def _format_convert(input_filename, output_filename):
"""
Examples
--------
import pytraj as pt
pt.io._format_convert('test.cpp4', 'test.dx')
"""
from pytraj.core.c_core import CpptrajState, Command
state = CpptrajState()
with Command() as command:
command.dispatch(state,
'readdata {} name mydata'.format(input_filename))
command.dispatch(state, 'writedata {} mydata '.format(output_filename))
def convert(input_filename, to):
"""convert datafile format (e.g .ccp4 to .dx, .dat to .xmgrace)
Examples
--------
>>> import pytraj as pt
>>> pt.datafiles.convert('test.cpp4', 'test.dx') # doctest: +SKIP
"""
from pytraj.core.c_core import CpptrajState, Command
state = CpptrajState()
with Command() as command:
command.dispatch(state,
'readdata {} name mydata'.format(input_filename))
command.dispatch(state, 'writedata {} mydata '.format(to))
def iterload_remd(filename, top=None, T="300.0"):
"""Load temperature remd trajectory for single temperature.
e.g: Suppose you have replica trajectoris remd.x.00{1-4}.
You want to load and extract only frames at 300 K, use this method
Parameters
----------
filename : str
top : {str, Topology}
T : {float, str}, default=300.0
Returns
-------
pytraj.traj.TrajectoryCpptraj
Notes
-----
"""
from pytraj.core.c_core import CpptrajState, Command
state = CpptrajState()
# add keyword 'remdtraj' to trick cpptraj
trajin = ' '.join(('trajin', filename, 'remdtraj remdtrajtemp', str(T)))
if isinstance(top, string_types):
top = load_topology(top)
else:
top = top
state.data.add('topology', 'remdtop')
# set topology
state.data['remdtop']._top = top
# load trajin
with Command() as cm:
cm.dispatch(state, trajin)
cm.dispatch(state, 'loadtraj name remdtraj')
# state.data.remove_set(state.data['remdtop'])
traj = state.data[-1]
# assign state to traj to avoid memory free
traj._base = state
return traj
def write_data(filename, data):
"""same as writedata in cpptraj. (this is work in progress, only support 1D-array for now)
Parameters
----------
filename : str
output filename. File format is deteced by its name.
data : ndarray
dtype : str, {'double', 'float', 'grid_float', 'grid_double'}, default 'double'
Examples
--------
>>> # xmgrace format
>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2()
>>> rmsd_data = pt.rmsd(traj, ref=0)
>>> pt.io.write_data('my.agr', rmsd_data)
>>> # gnu format
>>> pt.io.write_data('my.gnu', rmsd_data)
"""
data = np.asarray(data, dtype='f8')
dtype_map = {1: 'double', 3: 'grid_float'}
from pytraj.core.c_core import CpptrajState, Command
dtype = dtype_map[data.ndim]
if data.ndim == 3:
data = data.astype('f4')
state = CpptrajState()
dataset_name = 'my_data'
d0 = state.data.add(dtype=dtype, name=dataset_name)
d0.data = np.asarray(data)
cm = 'writedata {filename} {dataset_name}'.format(
filename=filename, dataset_name=dataset_name)
with Command() as command:
command.dispatch(state, cm)