done'))
log.info(T('reimaging'))
reimaged = traj.image_molecules(
inplace=False,
anchor_molecules=mols[:1],
other_molecules=mols[1:],
)
log.info(S('done'))
return reimaged
def _log_simtkimport_error():
msg = ("To use .cif files as Topologies taurenmd requires OpenMM, "
"which is currently not installed. "
"Please visit our Installation instruction at "
"https://taurenmd.readthedocs.io/")
log.error(T('Dependency Error'))
log.error(S(msg))
sys.exit(0)
def main(
topology,
trajectory,
# trajectories,
# additional args...
# ...
**kwargs):
"""Execute main client logic."""
log.info(T('starting'))
# write your logic here.
# use the log.info and log.debug registries to log and output
# information to the user.
# you can always refer to other clients for examples.
log.info(S('done'))
return
def mda_rmsf(
atom_group,
frame_slice=None,
):
"""
Calculate RMSFs.
Uses `MDAnalysis RMSF <https://www.mdanalysis.org/docs/documentation_pages/analysis/rms.html?highlight=rmsd#MDAnalysis.analysis.rms.RMSF>`_.
Parameters
----------
atom_group : MDAnalysis Atom Group.
`MDAnalysis Atom group <https://www.mdanalysis.org/docs/documentation_pages/core/groups.html?highlight=atom%20group#MDAnalysis.core.groups.AtomGroup>`_.
frame_slice : any, optional
Any argument that :py:func:`taurenmd.libs.libio.evaluate_to_slice` can receive.
Defaults to ``None``, considers all frames.
Returns
-------
Numpy Array
With the calculated RMSFs values, of shape (N,) where N are the
frames sliced from ``frame_slice``.
Raises
------
MDAnalysis Exceptions
Any exceptions that could come from MDAnalysis RMSF computation.
""" # noqa: E501
log.info(T('Calculating RMSFs'))
frame_slice = libio.evaluate_to_slice(value=frame_slice)
log.info(S('for trajectory slice: {}', frame_slice))
R = mdaRMSF(
atom_group,
start=frame_slice.start,
stop=frame_slice.stop,
step=frame_slice.step,
verbose=False,
)
R.run()
return R.rmsf
def report(universe):
"""
Report information about the Universe.
Example
-------
>>> u = libmda.load_universe('topology.pdb', 'trajectory.xtc')
>>> libmda.report(u)
Parameters
----------
universe : MDAnalysis Universe
`MDAnalysis universe <https://www.mdanalysis.org/docs/documentation_pages/core/universe.html?highlight=universe#core-object-universe-mdanalysis-core-universe>`_.
Returns
-------
None
""" # noqa: E501
log.info(T('Reporting'))
log.info(S('number of frames: {}', len(universe.trajectory)))
log.info(S('number of atoms: {}', len(universe.atoms)))
def main(topology,
trajectories,
plane_selection,
aunit='degrees',
ref_frame=0,
start=None,
stop=None,
step=None,
export=False,
plot=False,
plotvars=None,
**kwargs):
"""Execute main client logic."""
log.info(T('calculating angles'))
topology = Path(topology)
trajectories = [Path(t) for t in trajectories]
u = libmda.load_universe(topology, *trajectories)
frame_slice = libio.frame_slice(
start=start,
stop=stop,
step=step,
)
log.info(S('for slice {}', frame_slice))
log.info(T('calculating plane eq. for reference frame'))
log.info(S('using frame: {}', ref_frame))
u.trajectory[ref_frame]
reference_point_1 = u.select_atoms(plane_selection[0]).center_of_geometry()
reference_point_2 = u.select_atoms(plane_selection[1]).center_of_geometry()
reference_point_3 = u.select_atoms(plane_selection[2]).center_of_geometry()
ra, rb, rc, rd = libcalc.calc_plane_eq(
reference_point_1,
reference_point_2,
reference_point_3,
)
log.info(S('the equation is {}x + {}y + {}z = {}', ra, rb, rc, rd))
log.info(T('Calculating angles'))
angles = []
for _ts in u.trajectory[frame_slice]:
point1 = u.select_atoms(plane_selection[0]).center_of_geometry()
point2 = u.select_atoms(plane_selection[1]).center_of_geometry()
point3 = u.select_atoms(plane_selection[2]).center_of_geometry()
a, b, c, d = libcalc.calc_plane_eq(point1, point2, point3)
angles.append(
libcalc.calc_planes_angle(
ra,
rb,
rc,
a,
b,
c,
aunit=aunit,
))
log.info(S('calculated a total of {} angles.', len(angles)))
if export:
libio.export_data_to_file(
list(range(len(u.trajectory))[frame_slice]),
angles,
fname=export,
header=('# Angular oscillation between a plane representatives\n'
'# topology: {}\n'
'# trajectories: {}\n'
'# selections: {}\n'
'# frame,angle({})\n').format(
topology,
', '.join(t.resolve().str() for t in trajectories),
plane_selection,
aunit,
),
)
if plot:
plotvars = plotvars or dict()
plotvars.setdefault(
'labels',
'plane: {}'.format(' and '.join(plane_selection)),
)
log.info(T('plot params:'))
for k, v in plotvars.items():
log.info(S('{} = {!r}', k, v))
libplot.param(
list(range(len(u.trajectory))[frame_slice]),
angles,
**plotvars,
)
log.info(S('done'))
return
def main(topology, trajectories, insort=False, **kwargs):
"""Execute main client logic."""
log.info(T('reporting'))
libmda.load_universe(topology, *trajectories, insort=insort)
log.info(S('done'))
return
def main(topology,
trajectories,
start=None,
stop=None,
step=None,
selections=None,
export=False,
plot=False,
plotvars=None,
**kwargs):
"""Execute client main logic."""
log.info(T('starting RMSFs calculation'))
topology = Path(topology)
trajectories = [Path(t) for t in trajectories]
u = libmda.load_universe(topology, *trajectories)
frame_slice = libio.frame_slice(
start=start,
stop=stop,
step=step,
)
if selections is None:
selections = ['all']
if not isinstance(selections, list) or len(selections) == 0:
raise TypeError('selections must be LIST with at least one element')
log.info(T('calculating'))
for sel in selections:
labels = []
rmsfs = []
log.info(S('for selection: {}', sel))
atom_group = u.select_atoms(sel)
labels = libmda.draw_atom_label_from_atom_group(atom_group)
rmsfs = libcalc.mda_rmsf(
atom_group,
frame_slice=frame_slice,
)
if export:
libio.export_data_to_file(
labels,
rmsfs,
fname=export,
header=("# Date: {}\n"
"# Topology: {}\n"
"# Trajectories {}\n"
"# Atom,RMSF\n").format(
datetime.now().strftime("%d/%m/%Y, %H:%M:%S"),
Path(topology).resolve(),
', '.join(f.resolve().str() for f in trajectories),
),
)
if plot:
plotvars = plotvars or dict()
plotvars.setdefault('series_labels', selections)
log.info(T('plot params:'))
for k, v in plotvars.items():
log.info(S('{} = {!r}', k, v))
libplot.label_dots(
labels,
rmsfs,
**plotvars,
)
return
def main(
topology,
trajectories,
insort=False,
start=None,
stop=None,
step=None,
ref_frame=0,
selections=None,
export=False,
plot=False,
plotvars=None,
**kwargs
):
"""Execute main client logic."""
log.info(T('starting'))
u = libmda.load_universe(topology, *trajectories, insort=insort)
frame_slice = libio.frame_slice(
start=start,
stop=stop,
step=step,
)
if selections is None:
selections = ['all']
rmsds = []
for selection in selections:
rmsds.append(
libcalc.mda_rmsd(
u,
frame_slice=frame_slice,
selection=selection,
ref_frame=ref_frame,
)
)
if export:
libio.export_data_to_file(
list(range(len(u.trajectory))[frame_slice]),
*rmsds,
fname=export,
delimiter=',',
header=(
"# Date: {}\n'"
"# Topology: {}\n"
"# Trajectories : {}\n"
"# ref frame: {}\n"
"# frame number,{}\n"
).format(
datetime.now(),
Path(topology).resolve(),
', '.join(f.resolve().str() for f in trajectories),
ref_frame,
','.join(selections),
),
)
if plot:
plotvars = plotvars or dict()
plotvars.setdefault('labels', selections)
log.info(T('plot params:'))
for k, v in plotvars.items():
log.info(S('{} = {!r}', k, v))
libplot.param(
list(range(len(u.trajectory))[frame_slice]),
rmsds,
**plotvars,
)
return
def main(
topology,
trajectories,
insort=None,
start=None,
stop=None,
step=None,
selection='all',
traj_output='traj_out.dcd',
top_output=None,
unwrap=False,
unwrap_reference=None,
unwrap_compound='fragments',
align=False,
**kwargs,
):
"""Execute main client logic."""
log.info(T('editing trajectory'))
topology = Path(topology)
trajectories = [Path(t) for t in trajectories]
if insort:
trajectories = libio.sort_numbered_input(*trajectories)
u = libmda.load_universe(topology, *trajectories)
if unwrap:
log.info(T('unwrapping'))
log.info(S('set to: {}', unwrap))
log.info(S('reference: {}', unwrap_reference))
log.info(S('compound: {}', unwrap_compound))
if align:
log.info(T('Alignment'))
log.info(S('trajectory selection will be aligned to subselection:'))
log.info(S('- {}', align, indent=2))
align_reference = mda.Universe(Path(topology).str())
log.info(T('transformation'))
sliceObj = libio.frame_slice(start, stop, step)
log.info(S('selecting: {}', selection))
atom_selection = u.select_atoms(selection)
log.info(S('with {} atoms', atom_selection.n_atoms, indent=2))
log.info(T('saving trajectory'))
traj_output = Path(traj_output)
log.info(S('destination: {}', traj_output.resolve().str()))
with mda.Writer(traj_output.str(), atom_selection.n_atoms) as W:
for i, _ts in zip(
range(len(u.trajectory))[sliceObj],
u.trajectory[sliceObj],
):
log.info(S('working on frame: {}', i))
if unwrap:
log.debug(S('unwrapping', indent=2))
atom_selection.unwrap(
reference=unwrap_reference,
compound=unwrap_compound,
)
if align:
try:
libmda.mdaalignto(u, align_reference, selection=align)
except ZeroDivisionError:
_controlled_exit()
W.write(atom_selection)
log.info(S('trajectory saved'))
if top_output:
log.info(T('saving topology'))
fout = libio.parse_top_output(top_output, traj_output)
log.info(S('saving frame 0 to: {}', fout.resolve()))
with mda.Writer(fout.str(), atom_selection.n_atoms) as W:
for _ts in u.trajectory[sliceObj][0:1]:
if unwrap:
log.debug(S('unwrapping for topology', indent=2))
atom_selection.unwrap(
reference=unwrap_reference,
compound=unwrap_compound,
)
W.write(atom_selection)
log.info(S('Done'))
return
def main(topology,
trajectories,
insort=False,
sel1='all',
sel2='all',
start=None,
stop=None,
step=None,
export=False,
plot=False,
plotvars=None,
**kwargs):
"""Execute main client logic."""
log.info(T('measuring distances'))
topology = Path(topology)
trajectories = [Path(t) for t in trajectories]
u = libmda.load_universe(topology, *trajectories, insort=insort)
frame_slice = libio.frame_slice(
start=start,
stop=stop,
step=step,
)
log.info(T('defining atom seletions'))
log.info(S('atom selection #1: {}', sel1))
log.info(S('atom selection #2: {}', sel2))
atom_sel1 = u.select_atoms(sel1)
atom_sel2 = u.select_atoms(sel2)
distances = np.ones(len(u.trajectory[frame_slice]), dtype=np.float32)
log.info(T('Calculating distances'))
# https://www.mdanalysis.org/MDAnalysisTutorial/atomgroups.html
# https://www.mdanalysis.org/docs/documentation_pages/core/groups.html#MDAnalysis.core.groups.AtomGroup.center_of_geometry
with libcli.ProgressBar(distances.size, suffix='frames') as pb:
for i, _ts in enumerate(u.trajectory[frame_slice]):
distances[i] = np.linalg.norm(
np.subtract(
atom_sel1.center_of_geometry(),
atom_sel2.center_of_geometry(),
))
pb.increment()
log.info(S('calculated a total of {} distances.', len(distances)))
if export:
libio.export_data_to_file(
list(range(len(u.trajectory))[frame_slice]),
distances,
fname=export,
header=('# Distances between two selections centers of geomemtry\n'
'# topology: {}\n'
'# trajectories: {}\n'
'# selection #1: {}\n'
'# selection #2: {}\n'
'# frame,distance\n').format(
topology,
', '.join(t.resolve().str() for t in trajectories),
sel1,
sel2,
),
)
if plot:
plotvars = plotvars or dict()
plotvars.setdefault('labels', '{} dist {}'.format(sel1, sel2))
log.info(T('plot params:'))
for k, v in plotvars.items():
log.info(S('{} = {!r}', k, v))
libplot.param(
list(range(len(u.trajectory))[frame_slice]),
distances,
**plotvars,
)
log.info(S('done'))
return
def mda_rmsd(
universe,
frame_slice=None,
selection='all',
ref_frame=0,
):
"""
Calculate RMSDs observed for a selection.
Uses `MDAnalysis RMSD <https://www.mdanalysis.org/docs/documentation_pages/analysis/rms.html?highlight=rmsd#MDAnalysis.analysis.rms.RMSD>`_.
Example
-------
* Calculate RMSDs observed for the whole system along the whole trajectory.
>>> mda_rmsd(universe)
* Calculate the RMSDs observed for selection `segid A` for every 10 frames.
>>> mda_rmsd(universe, slice(0, None, 10), selection='segid A')
Parameters
----------
MDAnalysis Universe
The MDAnalysis `universe <https://www.mdanalysis.org/docs/documentation_pages/core/universe.html?highlight=universe#core-object-universe-mdanalysis-core-universe>`_.
frame_slice : any, optional
The frames in the trajectory to consider.
If ``None`` considers all frames.
Accepts any argument that
:py:func:`taurenmd.libs.libio.evaluate_to_slice` can receive.
Defaults to ``None``.
selection : str, optional
The selection upon which calculate the RMSDs.
Defaults to ``'all'``.
ref_frames : int, optional
The reference frame against which calculate the RMSDs.
Defaults to ``0``.
Returns
-------
Numpy Array
The array containing the calculated RMSDs of shape (N,), where
N is the number of frames.
Raises
------
ValueError
If ``frame_slice`` is not ``None`` or ``slice`` object.
MDAnalysis Exceptions
Any exceptions that could come from MDAnalysis RMSF computation.
""" # noqa: E501
log.info(T('Calculating RMSDs'))
frame_slice = libio.evaluate_to_slice(value=frame_slice)
log.info(S('for selection: {}', selection))
log.info(S('for trajectory slice: {}', frame_slice))
R = mdaRMSD(
universe,
universe,
select=selection,
groupselection=None,
ref_frame=ref_frame,
verbose=False,
)
R.run(verbose=False)
# rmsds[:, ii] = R.rmsd[:, 2][self._fslicer]
return R.rmsd[frame_slice, 2]
def main(
topology,
trajectories,
plane_selection,
aunit='degrees',
start=None,
stop=None,
step=None,
export=False,
**kwargs,
):
"""Execute main client logic."""
log.info(T('starting'))
topology = Path(topology)
trajectories = [Path(t) for t in trajectories]
u = libmda.load_universe(topology, *trajectories)
log.info(T('transformation'))
fSlice = libio.frame_slice(start=start, stop=stop, step=step)
origin_selection = ' or '.join(plane_selection)
pABC_atomG = u.select_atoms(origin_selection)
ABC_selections = plane_selection
# p stands for point
pA_atomG = u.select_atoms(ABC_selections[0])
pB_atomG = u.select_atoms(ABC_selections[1])
pC_atomG = u.select_atoms(ABC_selections[2])
u.trajectory[0]
# defining the center of reference
pABC_cog = pABC_atomG.center_of_geometry()
log.info(T('Original Center of Geometry'))
log.info(S('for frame: 0'))
log.info(S('for selection: {}', origin_selection))
log.info(S('pABC_cog: {}', pABC_cog))
log.info(T('Transfering'))
log.info(S('all coordinates of reference frame to the origin 0, 0, 0'))
pABC_atomG.positions = pABC_atomG.positions - pABC_cog
log.info(S('COG in origin: {}', pABC_atomG.center_of_geometry()))
log.info(T('defining the reference axes'))
pA_cog = pA_atomG.center_of_geometry()
pB_cog = pB_atomG.center_of_geometry()
pC_cog = pC_atomG.center_of_geometry()
log.info(S('plane points definition:'))
log.info(S('pA: {}', pA_cog))
log.info(S('pB: {}', pB_cog))
log.info(S('pC: {}', pC_cog))
log.info(T('defining the normal vector to reference plane'))
ref_plane_normal = libcalc.calc_plane_normal(pA_cog, pB_cog, pC_cog)
log.info(S('plane normal: {}', ref_plane_normal))
log.info(S('done'))
log.info(T('defining the cross product vector'))
ref_plane_cross = np.cross(pA_cog, ref_plane_normal)
log.info(S('np cross: {}', ref_plane_cross))
roll_angles = []
pitch_angles = []
yaw_angles = []
for i, _ts in enumerate(u.trajectory[fSlice]):
print(f'.. working for frame :{i}')
pABC_cog_ts = pABC_atomG.center_of_geometry()
pABC_atomG.positions = pABC_atomG.positions - pABC_cog_ts
pA_cog_ts = pA_atomG.center_of_geometry()
pB_cog_ts = pB_atomG.center_of_geometry()
pC_cog_ts = pC_atomG.center_of_geometry()
ts_plane_normal = libcalc.calc_plane_normal(
pA_cog_ts,
pB_cog_ts,
pC_cog_ts,
)
ts_plane_cross = np.cross(pA_cog_ts, ts_plane_normal)
# Calculating Quaternion Rotations
roll_Qs_tuples = libcalc.generate_quaternion_rotations(
ref_plane_normal,
pA_cog_ts,
)
pitch_Qs_tuples = libcalc.generate_quaternion_rotations(
ref_plane_cross,
ts_plane_normal,
)
yaw_Qs_tuples = libcalc.generate_quaternion_rotations(
pA_cog,
ts_plane_cross,
)
roll_minimum = libcalc.sort_by_minimum_Qdistances(
roll_Qs_tuples,
pA_cog,
)[0][0]
pitch_minimum = libcalc.sort_by_minimum_Qdistances(
pitch_Qs_tuples,
ref_plane_normal,
)[0][0]
yaw_minimum = libcalc.sort_by_minimum_Qdistances(
yaw_Qs_tuples,
ref_plane_cross,
)[0][0]
if aunit == 'degrees':
roll_angles.append(round(roll_minimum.degrees, 3))
pitch_angles.append(round(pitch_minimum.degrees, 3))
yaw_angles.append(round(yaw_minimum.degrees, 3))
else:
roll_angles.append(round(roll_minimum.radians, 3))
pitch_angles.append(round(pitch_minimum.radians, 3))
yaw_angles.append(round(yaw_minimum.radians, 3))
if export:
file_names = []
for _fname in ['roll', 'pitch', 'yaw']:
file_names.append(
libio.add_prefix_to_path(
export,
f"{_fname}_angles_",
)
)
log.info(T('Saving data to files'))
for data, fname in zip(
[roll_angles, pitch_angles, yaw_angles],
file_names,
):
log.info(S('saving {}', fname))
libio.export_data_to_file(
list(range(len(u.trajectory))[fSlice]),
data,
fname=fname,
header=(
'# Topology: {}\n'
'# Trajectories: {}\n'
'# Plane Selection: {}\n'
'# frame,ange{}\n'
).format(
topology,
', '.join(t.resolve().str() for t in trajectories),
origin_selection,
aunit,
),
)
log.info(S('done'))
return