def test_modify_frame_use_Pipeline(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
dslist = CpptrajDatasetList()
dslist.add_new('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = ['autoimage', 'strip :WAT', 'createcrd mycrd', ]
actlist = Pipeline(commands, top=traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(dslist['mycrd'].xyz,
pt.get_coordinates(traj,
mask='!:WAT',
autoimage=True))
def test_modify_frame_use_Pipeline(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
dslist = CpptrajDatasetList()
dslist.add('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = [
'autoimage',
'strip :WAT',
'createcrd mycrd',
]
actlist = Pipeline(commands, top=traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(dslist['mycrd'].xyz,
pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def strip_prmtop(prmtop, mask=":WAT,:Na+,:Cl-"):
"""Strip residues from a structure and write a new parameter file. This could probably also be done with ParmEd.
Parameters
----------
prmtop : os.PathLike
Existing Amber parameter file.
mask : str, optional, default=':WAT,:Na+,:Cl-'
The list of atom masks to strip.
Returns
-------
stripped: :class:`pytraj.topology`
The stripped topology that can be used to read stripped trajectories with :class:`pytraj`.
"""
structure = pt.load_topology(os.path.normpath(prmtop))
stripped = pt.strip(mask, structure)
# stripped_name = os.path.join(os.path.splitext(prmtop)[0], '-stripped', os.path.splitext(prmtop)[1])
# stripped.save(filename=stripped_name)
# logger.debug('Stripping {} from parameter file and writing {}...'.format(mask, stripped_name))
return stripped
def strip_prmtop(prmtop, mask=":WAT,:Na+,:Cl-"):
"""Strip residues from a structure and write a new parameter file. This could probably also be done with ParmEd.
Parameters:
----------
prmtop : {str}
Existing parameter file
mask : {str}, optional
The list of atom masks to strip (the default is [':WAT,:Na+,:Cl-'])
Returns:
-------
stripped.topology
The stripped topology that can be used to read stripped trajectories with `pytraj`
"""
structure = pt.load_topology(os.path.normpath(prmtop))
stripped = pt.strip(mask, structure)
# stripped_name = os.path.join(os.path.splitext(prmtop)[0], '-stripped', os.path.splitext(prmtop)[1])
# stripped.save(filename=stripped_name)
# log.debug('Stripping {} from parameter file and writing {}...'.format(mask, stripped_name))
return stripped
stop = 2950
every = 50
trajectory = '../../../1-408cent1_skip100.nc'
topology = '../../../PHYb_ff14.prmtop'
stripmask = ':505-1008,Na+'
#solvmask is the mask for the atom around which you can keep the closest waters
solvmask = ':504@CHC'
wat2keep = 390
##########################################################
##########################################################
traj = pt.iterload(trajectory, top=topology)
top = pt.load_topology(topology)
stripped_prm = pt.strip(top, mask=stripmask)
stripped_traj = pt.strip(traj, stripmask)
print stripmask, "stripped"
print "selecting closest", wat2keep, "water molecules ..."
closest_traj = pt.closest(stripped_traj,
mask=solvmask,
n_solvents=wat2keep,
dtype='trajectory')
# NOTE: framelist here starts from zero!
framelist = range(start - 1, stop, every)
for frame in framelist:
# NOTE: output files have numbering starting from one!
from __future__ import print_function
from parmed.utils.netcdf import netcdf_file
import pytraj as pt
import numpy as np
fh = netcdf_file('data/mdfrc',
mmap=False) # change mdfrc to your force filename
forces = fh.variables['forces']
# do similar thing for velocities
top = pt.load_topology(
'data/mdfrc.prmtop') # change prmtop to your parm7 filename
traj = pt.Trajectory(xyz=np.ascontiguousarray(forces[:], dtype='f8'), top=top)
print('original trajectory', traj)
# strip atom atoms
# change ':1-100' to your mask (e.g ':WAT')
new_traj = pt.strip(':1-100', traj)
print('stripped trajectory', new_traj)
# write trajectory
new_traj.save('test.nc', overwrite=True)
