13726590978

Committed 07 Mar 2025 06:07PM UTC coverage: 1.726%. First build

Build # 13726590978

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push

github

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web-flow

Commit Message

Merge pull request #45 from CCPBioSim/39-implement-ci-pipeline-pre-commit-hooks

Implement CI pipeline pre-commit hooks

Run Details

27 of 1135 new or added lines in 23 files covered. (2.38%)

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0.0

/CodeEntropy/MDAUniverseHelper.py

import pickle

import MDAnalysis as mda
from MDAnalysis.analysis.base import AnalysisFromFunction
from MDAnalysis.coordinates.memory import MemoryReader


def new_U_select_frame(u, start=None, end=None, step=1):
    """Create a reduced universe by dropping frames according to user selection

    Parameters
    ----------
    u : MDAnalyse.Universe
        A Universe object will all topology, dihedrals,coordinates and force information
    start : int or None, Optional, default: None
        Frame id to start analysis. Default None will start from frame 0
    end : int or None, Optional, default: None
        Frame id to end analysis. Default None will end at last frame
    step : int, Optional, default: 1
        Steps between frame.

    Returns
    -------
        u2 : MDAnalysis.Universe
            reduced universe
    """
    if start is None:
        start = 0
    if end is None:
        end = len(u.trajectory)
    select_atom = u.select_atoms("all", updating=True)
    coordinates = (
        AnalysisFromFunction(lambda ag: ag.positions.copy(), select_atom)
        .run()
        .results["timeseries"][start:end:step]
    )
    forces = (
        AnalysisFromFunction(lambda ag: ag.forces.copy(), select_atom)
        .run()
        .results["timeseries"][start:end:step]
    )
    dimensions = (
        AnalysisFromFunction(lambda ag: ag.dimensions.copy(), select_atom)
        .run()
        .results["timeseries"][start:end:step]
    )
    u2 = mda.Merge(select_atom)
    u2.load_new(coordinates, format=MemoryReader, forces=forces, dimensions=dimensions)
    return u2


def new_U_select_atom(u, select_string="all"):
    """Create a reduced universe by dropping atoms according to user selection

    Parameters
    ----------
    u : MDAnalyse.Universe
        A Universe object will all topology, dihedrals,coordinates and force information
    select_string : str, Optional, default: 'all'
        MDAnalysis.select_atoms selection string.

    Returns
    -------
        u2 : MDAnalysis.Universe
            reduced universe

    """
    select_atom = u.select_atoms(select_string, updating=True)
    coordinates = (
        AnalysisFromFunction(lambda ag: ag.positions.copy(), select_atom)
        .run()
        .results["timeseries"]
    )
    forces = (
        AnalysisFromFunction(lambda ag: ag.forces.copy(), select_atom)
        .run()
        .results["timeseries"]
    )
    dimensions = (
        AnalysisFromFunction(lambda ag: ag.dimensions.copy(), select_atom)
        .run()
        .results["timeseries"]
    )
    u2 = mda.Merge(select_atom)
    u2.load_new(coordinates, format=MemoryReader, forces=forces, dimensions=dimensions)
    return u2


def write_universe(u, name="default"):
    """Write a universe to working directories as pickle

    Parameters
    ----------
    u : MDAnalyse.Universe
        A Universe object will all topology, dihedrals,coordinates and force information
    name : str, Optional. default: 'default'
        The name of file with sub file name .pkl

    Returns
    -------
        name : str
            filename of saved universe
    """
    filename = f"{name}.pkl"
    pickle.dump(u, open(filename, "wb"))
    return name


def read_universe(path):
    """read a universe to working directories as pickle

    Parameters
    ----------
    path : str
        The path to file.

    Returns
    -------
        u : MDAnalysis.Universe
            A Universe object will all topology, dihedrals,coordinates and force
            information.
    """
    u = pickle.load(open(path, "rb"))
    return u

1	import pickle	×
2
NEW 3	import MDAnalysis as mda	×
4	from MDAnalysis.analysis.base import AnalysisFromFunction	×
5	from MDAnalysis.coordinates.memory import MemoryReader	×
6
7
8	def new_U_select_frame(u, start=None, end=None, step=1):	×
9	"""Create a reduced universe by dropping frames according to user selection
10
11	Parameters
12	----------
13	u : MDAnalyse.Universe
14	A Universe object will all topology, dihedrals,coordinates and force information
15	start : int or None, Optional, default: None
16	Frame id to start analysis. Default None will start from frame 0
17	end : int or None, Optional, default: None
18	Frame id to end analysis. Default None will end at last frame
19	step : int, Optional, default: 1
20	Steps between frame.
21
22	Returns
23	-------
24	u2 : MDAnalysis.Universe
25	reduced universe
26	"""
NEW 27	if start is None:	×
28	start = 0	×
NEW 29	if end is None:	×
30	end = len(u.trajectory)	×
NEW 31	select_atom = u.select_atoms("all", updating=True)	×
NEW 32	coordinates = (	×
33	AnalysisFromFunction(lambda ag: ag.positions.copy(), select_atom)
34	.run()
35	.results["timeseries"][start:end:step]
36	)
NEW 37	forces = (	×
38	AnalysisFromFunction(lambda ag: ag.forces.copy(), select_atom)
39	.run()
40	.results["timeseries"][start:end:step]
41	)
NEW 42	dimensions = (	×
43	AnalysisFromFunction(lambda ag: ag.dimensions.copy(), select_atom)
44	.run()
45	.results["timeseries"][start:end:step]
46	)
47	u2 = mda.Merge(select_atom)	×
NEW 48	u2.load_new(coordinates, format=MemoryReader, forces=forces, dimensions=dimensions)	×
49	return u2	×
50
51
NEW 52	def new_U_select_atom(u, select_string="all"):	×
53	"""Create a reduced universe by dropping atoms according to user selection
54
55	Parameters
56	----------
57	u : MDAnalyse.Universe
58	A Universe object will all topology, dihedrals,coordinates and force information
59	select_string : str, Optional, default: 'all'
60	MDAnalysis.select_atoms selection string.
61
62	Returns
63	-------
64	u2 : MDAnalysis.Universe
65	reduced universe
66
67	"""
68	select_atom = u.select_atoms(select_string, updating=True)	×
NEW 69	coordinates = (	×
70	AnalysisFromFunction(lambda ag: ag.positions.copy(), select_atom)
71	.run()
72	.results["timeseries"]
73	)
NEW 74	forces = (	×
75	AnalysisFromFunction(lambda ag: ag.forces.copy(), select_atom)
76	.run()
77	.results["timeseries"]
78	)
NEW 79	dimensions = (	×
80	AnalysisFromFunction(lambda ag: ag.dimensions.copy(), select_atom)
81	.run()
82	.results["timeseries"]
83	)
84	u2 = mda.Merge(select_atom)	×
85	u2.load_new(coordinates, format=MemoryReader, forces=forces, dimensions=dimensions)	×
NEW 86	return u2	×
87
88
NEW 89	def write_universe(u, name="default"):	×
90	"""Write a universe to working directories as pickle
91
92	Parameters
93	----------
94	u : MDAnalyse.Universe
95	A Universe object will all topology, dihedrals,coordinates and force information
96	name : str, Optional. default: 'default'
97	The name of file with sub file name .pkl
98
99	Returns
100	-------
101	name : str
102	filename of saved universe
103	"""
104	filename = f"{name}.pkl"	×
105	pickle.dump(u, open(filename, "wb"))	×
106	return name	×
107
108
109	def read_universe(path):	×
110	"""read a universe to working directories as pickle
111
112	Parameters
113	----------
114	path : str
115	The path to file.
116
117	Returns
118	-------
119	u : MDAnalysis.Universe
120	A Universe object will all topology, dihedrals,coordinates and force
121	information.
122	"""
123	u = pickle.load(open(path, "rb"))	×
124	return u	×

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