def test_param():
"""Test param plot."""
p = Path('param.pdf')
lplt.param(
list(range(10)),
list(range(10)),
filename='param.pdf',
)
assert p.exists()
p.unlink()
def test_label_dots():
"""Test label_dots plot."""
p = Path('label_dots.pdf')
lplt.param(
['a', 'b', 'c'],
list(range(3)),
filename='label_dots.pdf',
)
assert p.exists()
p.unlink()
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,
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=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