def inner(*args, **kwd):
args = list(args)
traj = kwd.get('traj', args[0])
frame_indices = kwd.get('frame_indices')
ref = kwd.get('ref')
top = kwd.get('top')
if 'mask' in kwd.keys():
mask = kwd.get('mask')
else:
mask = args[1]
# overwrite
kwd['top'] = get_topology(traj, top)
if ref is not None:
kwd['ref'] = get_reference(traj, ref)
if 'traj' in kwd.keys():
kwd['traj'] = get_fiterator(traj, frame_indices)
else:
args[0] = get_fiterator(traj, frame_indices)
if not isinstance(mask, string_types):
mask = array_to_cpptraj_atommask(mask)
if 'mask' in kwd.keys():
kwd['mask'] = mask
else:
args[1] = mask
return f(*args, **kwd)
def vector(traj=None,
command="",
frame_indices=None,
dtype='ndarray',
top=None):
"""perform vector calculation. See example below. Same as 'vector' command in cpptraj.
Parameters
----------
traj : Trajectory-like or iterable that produces :class:`pytraj.Frame`
command : str or a list of strings, cpptraj command
frame_indices : array-like, optional, default None
only perform calculation for given frame indices
dtype : output's dtype, default 'ndarray'
top : Topology, optional, default None
Returns
-------
out : numpy ndarray, shape (n_frames, 3) if command is a string
numpy ndarray, shape (n_vectors, n_frames, 3) if command is a list of strings
Examples
--------
>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> data = pt.vector.vector(traj, "@CA @CB")
>>> data = pt.vector.vector(traj, [("@CA @CB"),])
>>> data = pt.vector.vector(traj, "principal z")
>>> data = pt.vector.vector(traj, "principal x")
>>> data = pt.vector.vector(traj, "ucellx")
>>> data = pt.vector.vector(traj, "boxcenter")
>>> data = pt.vector.vector(traj, "box")
Notes
-----
It's faster to calculate with a list of commands.
For example, if you need to perform 3 calculations for 'ucellx', 'boxcenter', 'box'
like below:
>>> data = pt.vector.vector(traj, "ucellx")
>>> data = pt.vector.vector(traj, "boxcenter")
>>> data = pt.vector.vector(traj, "box")
You should use a list of commands for faster calculation.
>>> comlist = ['ucellx', 'boxcenter', 'box']
>>> data = pt.vector.vector(traj, comlist)
"""
c_dslist = CpptrajDatasetList()
top_ = get_topology(traj, top)
list_of_commands = get_list_of_commands(command)
fi = get_fiterator(traj, frame_indices)
actlist = ActionList()
for command in list_of_commands:
act = c_action.Action_Vector()
actlist.add(act, command, top_, dslist=c_dslist)
actlist.compute(fi)
return get_data_from_dtype(c_dslist, dtype=dtype)
def __init__(self,
filename=None,
top=None,
xyz=None,
velocity=None,
force=None,
time=None):
self._top = get_topology(filename, top)
if velocity is not None:
velocity = np.asarray(velocity, dtype='f8')
if force is not None:
force = np.asarray(force, dtype='f8')
if time is not None:
time = np.asarray(time, dtype='f8')
self.velocities = velocity
self.forces = force
self.time = time
if self._top is None:
self._top = Topology()
self._xyz = None
self._boxes = None
# use those to keep lifetime of Frame
self._life_holder = None
self._frame_holder = None
if filename is None or filename == "":
if xyz is not None:
if self.top.is_empty():
raise ValueError("must have a non-empty Topology")
else:
assert self.top.n_atoms == xyz.shape[
1], "must have the same n_atoms"
self._xyz = np.asarray(xyz)
else:
self._xyz = None
elif hasattr(filename, 'xyz'):
# make sure to use `float64`
self._xyz = filename.xyz.astype(np.float64)
elif isinstance(filename, (string_types, list, tuple)):
self.load(filename)
else:
raise ValueError('filename must be None, a Trajectory or a string')
if hasattr(self._xyz, 'shape'):
assert self.top.n_atoms == self._xyz.shape[
1], "must have the same n_atoms"
if hasattr(filename, 'unitcells'):
self._boxes = filename.unitcells
def _dbscan(traj=None,
mask='*',
minpoints=None,
epsilon=0.,
sievetoframe=False,
random_sieveseed=1,
kdist=None,
kfile=None,
sieve=1,
metric='rms',
top=None,
options=''):
'''perform clustering and return cluster index for each frame
Parameters
----------
traj : Trajectory-like or iterable that produces Frame
mask : str, default: * (all atoms)
n_clusters: int, default: 10
random_point : bool, default: True
maxit : int, default: 100
max iterations
metric : str, {'rms', 'dme'}
distance metric
top : Topology, optional, default: None
only need to provide this Topology if ``traj`` does not have one
options : option to save data to files.
Returns
-------
1D numpy array of frame indices
'''
# don't need to get_topology
_top = get_topology(traj, top)
_clusters = 'dbscan minpoints ' + str(minpoints)
_mask = mask
_epsilon = 'epsilon ' + str(epsilon)
_sievetoframe = 'sievetoframe' if sievetoframe else ''
_kdist = 'kdist' + str(kdist) if kdist is not None else ''
_kfile = kfile if kfile is not None else ''
_sieve = 'sieve ' + str(sieve)
_metric = metric
_random_sieveseed = 'random ' + str(random_sieveseed)
_output = options
command = ' '.join((_clusters, _epsilon, _sievetoframe, _kdist, _sieve,
_kfile, _metric, _random_sieveseed, _mask, _output))
return _cluster(traj, command, top=_top, dtype='ndarray')
def read_gaussian_output(filename=None, top=None):
"""return a `pytraj.trajectory.Trajectory` object
Parameters
----------
fname : str, filename
top : {str, Topology}, optional, default None
pytraj.Topology or a filename or None
if None, use `antechamber` to generate mol2 file, need set $AMBERHOME env
Requires
--------
cclib (``pip install cclib``)
>>> import pytraj as pt
>>> pt.tools.read_gaussian_output("gau.out", "mytest.pdb") # doctest: +SKIP
"""
import cclib
from pytraj.trajectory.trajectory import Trajectory
from pytraj.utils.context import tempfolder
from pytraj.utils.get_common_objects import get_topology
_top = get_topology(None, top)
gau = cclib.parser.Gaussian(filename)
go = gau.parse()
if _top is None: # pragma: no cover
try:
amberhome = os.environ['AMBERHOME']
except KeyError:
raise KeyError("must set AMBERHOME")
fpath = os.path.abspath(filename)
with tempfolder():
at = amberhome + "/bin/antechamber"
out = "-i %s -fi gout -o tmp.mol2 -fo mol2 -at amber" % fpath
cm = " ".join((at, out))
os.system(cm)
return Trajectory(xyz=go.atomcoords, top="tmp.mol2")
else:
return Trajectory(xyz=go.atomcoords, top=_top)
def vector_mask(traj=None,
mask="",
frame_indices=None,
dtype='ndarray',
top=None):
"""compute vector between two maskes
Parameters
----------
traj : Trajectory-like or iterable that produces Frame
mask: str or array of string or array of intergers, shape (n_vectors, 2)
vector maskes
frame_indices : array-like or iterable that produces integer number
frame indices
dtype : str, default 'ndarray'
output dtype
top : Topology, optional, default None
Returns
-------
if mask is a string, return 2D ndarray, shape (n_frames, 3)
if mask is a list of strings or a 2D ndarray, return 3D ndarray, shape (n_vectors, n_frames, 3)
Examples
--------
>>> # calcualte N-H vector
>>> import pytraj as pt
>>> import numpy as np
>>> traj = pt.load_sample_data('tz2')
>>> from pytraj import vector as va
>>> n_indices = pt.select_atoms('@N', traj.top)
>>> h_indices = n_indices + 1
>>> # create n-h pair for vector calculation
>>> n_h_pairs = np.array(list(zip(n_indices, h_indices)))
>>> data_vec = va.vector_mask(traj, n_h_pairs, dtype='ndarray')
>>> # compute vectors for specific frame indices (0, 4)
>>> data_vec = va.vector_mask(traj, n_h_pairs, frame_indices=[0, 4], dtype='ndarray')
"""
from pytraj.utils.get_common_objects import get_topology, get_data_from_dtype, get_fiterator
from pytraj.utils.get_common_objects import get_list_of_commands
from pytraj.datasets.c_datasetlist import DatasetList as CpptrajDatasetList
from pytraj.analysis.c_action.c_action import Action_Vector
from pytraj.analysis.c_action.actionlist import ActionList
fi = get_fiterator(traj, frame_indices)
_top = get_topology(fi, top)
dslist = CpptrajDatasetList()
template_command = ' mask '
cm_arr = np.asarray(mask)
if cm_arr.dtype.kind != 'i':
list_of_commands = get_list_of_commands(mask)
else:
if cm_arr.ndim != 2:
raise ValueError(
'if mask is a numpy.ndarray, it must have ndim = 2')
list_of_commands = _2darray_to_atommask_groups(cm_arr)
actlist = ActionList()
for command in list_of_commands:
act = Action_Vector()
_command = command + template_command
actlist.add(act, _command, _top, dslist=dslist)
actlist.compute(fi)
return get_data_from_dtype(dslist, dtype=dtype)