.. code-block:: python
- pywindow.MolecularSystem.load_file(`filepath`)
+ pywindow.molecular.MolecularSystem.load_file(`filepath`)
2. Using RDKit molecule object as an input:
.. code-block:: python
- pywindow.MolecularSystem.load_rdkit_mol(rdkit.Chem.rdchem.Mol)
+ pywindow.molecular.MolecularSystem.load_rdkit_mol(rdkit.Chem.rdchem.Mol)
3. Using a dictionary (or another :attr:`MoleculeSystem.system`) as input:
.. code-block:: python
- pywindow.MolecularSystem.load_system({...})
+ pywindow.molecular.MolecularSystem.load_system({...})
Attributes
----------
@@ -1076,7 +1076,7 @@ Source code for pywindow.molecular
.. code-block:: python
- pywindow.MolecularSystem.swap_atom_keys({'he': 'H'})
+ pywindow.molecular.MolecularSystem.swap_atom_keys({'he': 'H'})
Parameters
----------
diff --git a/docs/_modules/pywindow/trajectory.html b/docs/_modules/pywindow/trajectory.html
index 4c0f22f..db04c08 100644
--- a/docs/_modules/pywindow/trajectory.html
+++ b/docs/_modules/pywindow/trajectory.html
@@ -139,7 +139,39 @@
Source code for pywindow.trajectory
-"""Module intended for the analysis of molecular dynamics trajectories."""
+"""
+Module intended for the analysis of molecular dynamics trajectories.
+
+The trajectory file (DL_POLY_C:HISTORY, PDB or XYZ) should be loaded with
+the one of the corresponding classes (DLPOLY, PDB or XYZ, respectively).
+
+Example
+-------
+In this example a DL_POLY_C HISTORY trajectory file is loaded.
+
+.. code-block:: python
+
+ pywindow.trajectory.DLPOLY('path/to/HISTORY')
+
+Then, each of the trajectory frames can be extracted and returned as a
+:class:`pywindow.molecular.MolecularSystem` object for analysis. See
+:mod:`pywindow.molecular` docstring for more information.
+
+Alternatively, the analysis can be performed on a whole or a chunk of
+the trajectory with the :func:`analysis()` function. The benefit is
+that the analysis can be performed in parallel and the results stored as a
+single JSON dictionary in a straightforward way. Also, the deciphering of the
+force field atom ids and the rebuilding of molecules can be applied to each
+frame in a consitent and automated manner. The downfall is that at the
+moment it is not possible to choose the set of parameters that are being
+calculated in the :class:`pywindow.molecular.Molecule` as the
+:func:`pywindow.molecular.Molecule.full_analysis()` is invoked by default.
+However, the computational cost of calculating majority of the structural
+properties is miniscule and it is usually the
+:func:`pywindow.molecular.MolecularSystem.rebuild_system()` step that is the
+bottleneck.
+
+"""
import os
import numpy as np
from copy import deepcopy
@@ -175,12 +207,65 @@ Source code for pywindow.trajectory
[docs]def make_supercell(system, matrix, supercell=[1, 1, 1]):
+
"""
+
Return a supercell.
+
+
This functions takes the input unitcell and creates a supercell of it that
+
is returned as a new :class:`pywindow.molecular.MolecularSystem`.
+
+
Parameters
+
----------
+
system : :attr:`pywindow.molecular.MolecularSystem.system`
+
The unit cell for creation of the supercell
+
+
matrix : :class:`numpy.array`
+
The unit cell parameters in form of a lattice.
+
+
supercell : :class:`list`, optional
+
A list that specifies the size of the supercell in the a, b and c
+
direction. (default=[1, 1, 1])
+
+
Returns
+
-------
+
:class:`pywindow.molecular.MolecularSystem`
+
Returns the created supercell as a new :class:`MolecularSystem`.
+
+
"""
user_supercell = [[1, supercell[0]], [1, supercell[1]], [1, supercell[1]]]
system = create_supercell(system, matrix, supercell=user_supercell)
return MolecularSystem.load_system(system)
[docs]class DLPOLY(object):
+
"""
+
A container for a DL_POLY_C type trajectory (HISTORY).
+
+
This function takes a DL_POLY_C trajectory file and maps it for the
+
binary points in the file where each frame starts/ends. This way the
+
process is fast, as it not require loading the trajectory into computer
+
memory. When a frame is being extracted, it is only this frame that gets
+
loaded to the memory.
+
+
Frames can be accessed individually and loaded as an unmodified string,
+
returned as a :class:`pywindow.molecular.MolecularSystem` (and analysed),
+
dumped as PDB or XYZ or JSON (if dumped as a
+
:attr:`pywindow.molecular.MolecularSystem.system`)
+
+
Attributes
+
----------
+
filepath : :class:`str`
+
The filepath.
+
+
system_id : :class:`str`
+
The system id inherited from the filename.
+
+
frames : :class:`dict`
+
A dictionary that is populated, on the fly, with the extracted frames.
+
+
analysis_output : :class:`dict`
+
A dictionary that is populated, on the fly, with the analysis output.
+
+
"""
def __init__(self, filepath):
# Image conventions - periodic boundary key.
self._imcon = {
@@ -270,7 +355,50 @@
Source code for pywindow.trajectory
self.no_of_atoms = header[2]
return header
-[docs] def get_frames(self, frames, override=False, **kwargs):
+
[docs] def get_frames(self, frames='all', override=False, **kwargs):
+
"""
+
Extract frames from the trajectory file.
+
+
Depending on the passed parameters a frame, a list of particular
+
frames, a range of frames (from, to), or all frames can be extracted
+
with this function.
+
+
Parameters
+
----------
+
frames : :class:`int` or :class:`list` or :class:`touple` or :class:`str`
+
Specified frame (:class:`int`), or frames (:class:`list`), or
+
range (:class:`touple`), or `all`/`everything` (:class:`str`).
+
(default=`all`)
+
+
override : :class:`bool`
+
If True, a frame already storred in :attr:`frames` can be override.
+
(default=False)
+
+
extract_data : :class:`bool`, optional
+
If False, a frame is returned as a :class:`str` block as in the
+
trajectory file. Ohterwise, it is extracted and returned as
+
:class:`pywindow.molecular.MolecularSystem`. (default=True)
+
+
swap_atoms : :class:`dict`, optional
+
If this kwarg is passed with an appropriate dictionary a
+
:func:`pywindow.molecular.MolecularSystem.swap_atom_keys()` will
+
be applied to the extracted frame.
+
+
forcefield : :class:`str`, optional
+
If this kwarg is passed with appropriate forcefield keyword a
+
:func:`pywindow.molecular.MolecularSystem.decipher_atom_keys()`
+
will be applied to the extracted frame.
+
+
Returns
+
-------
+
:class:`pywindow.molecular.MolecularSystem`
+
If a single frame is extracted.
+
+
None : :class:`NoneType`
+
If more than one frame is extracted, the frames are returned to
+
:attr:`frames`
+
+
"""
if override is True:
self.frames = {}
if isinstance(frames, int):
@@ -382,7 +510,74 @@
Source code for pywindow.trajectory
[docs] def analysis(
self, frames='all', ncpus=1, _ncpus=1, override=False, **kwargs
):
-
""" """
+
"""
+
Perform structural analysis on a frame/ set of frames.
+
+
Depending on the passed parameters a frame, a list of particular
+
frames, a range of frames (from, to), or all frames can be analysed
+
with this function.
+
+
The analysis is performed on each frame and each discrete molecule in
+
that frame separately. The steps are as follows:
+
+
1. A frame is extracted and returned as a :class:`MolecularSystem`.
+
2. If `swap_atoms` is set the atom ids are swapped.
+
3. If `forcefield` is set the atom ids are deciphered.
+
4. If `rebuild` is set the molecules in the system are rebuild.
+
5. Each discrete molecule is extracted as :class:`Molecule`
+
6. Each molecule is analysed with :func:`Molecule.full_analysis()`
+
7. Analysis output populates the :attr:`analysis_output` dictionary.
+
+
As the analysis of trajectories often have to be unique, many options
+
are conditional.
+
+
A side effect of this function is that the analysed frames are also
+
returned to the :attr:`frames` mimicking the behaviour of the
+
:func:`get_frames()`.
+
+
Parameters
+
----------
+
frames : :class:`int` or :class:`list` or :class:`touple` or :class:`str`
+
Specified frame (:class:`int`), or frames (:class:`list`), or
+
range (:class:`touple`), or `all`/`everything` (:class:`str`).
+
(default='all')
+
+
override : :class:`bool`
+
If True, an output already storred in :attr:`analysis_output` can
+
be override. (default=False)
+
+
swap_atoms : :class:`dict`, optional
+
If this kwarg is passed with an appropriate dictionary a
+
:func:`pywindow.molecular.MolecularSystem.swap_atom_keys()` will
+
be applied to the extracted frame.
+
+
forcefield : :class:`str`, optional
+
If this kwarg is passed with appropriate forcefield keyword a
+
:func:`pywindow.molecular.MolecularSystem.decipher_atom_keys()`
+
will be applied to the extracted frame.
+
+
modular : :class:`bool`, optional
+
If this kwarg is passed a
+
:func:`pywindow.molecular.MolecularSystem.make_modular()`
+
will be applied to the extracted frame. (default=False)
+
+
rebuild : :class:`bool`, optional
+
If this kwarg is passed a `rebuild=True` is passed to
+
:func:`pywindow.molecular.MolecularSystem.make_modular()` that
+
will be applied to the extracted frame. (default=False)
+
+
ncpus : :class:`int`, optional
+
If ncpus > 1, then the analysis is performed in parallel for the
+
specified number of parallel jobs. Otherwise, it runs in serial.
+
(default=1)
+
+
Returns
+
-------
+
None : :class:`NoneType`
+
The function returns `None`, the analysis output is
+
returned to :attr:`analysis_output` dictionary.
+
+
"""
frames_for_analysis = []
# First populate the frames_for_analysis list.
if isinstance(frames, int):
@@ -617,6 +812,18 @@
Source code for pywindow.trajectory
raise _TrajectoryError(error)
[docs] def save_analysis(self, filepath=None, **kwargs):
+
"""
+
Dump the content of :attr:`analysis_output` as JSON dictionary.
+
+
Parameters
+
----------
+
filepath : :class:`str`
+
The filepath for the JSON file.
+
+
Returns
+
-------
+
None : :class:`NoneType`
+
"""
# We pass a copy of the analysis attribute dictionary.
dict_obj = deepcopy(self.analysis_output)
# If no filepath is provided we create one.
@@ -682,6 +889,38 @@
Source code for pywindow.trajectory
[docs]class XYZ(object):
+
"""
+
A container for an XYZ type trajectory.
+
+
This function takes an XYZ trajectory file and maps it for the
+
binary points in the file where each frame starts/ends. This way the
+
process is fast, as it not require loading the trajectory into computer
+
memory. When a frame is being extracted, it is only this frame that gets
+
loaded to the memory.
+
+
Frames can be accessed individually and loaded as an unmodified string,
+
returned as a :class:`pywindow.molecular.MolecularSystem` (and analysed),
+
dumped as PDB or XYZ or JSON (if dumped as a
+
:attr:`pywindow.molecular.MolecularSystem.system`)
+
+
Attributes
+
----------
+
filepath : :class:`str`
+
The filepath.
+
+
filename : :class:`str`
+
The filename.
+
+
system_id : :class:`str`
+
The system id inherited from the filename.
+
+
frames : :class:`dict`
+
A dictionary that is populated, on the fly, with the extracted frames.
+
+
analysis_output : :class:`dict`
+
A dictionary that is populated, on the fly, with the analysis output.
+
+
"""
def __init__(self, filepath):
self.filepath = filepath
self.filename = os.path.basename(filepath)
@@ -726,7 +965,50 @@
Source code for pywindow.trajectory
progress = progress + len(bline)
self.no_of_frames = frame + 1
-[docs] def get_frames(self, frames, override=False, **kwargs):
+
[docs] def get_frames(self, frames='all', override=False, **kwargs):
+
"""
+
Extract frames from the trajectory file.
+
+
Depending on the passed parameters a frame, a list of particular
+
frames, a range of frames (from, to), or all frames can be extracted
+
with this function.
+
+
Parameters
+
----------
+
frames : :class:`int` or :class:`list` or :class:`touple` or :class:`str`
+
Specified frame (:class:`int`), or frames (:class:`list`), or
+
range (:class:`touple`), or `all`/`everything` (:class:`str`).
+
(default=`all`)
+
+
override : :class:`bool`
+
If True, a frame already storred in :attr:`frames` can be override.
+
(default=False)
+
+
extract_data : :class:`bool`, optional
+
If False, a frame is returned as a :class:`str` block as in the
+
trajectory file. Ohterwise, it is extracted and returned as
+
:class:`pywindow.molecular.MolecularSystem`. (default=True)
+
+
swap_atoms : :class:`dict`, optional
+
If this kwarg is passed with an appropriate dictionary a
+
:func:`pywindow.molecular.MolecularSystem.swap_atom_keys()` will
+
be applied to the extracted frame.
+
+
forcefield : :class:`str`, optional
+
If this kwarg is passed with appropriate forcefield keyword a
+
:func:`pywindow.molecular.MolecularSystem.decipher_atom_keys()`
+
will be applied to the extracted frame.
+
+
Returns
+
-------
+
:class:`pywindow.molecular.MolecularSystem`
+
If a single frame is extracted.
+
+
None : :class:`NoneType`
+
If more than one frame is extracted, the frames are returned to
+
:attr:`frames`
+
+
"""
if override is True:
self.frames = {}
if isinstance(frames, int):
@@ -800,6 +1082,74 @@
Source code for pywindow.trajectory
return frame_data
[docs] def analysis(self, frames='all', ncpus=1, override=False, **kwargs):
+
"""
+
Perform structural analysis on a frame/ set of frames.
+
+
Depending on the passed parameters a frame, a list of particular
+
frames, a range of frames (from, to), or all frames can be analysed
+
with this function.
+
+
The analysis is performed on each frame and each discrete molecule in
+
that frame separately. The steps are as follows:
+
+
1. A frame is extracted and returned as a :class:`MolecularSystem`.
+
2. If `swap_atoms` is set the atom ids are swapped.
+
3. If `forcefield` is set the atom ids are deciphered.
+
4. If `rebuild` is set the molecules in the system are rebuild.
+
5. Each discrete molecule is extracted as :class:`Molecule`
+
6. Each molecule is analysed with :func:`Molecule.full_analysis()`
+
7. Analysis output populates the :attr:`analysis_output` dictionary.
+
+
As the analysis of trajectories often have to be unique, many options
+
are conditional.
+
+
A side effect of this function is that the analysed frames are also
+
returned to the :attr:`frames` mimicking the behaviour of the
+
:func:`get_frames()`.
+
+
Parameters
+
----------
+
frames : :class:`int` or :class:`list` or :class:`touple` or :class:`str`
+
Specified frame (:class:`int`), or frames (:class:`list`), or
+
range (:class:`touple`), or `all`/`everything` (:class:`str`).
+
(default='all')
+
+
override : :class:`bool`
+
If True, an output already storred in :attr:`analysis_output` can
+
be override. (default=False)
+
+
swap_atoms : :class:`dict`, optional
+
If this kwarg is passed with an appropriate dictionary a
+
:func:`pywindow.molecular.MolecularSystem.swap_atom_keys()` will
+
be applied to the extracted frame.
+
+
forcefield : :class:`str`, optional
+
If this kwarg is passed with appropriate forcefield keyword a
+
:func:`pywindow.molecular.MolecularSystem.decipher_atom_keys()`
+
will be applied to the extracted frame.
+
+
modular : :class:`bool`, optional
+
If this kwarg is passed a
+
:func:`pywindow.molecular.MolecularSystem.make_modular()`
+
will be applied to the extracted frame. (default=False)
+
+
rebuild : :class:`bool`, optional
+
If this kwarg is passed a `rebuild=True` is passed to
+
:func:`pywindow.molecular.MolecularSystem.make_modular()` that
+
will be applied to the extracted frame. (default=False)
+
+
ncpus : :class:`int`, optional
+
If ncpus > 1, then the analysis is performed in parallel for the
+
specified number of parallel jobs. Otherwise, it runs in serial.
+
(default=1)
+
+
Returns
+
-------
+
None : :class:`NoneType`
+
The function returns `None`, the analysis output is
+
returned to :attr:`analysis_output` dictionary.
+
+
"""
if override is True:
self.analysis_output = {}
if isinstance(frames, int):
@@ -932,6 +1282,18 @@
Source code for pywindow.trajectory
raise _ParallelAnalysisError("Parallel analysis failed.")
[docs] def save_analysis(self, filepath=None, **kwargs):
+
"""
+
Dump the content of :attr:`analysis_output` as JSON dictionary.
+
+
Parameters
+
----------
+
filepath : :class:`str`
+
The filepath for the JSON file.
+
+
Returns
+
-------
+
None : :class:`NoneType`
+
"""
# We pass a copy of the analysis attribute dictionary.
dict_obj = deepcopy(self.analysis_output)
# If no filepath is provided we create one.
@@ -942,11 +1304,94 @@
Source code for pywindow.trajectory
filepath = '/'.join((os.getcwd(), filepath))
# Dump the dictionary to json file.
Output().dump2json(dict_obj, filepath, default=to_list, **kwargs)
- return
+ return
+
+
[docs] def save_frames(self, frames, filepath=None, filetype='pdb', **kwargs):
+
settings = {
+
"pdb": Output()._save_pdb,
+
"xyz": Output()._save_xyz,
+
"decipher": True,
+
"forcefield": None,
+
}
+
settings.update(kwargs)
+
if filetype.lower() not in settings.keys():
+
raise _FormatError("The '{0}' file format is not supported".format(
+
filetype))
+
frames_to_get = []
+
if isinstance(frames, int):
+
frames_to_get.append(frames)
+
if isinstance(frames, list):
+
frames_to_get = frames
+
if isinstance(frames, tuple):
+
for frame in range(frames[0], frames[1]):
+
frames_to_get.append(frame)
+
if isinstance(frames, str):
+
if frames in ['all', 'everything']:
+
for frame in range(0, self.no_of_frames):
+
frames_to_get.append(frame)
+
for frame in frames_to_get:
+
if frame not in self.frames.keys():
+
_ = self.get_frames(frame)
+
# If no filepath is provided we create one.
+
if filepath is None:
+
filepath = '/'.join((os.getcwd(), str(self.system_id)))
+
for frame in frames_to_get:
+
frame_molsys = self.frames[frame]
+
if settings[
+
'decipher'] is True and settings['forcefield'] is not None:
+
if "swap_atoms" in settings.keys():
+
if isinstance(settings["swap_atoms"], dict):
+
frame_molsys.swap_atom_keys(settings["swap_atoms"])
+
else:
+
raise _FunctionError(
+
"The swap_atom_keys function only accepts "
+
"'swap_atoms' argument in form of a dictionary.")
+
frame_molsys.decipher_atom_keys(settings["forcefield"])
+
ffilepath = '_'.join((filepath, str(frame)))
+
if 'elements' not in frame_molsys.system.keys():
+
raise _FunctionError(
+
"The frame (MolecularSystem object) needs to have "
+
"'elements' attribute within the system dictionary. "
+
"It is, therefore, neccessary that you set a decipher "
+
"keyword to True. (see manual)")
+
settings[filetype.lower()](frame_molsys.system, ffilepath, **
+
kwargs)
[docs]class PDB(object):
def __init__(self, filepath):
+
"""
+
A container for an PDB type trajectory.
+
+
This function takes an PDB trajectory file and maps it for the
+
binary points in the file where each frame starts/ends. This way the
+
process is fast, as it not require loading the trajectory into computer
+
memory. When a frame is being extracted, it is only this frame that gets
+
loaded to the memory.
+
+
Frames can be accessed individually and loaded as an unmodified string,
+
returned as a :class:`pywindow.molecular.MolecularSystem` (and analysed),
+
dumped as PDB or XYZ or JSON (if dumped as a
+
:attr:`pywindow.molecular.MolecularSystem.system`)
+
+
Attributes
+
----------
+
filepath : :class:`str`
+
The filepath.
+
+
filename : :class:`str`
+
The filename.
+
+
system_id : :class:`str`
+
The system id inherited from the filename.
+
+
frames : :class:`dict`
+
A dictionary that is populated, on the fly, with the extracted frames.
+
+
analysis_output : :class:`dict`
+
A dictionary that is populated, on the fly, with the analysis output.
+
+
"""
self.filepath = filepath
self.filename = os.path.basename(filepath)
self.system_id = self.filename.split(".")[0]
@@ -992,7 +1437,50 @@
Source code for pywindow.trajectory
progress = progress + len(bline)
self.no_of_frames = frame
-[docs] def get_frames(self, frames, override=False, **kwargs):
+
[docs] def get_frames(self, frames='all', override=False, **kwargs):
+
"""
+
Extract frames from the trajectory file.
+
+
Depending on the passed parameters a frame, a list of particular
+
frames, a range of frames (from, to), or all frames can be extracted
+
with this function.
+
+
Parameters
+
----------
+
frames : :class:`int` or :class:`list` or :class:`touple` or :class:`str`
+
Specified frame (:class:`int`), or frames (:class:`list`), or
+
range (:class:`touple`), or `all`/`everything` (:class:`str`).
+
(default=`all`)
+
+
override : :class:`bool`
+
If True, a frame already storred in :attr:`frames` can be override.
+
(default=False)
+
+
extract_data : :class:`bool`, optional
+
If False, a frame is returned as a :class:`str` block as in the
+
trajectory file. Ohterwise, it is extracted and returned as
+
:class:`pywindow.molecular.MolecularSystem`. (default=True)
+
+
swap_atoms : :class:`dict`, optional
+
If this kwarg is passed with an appropriate dictionary a
+
:func:`pywindow.molecular.MolecularSystem.swap_atom_keys()` will
+
be applied to the extracted frame.
+
+
forcefield : :class:`str`, optional
+
If this kwarg is passed with appropriate forcefield keyword a
+
:func:`pywindow.molecular.MolecularSystem.decipher_atom_keys()`
+
will be applied to the extracted frame.
+
+
Returns
+
-------
+
:class:`pywindow.molecular.MolecularSystem`
+
If a single frame is extracted.
+
+
None : :class:`NoneType`
+
If more than one frame is extracted, the frames are returned to
+
:attr:`frames`
+
+
"""
if override is True:
self.frames = {}
if isinstance(frames, int):
@@ -1073,6 +1561,74 @@
Source code for pywindow.trajectory
return frame_data
[docs] def analysis(self, frames='all', ncpus=1, override=False, **kwargs):
+
"""
+
Perform structural analysis on a frame/ set of frames.
+
+
Depending on the passed parameters a frame, a list of particular
+
frames, a range of frames (from, to), or all frames can be analysed
+
with this function.
+
+
The analysis is performed on each frame and each discrete molecule in
+
that frame separately. The steps are as follows:
+
+
1. A frame is extracted and returned as a :class:`MolecularSystem`.
+
2. If `swap_atoms` is set the atom ids are swapped.
+
3. If `forcefield` is set the atom ids are deciphered.
+
4. If `rebuild` is set the molecules in the system are rebuild.
+
5. Each discrete molecule is extracted as :class:`Molecule`
+
6. Each molecule is analysed with :func:`Molecule.full_analysis()`
+
7. Analysis output populates the :attr:`analysis_output` dictionary.
+
+
As the analysis of trajectories often have to be unique, many options
+
are conditional.
+
+
A side effect of this function is that the analysed frames are also
+
returned to the :attr:`frames` mimicking the behaviour of the
+
:func:`get_frames()`.
+
+
Parameters
+
----------
+
frames : :class:`int` or :class:`list` or :class:`touple` or :class:`str`
+
Specified frame (:class:`int`), or frames (:class:`list`), or
+
range (:class:`touple`), or `all`/`everything` (:class:`str`).
+
(default='all')
+
+
override : :class:`bool`
+
If True, an output already storred in :attr:`analysis_output` can
+
be override. (default=False)
+
+
swap_atoms : :class:`dict`, optional
+
If this kwarg is passed with an appropriate dictionary a
+
:func:`pywindow.molecular.MolecularSystem.swap_atom_keys()` will
+
be applied to the extracted frame.
+
+
forcefield : :class:`str`, optional
+
If this kwarg is passed with appropriate forcefield keyword a
+
:func:`pywindow.molecular.MolecularSystem.decipher_atom_keys()`
+
will be applied to the extracted frame.
+
+
modular : :class:`bool`, optional
+
If this kwarg is passed a
+
:func:`pywindow.molecular.MolecularSystem.make_modular()`
+
will be applied to the extracted frame. (default=False)
+
+
rebuild : :class:`bool`, optional
+
If this kwarg is passed a `rebuild=True` is passed to
+
:func:`pywindow.molecular.MolecularSystem.make_modular()` that
+
will be applied to the extracted frame. (default=False)
+
+
ncpus : :class:`int`, optional
+
If ncpus > 1, then the analysis is performed in parallel for the
+
specified number of parallel jobs. Otherwise, it runs in serial.
+
(default=1)
+
+
Returns
+
-------
+
None : :class:`NoneType`
+
The function returns `None`, the analysis output is
+
returned to :attr:`analysis_output` dictionary.
+
+
"""
if override is True:
self.analysis_output = {}
if isinstance(frames, int):
@@ -1205,6 +1761,18 @@
Source code for pywindow.trajectory
raise _ParallelAnalysisError("Parallel analysis failed.")
[docs] def save_analysis(self, filepath=None, **kwargs):
+
"""
+
Dump the content of :attr:`analysis_output` as JSON dictionary.
+
+
Parameters
+
----------
+
filepath : :class:`str`
+
The filepath for the JSON file.
+
+
Returns
+
-------
+
None : :class:`NoneType`
+
"""
# We pass a copy of the analysis attribute dictionary.
dict_obj = deepcopy(self.analysis_output)
# If no filepath is provided we create one.
@@ -1215,7 +1783,58 @@
Source code for pywindow.trajectory
filepath = '/'.join((os.getcwd(), filepath))
# Dump the dictionary to json file.
Output().dump2json(dict_obj, filepath, default=to_list, **kwargs)
- return
+ return
+
+
[docs] def save_frames(self, frames, filepath=None, filetype='pdb', **kwargs):
+
settings = {
+
"pdb": Output()._save_pdb,
+
"xyz": Output()._save_xyz,
+
"decipher": True,
+
"forcefield": None,
+
}
+
settings.update(kwargs)
+
if filetype.lower() not in settings.keys():
+
raise _FormatError("The '{0}' file format is not supported".format(
+
filetype))
+
frames_to_get = []
+
if isinstance(frames, int):
+
frames_to_get.append(frames)
+
if isinstance(frames, list):
+
frames_to_get = frames
+
if isinstance(frames, tuple):
+
for frame in range(frames[0], frames[1]):
+
frames_to_get.append(frame)
+
if isinstance(frames, str):
+
if frames in ['all', 'everything']:
+
for frame in range(0, self.no_of_frames):
+
frames_to_get.append(frame)
+
for frame in frames_to_get:
+
if frame not in self.frames.keys():
+
_ = self.get_frames(frame)
+
# If no filepath is provided we create one.
+
if filepath is None:
+
filepath = '/'.join((os.getcwd(), str(self.system_id)))
+
for frame in frames_to_get:
+
frame_molsys = self.frames[frame]
+
if settings[
+
'decipher'] is True and settings['forcefield'] is not None:
+
if "swap_atoms" in settings.keys():
+
if isinstance(settings["swap_atoms"], dict):
+
frame_molsys.swap_atom_keys(settings["swap_atoms"])
+
else:
+
raise _FunctionError(
+
"The swap_atom_keys function only accepts "
+
"'swap_atoms' argument in form of a dictionary.")
+
frame_molsys.decipher_atom_keys(settings["forcefield"])
+
ffilepath = '_'.join((filepath, str(frame)))
+
if 'elements' not in frame_molsys.system.keys():
+
raise _FunctionError(
+
"The frame (MolecularSystem object) needs to have "
+
"'elements' attribute within the system dictionary. "
+
"It is, therefore, neccessary that you set a decipher "
+
"keyword to True. (see manual)")
+
settings[filetype.lower()](frame_molsys.system, ffilepath, **
+
kwargs)
diff --git a/docs/genindex.html b/docs/genindex.html
index 5474450..3986cba 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -181,6 +181,12 @@
A
|