13726590978

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

Build # 13726590978

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Commit Message

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

Implement CI pipeline pre-commit hooks

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

53 of 3071 relevant lines covered (1.73%)

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/CodeEntropy/PoseidonHelper.py

1	import logging	×
NEW 2	import sys	×
NEW 3	from datetime import datetime	×
4
5	# from CodeEntropy.poseidon.analysis.EECalculation import processEE
6	# from CodeEntropy.poseidon.analysis.helper import memoryInfo, weightingPopulation
7	# from CodeEntropy.poseidon.analysis.populateClasses import classPopulation
NEW 8	from CodeEntropy.poseidon.extractData.dihedrals import calculateDihedrals	×
NEW 9	from CodeEntropy.poseidon.extractData.forceTorques import calculateFTMatrix	×
10
11	# # Energy is not needed
12	# from CodeEntropy.poseidon.extractData.readFiles import populateEnergy, UAEnergyGroup
NEW 13	from CodeEntropy.poseidon.extractData.HBRAD import HBCalc, UALevelRAD, distCutoffNc	×
14	from CodeEntropy.poseidon.extractData.mainClass import clearClass	×
NEW 15	from CodeEntropy.poseidon.extractData.nearestNonlike2 import (	×
16	getShellAssignment,
17	moleculePositionRankingRAD,
18	)
19
20	# from CodeEntropy.poseidon.extractData.outputFiles import moleculeObjectPopulation
NEW 21	from CodeEntropy.poseidon.extractData.readFiles import ( # populateTopology,	×
22	getCoordsForces,
23	getDistArray,
24	)
25
26
NEW 27	def frame_iteration(	×
28	container,
29	all_data,
30	dimensions,
31	startTime,
32	verbosePrint,
33	waterTuple,
34	cutShell,
35	excludedResnames,
36	frame,
37	):
38	clearClass(all_data)	×
39	print(f"frame = {frame}")	×
40
NEW 41	all_data, dimensions = getCoordsForces(	×
42	container, all_data, dimensions, frame, startTime, verbosePrint
43	)
44	# # Energy is not needed
45	# populateEnergy(container, all_data,
46	# dimensions, frame, startTime, verbosePrint)
47	# UAEnergyGroup(all_data)
48
49	calculateDihedrals(all_data, dimensions)	×
NEW 50	verbosePrint("DIH")	×
51	verbosePrint(datetime.now() - startTime)	×
52	sys.stdout.flush()	×
53
54	traj = container.trajectory[frame]	×
55	neighbour_coords = None	×
56	neighbour_coords = traj.positions	×
57
58	max_cutoff = 10	×
59	for x in range(0, len(all_data)):	×
60	atom = all_data[x]	×
61	# start nearest array from solutes
62	if atom.resname not in waterTuple:	×
NEW 63	getDistArray(	×
64	atom,
65	all_data,
66	traj,
67	max_cutoff,
68	dimensions,
69	neighbour_coords,
70	startTime,
71	verbosePrint,
72	)
73	# find nearest array for solute neighbours that are solvent
74	for nearDist in atom.nearest_all_atom_array[0:20]:	×
75	neighbour = all_data[nearDist[0]]	×
NEW 76	if (	×
77	neighbour.resname in waterTuple
78	and neighbour.nearest_all_atom_array is None
79	):
NEW 80	getDistArray(	×
81	neighbour,
82	all_data,
83	traj,
84	max_cutoff,
85	dimensions,
86	neighbour_coords,
87	startTime,
88	verbosePrint,
89	)
90	# find solvent neighbours neighbours nearest array
NEW 91	if neighbour.nearest_all_atom_array is not None:	×
92	for nearDist2 in neighbour.nearest_all_atom_array[0:20]:	×
93	neighbour2 = all_data[nearDist2[0]]	×
NEW 94	if (	×
95	neighbour2.resname in waterTuple
96	and neighbour2.nearest_all_atom_array is None
97	):
NEW 98	getDistArray(	×
99	neighbour2,
100	all_data,
101	traj,
102	max_cutoff,
103	dimensions,
104	neighbour_coords,
105	startTime,
106	verbosePrint,
107	)
108	else:
109	continue	×
110	else:
111	continue	×
112	else:
113	continue	×
NEW 114	verbosePrint("NEAREST ARRAYS")	×
115	verbosePrint(datetime.now() - startTime)	×
116	sys.stdout.flush()	×
117
NEW 118	if cutShell is not None:	×
119	# Used for fixed cut-off coordination shells
120	try:	×
121	cutoff_dist = float(cutShell)	×
122	distCutoffNc(all_data, dimensions, cutoff_dist)	×
123	# #don't know what this is it is not defined anywhere
124	# NcPairs(all_data, dimensions)
NEW 125	verbosePrint("distCutoffNc")	×
126	verbosePrint(datetime.now() - startTime)	×
NEW 127	sys.stdout.flush()	×
128	except ValueError:	×
NEW 129	logging.error("Cutoff distance needs to be a float")	×
130
NEW 131	if cutShell is None:	×
132	UALevelRAD(all_data, dimensions)	×
NEW 133	verbosePrint("RAD")	×
134	verbosePrint(datetime.now() - startTime)	×
135
136	# if inputType != 'pdb':
137	HBCalc(all_data, waterTuple, dimensions)	×
NEW 138	verbosePrint("HB")	×
139	verbosePrint(datetime.now() - startTime)	×
NEW 140	sys.stdout.flush()	×
141
NEW 142	getShellAssignment(all_data, excludedResnames, dimensions, startTime, verbosePrint)	×
NEW 143	verbosePrint("PROX")	×
144	verbosePrint(datetime.now() - startTime)	×
145	sys.stdout.flush()	×
146
147	# if (force is not None):
148	calculateFTMatrix(all_data, dimensions)	×
NEW 149	verbosePrint("FTMATRIX")	×
150	verbosePrint(datetime.now() - startTime)	×
151	sys.stdout.flush()	×
152
153	moleculePositionRankingRAD(all_data, waterTuple, dimensions)	×
NEW 154	verbosePrint("ORIENTS")	×
155	verbosePrint(datetime.now() - startTime)	×
156	sys.stdout.flush()	×
157
NEW 158	"""	×
159	if iterations == 1:
160	verbosePrint('Generating .pdb file for frame %s' % (frame+1))
161	pdbGenerate(all_data, ('frame_%s' % (frame+1)), dimensions)
162	"""
163	# print(all_data, frame, dimensions)
164	return (all_data, frame, dimensions)	×

CCPBioSim / CodeEntropy / 13726590978

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