def calc_density(traj=None,
command="",
top=None,
dtype='ndarray',
frame_indices=None):
# NOTE: trick cpptraj to write to file first and the reload
'''
Examples
--------
>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> pt.density(traj, 'charge')
'''
with tempfolder():
def _calc_density(traj, command):
# TODO: update this method if cpptraj save data to
# CpptrajDatasetList
dflist = DataFileList()
tmp_filename = "tmp_pytraj_out.txt"
command = "out " + tmp_filename + " " + command
act = c_action.Action_Density()
act(command, traj, top=top, dflist=dflist)
act.post_process()
dflist.write_all_datafiles()
absolute_path_tmp = os.path.abspath(tmp_filename)
return absolute_path_tmp
dslist = CpptrajDatasetList()
fname = _calc_density(traj, command)
dslist.read_data(fname)
return get_data_from_dtype(dslist, dtype)
def calc_density(traj=None,
command="",
top=None,
dtype='ndarray',
frame_indices=None):
# NOTE: trick cpptraj to write to file first and the reload
'''
Examples
--------
>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> pt.density(traj, 'charge')
'''
with tempfolder():
def _calc_density(traj, command):
# TODO: update this method if cpptraj save data to
# CpptrajDatasetList
dflist = DataFileList()
tmp_filename = "tmp_pytraj_out.txt"
command = "out " + tmp_filename + " " + command
act = c_action.Action_Density()
act(command, traj, top=top, dflist=dflist)
act.post_process()
dflist.write_all_datafiles()
absolute_path_tmp = os.path.abspath(tmp_filename)
return absolute_path_tmp
dslist = CpptrajDatasetList()
fname = _calc_density(traj, command)
dslist.read_data(fname)
return get_data_from_dtype(dslist, dtype)
def read_data(filename, options=''):
"""same as readdata in cpptraj
Returns
-------
out : CpptrajDatasetList
"""
from pytraj.datasets import CpptrajDatasetList
cdslist = CpptrajDatasetList()
cdslist.read_data(filename, options)
return cdslist
