def worker_by_state(rank, n_cores=1, traj=None, lines=None, dtype='dict'):
'''worker for CpptrajState
'''
# need to make a copy if lines since python's list is dangerous
# it's easy to mess up with mutable list
# do not use lines.copy() since this is not available in py2.7
if lines is None:
lines = []
my_lines = [line for line in lines]
from pytraj.utils import split_range
from pytraj.core.c_core import _load_batch
mylist = split_range(n_cores, 0, traj.n_frames)[rank]
start, stop = mylist
crdframes_string = 'crdframes ' + ','.join((str(start + 1), str(stop)))
for idx, line in enumerate(my_lines):
if not line.lstrip().startswith('reference'):
my_lines[idx] = ' '.join(
('crdaction traj', line, crdframes_string))
# do not use 'extend' in this case
# will get weird output
my_lines = [
'loadtraj name traj',
] + my_lines
state = _load_batch(my_lines, traj)
state.run()
if dtype == 'dict':
# exclude DatasetTopology and TrajectoryCpptraj
return (rank, state.data[2:].to_dict())
else:
raise ValueError('must use dtype="dict"')
def load_cpptraj_state(txt, traj=None):
"""load text to CpptrajState
Examples
--------
>>> # load from string
>>> import pytraj as pt
>>> state = pt.datafiles.load_cpptraj_state('''
... parm data/tz2.ortho.parm7
... trajin data/tz2.ortho.nc
... autoimage
... center origin
... rms''')
>>> state.run()
CpptrajState, include:
<datasetlist: 2 datasets>
>>> # load from string with given TrajectoryIterator
>>> traj = pt.datafiles.load_tz2_ortho()
>>> state = pt.datafiles.load_cpptraj_state('''
... autoimage
... center origin
... rms''', traj=traj)
>>> state.run()
CpptrajState, include:
<datasetlist: 2 datasets>
"""
from pytraj.core.c_core import _load_batch
return _load_batch(txt, traj=traj)
def load_cpptraj_state(txt, traj=None):
"""load text to CpptrajState
Examples
--------
>>> # load from string
>>> import pytraj as pt
>>> state = pt.datafiles.load_cpptraj_state('''
... parm data/tz2.ortho.parm7
... trajin data/tz2.ortho.nc
... autoimage
... center origin
... rms''')
>>> state.run()
CpptrajState, include:
<datasetlist: 2 datasets>
>>> # load from string with given TrajectoryIterator
>>> traj = pt.datafiles.load_tz2_ortho()
>>> state = pt.datafiles.load_cpptraj_state('''
... autoimage
... center origin
... rms''', traj=traj)
>>> state.run()
CpptrajState, include:
<datasetlist: 2 datasets>
"""
if os.path.exists(txt):
# txt is a file
return load_cpptraj_file(txt)
else:
from pytraj.core.c_core import _load_batch
return _load_batch(txt, traj=traj)
def worker_state(rank, n_cores=1, traj=None, lines=None, dtype='dict'):
'''worker for CpptrajState
'''
# need to make a copy if lines since python's list is dangerous
# it's easy to mess up with mutable list
# do not use lines.copy() since this is not available in py2.7
if lines is None:
lines = []
my_lines = [line for line in lines]
from pytraj.utils import split_range
from pytraj.core.c_core import _load_batch
mylist = split_range(n_cores, 0, traj.n_frames)[rank]
start, stop = mylist
crdframes_string = 'crdframes ' + ','.join((str(start + 1), str(stop)))
for idx, line in enumerate(my_lines):
if not line.lstrip().startswith('reference'):
my_lines[idx] = ' '.join(('crdaction traj', line, crdframes_string
))
# do not use 'extend' in this case
# will get weird output
my_lines = ['loadtraj name traj', ] + my_lines
state = _load_batch(my_lines, traj)
state.run()
if dtype == 'dict':
# exclude DatasetTopology and TrajectoryCpptraj
return (rank, state.data[2:].to_dict())
else:
raise ValueError('must use dtype="dict"')
def load_cpptraj_output(txt, dtype=None):
"""load output from cpptraj
Parameters
----------
txt : str
cpptraj's trajin
dtype : str, return data type
Returns
-------
if dtype is 'state', return CpptrajState
if dtype is 'ndarray', return ndarray and so on
"""
from pytraj.core.c_core import _load_batch
from pytraj.datasetlist import DatasetList
from pytraj import ArgList
commands = list(filter(lambda x: x, txt.split("\n")))
for idx, line in enumerate(commands):
if 'parm' in line:
arglist = ArgList(line)
# use absolute path
fname = os.path.abspath(arglist.get_string_key('parm'))
commands[idx] = " ".join(('parm', fname))
if 'trajin' in line:
arglist = ArgList(line)
# use absolute path
relative_fname = arglist.get_string_key('trajin')
the_rest_of_line = ' '.join(line.split(relative_fname)[1:])
fname = os.path.abspath(relative_fname)
commands[idx] = " ".join(('trajin', fname, the_rest_of_line))
txt = "\n".join([line for line in commands])
state = _load_batch(txt, traj=None)
state.run()
if dtype == 'state':
out = state
else:
out = DatasetList(state.datasetlist)
return out