4607244921

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Adding examples (#77)

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0.0

/src/SOAPify/cli.py

1	"""submodule containing the command line interfaces of SOAPify"""
NEW 2	from argparse import ArgumentParser	×
3
4
NEW 5	def getDictFromList(nameAndValues: list) -> dict:	×
6	"""generates a dictionary from a list of couples [name, value]
7
8	Args:
9	nameAndValues (list):
10	the list of couples [name, value]
11
12	Returns:
13	dict:
14	the dictionary, for example {name0:value0, name1:value1}
15	"""
NEW 16	myDict = {}	×
NEW 17	for attr in nameAndValues:	×
NEW 18	myDict[attr[0]] = attr[1]	×
NEW 19	return myDict	×
20
21
NEW 22	def createTrajectory():	×
23	"""Creates or overide an hdf5 file containing a given trajectory
24
25	if you are creating ahdf5 file from a data+dump from a soap simulation
26	remember to add `-u atom_style "id type x y z"` to the arguments
27
28	defaults trajChunkSize=1000"""
NEW 29	from MDAnalysis import Universe as mdaUniverse	×
30
NEW 31	from SOAPify.HDF5er import MDA2HDF5	×
NEW 32	from os import path	×
33
NEW 34	parser = ArgumentParser(description=createTrajectory.__doc__)	×
NEW 35	parser.add_argument("topology", help="the topology file")	×
NEW 36	parser.add_argument("hdf5File", help="the file where to putput the trajectory")	×
NEW 37	parser.add_argument(	×
38	"-t",
39	"--trajectory",
40	help="the trajectory file(s)",
41	metavar="trajectory",
42	action="append",
43	default=[],
44	)
NEW 45	parser.add_argument(	×
46	"-n",
47	"--name",
48	metavar="name",
49	help="the name of the trajectory to save",
50	)
NEW 51	parser.add_argument(	×
52	"--types",
53	metavar="atomNames",
54	help="list of the atoms names",
55	nargs="+",
56	dest="atomTypes",
57	)
NEW 58	parser.add_argument(	×
59	"-a",
60	"--attribute",
61	nargs=2,
62	action="append",
63	dest="extraAttributes",
64	metavar=("name", "value"),
65	help="extra attributes to store in the trajectory, saved as strings",
66	)
NEW 67	parser.add_argument(	×
68	"-u",
69	"--universe-options",
70	nargs=2,
71	action="append",
72	dest="universeOPTs",
73	metavar=("name", "value"),
74	help="extra option to pass to the MDA universe, compatible only with string"
75	" values, use the python script if you need to pass more other settings",
76	)
NEW 77	parser.add_argument(	×
78	"-d",
79	"--dry-run",
80	action="store_true",
81	help="just print the output without making any action",
82	)
NEW 83	args = parser.parse_args()	×
84	# print(args)
85	# arguments
NEW 86	trajectoryFiles = args.trajectory	×
NEW 87	filename = args.hdf5File	×
NEW 88	topo = args.topology	×
NEW 89	name = args.name	×
NEW 90	if name is None:	×
NEW 91	name = path.basename(topo)	×
NEW 92	name = name.split(".")[0]	×
93
NEW 94	print(	×
95	f'from topology "{topo}"',
96	f'and trajectory "{trajectoryFiles}":',
97	"and creating a new trajectory in",
98	)
99
NEW 100	print(f'"{filename}/Trajectories/{name}"')	×
NEW 101	extraAttrs = None	×
NEW 102	if args.extraAttributes:	×
NEW 103	extraAttrs = getDictFromList(args.extraAttributes)	×
NEW 104	print("extra attributes:", extraAttrs)	×
NEW 105	universeOptions = {}	×
NEW 106	if args.universeOPTs:	×
NEW 107	universeOptions = getDictFromList(args.universeOPTs)	×
108
NEW 109	if args.dry_run:	×
NEW 110	exit()	×
111
NEW 112	u = mdaUniverse(topo, trajectoryFiles, *universeOptions)	×
NEW 113	if args.atomTypes:	×
NEW 114	ntypes = len(args.atomTypes)	×
NEW 115	if len(u.atoms) % ntypes != 0:	×
NEW 116	raise ValueError(	×
117	f"The number of atom types is not compatible with the number"
118	f" of atoms:{len(u.atoms)} % {ntypes} = {len(u.atoms) % ntypes}"
119	)
NEW 120	u.atoms.types = args.atomTypes * (len(u.atoms) // ntypes)	×
121
NEW 122	MDA2HDF5(u, filename, name, trajChunkSize=1000, attrs=extraAttrs)	×
123	# TODO: implement this:
124	# from MDAnalysis import transformations
125	# ref = mdaUniverse(topo, atom_style="id type x y z")
126	# u.trajectory.add_transformations(transformations.fit_rot_trans(u, ref))
127	# MDA2HDF5(u, name + "_fitted.hdf5", f"{name}_fitted", trajChunkSize=1000))
128
129
NEW 130	def traj2SOAP():	×
131	"""Given an hdf5 file containing trajectories calculates SOAP of the contained trajectories
132
133
134	default SOAP engine is dscribe"""
135
NEW 136	from SOAPify import saponifyTrajectory	×
NEW 137	from SOAPify.HDF5er import isTrajectoryGroup	×
NEW 138	import h5py	×
139
NEW 140	parser = ArgumentParser(description=traj2SOAP.__doc__)	×
NEW 141	parser.add_argument(	×
142	"trajFile",
143	help="the file containing the trajectories",
144	)
NEW 145	parser.add_argument(	×
146	"-s",
147	"--SOAPFile",
148	help="The file were to save the SOAP fingerprints, if not specified"
149	" creates a SOAP group in within the trajFile",
150	)
NEW 151	parser.add_argument(	×
152	"-t",
153	"--trajectory",
154	default="Trajectories",
155	help="Specify the group containing the trajectories groups or the"
156	" trajectory group tha you wnat to calculate the SOAP fingerprints",
157	)
NEW 158	parser.add_argument(	×
159	"-e",
160	"--engine",
161	choices=["dscribe", "quippy"],
162	default="dscribe",
163	help="the engine used to calculate SOAP",
164	)
NEW 165	parser.add_argument(	×
166	"-l",
167	"--lMax",
168	type=int,
169	default=8,
170	help="the lmax parameter, defaults to 8",
171	)
NEW 172	parser.add_argument(	×
173	"-n",
174	"--nMax",
175	type=int,
176	default=8,
177	help="the nmax parameter, defaults to 8",
178	)
NEW 179	parser.add_argument(	×
180	"-r",
181	"--rCut",
182	type=float,
183	default=10.0,
184	help="the rcut parameter, defaults to 10.0 Å",
185	)
NEW 186	parser.add_argument(	×
187	"-j",
188	"--jobs",
189	type=int,
190	default=1,
191	help="the number of jobs to use, defaults to 1",
192	)
NEW 193	parser.add_argument(	×
194	"-d",
195	"--dry-run",
196	action="store_true",
197	help="just print the output without making any action",
198	)
NEW 199	args = parser.parse_args()	×
200	# print(args)
201
NEW 202	trajGroupLocation = args.trajectory	×
203
NEW 204	def worker(group: "h5py.Group\|h5py.Dataset", soapFile: h5py.File):	×
NEW 205	print(	×
206	f"\"{group.name}\" is {'' if isTrajectoryGroup(group) else 'not '}a trajectory group"
207	)
NEW 208	if isTrajectoryGroup(group):	×
NEW 209	if args.dry_run:	×
NEW 210	return	×
NEW 211	saponifyTrajectory(	×
212	trajContainer=group,
213	SOAPoutContainer=soapFile.require_group("SOAP"),
214	SOAPOutputChunkDim=1000,
215	SOAPnJobs=args.jobs,
216	SOAPrcut=args.rCut,
217	SOAPnmax=args.nMax,
218	SOAPlmax=args.lMax,
219	useSoapFrom=args.engine,
220	)
221
NEW 222	SOAPFile = args.SOAPFile	×
NEW 223	if args.SOAPFile is None:	×
NEW 224	SOAPFile = args.trajFile	×
NEW 225	with h5py.File(	×
226	args.trajFile, "r" if SOAPFile != args.trajFile else "a"
227	) as workFile, h5py.File(SOAPFile, "a") as SOAPFile:
NEW 228	trajGroup = workFile[trajGroupLocation]	×
NEW 229	if isTrajectoryGroup(trajGroup):	×
NEW 230	worker(trajGroup, SOAPFile)	×
231	else:
NEW 232	for _, group in trajGroup.items():	×
NEW 233	worker(group, SOAPFile)	×

GMPavanLab / SOAPify / 4607244921

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