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 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 test_parse_top_output(top, traj, expected):
"""Test parse topology output."""
result = io.parse_top_output(top, traj_output=traj)
assert isinstance(result, Path)
assert result.name == expected