13726590978

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

Build # 13726590978

Build Type

push

github

Committed by

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%)

53 of 3071 relevant lines covered (1.73%)

0.05 hits per line

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0.0

/CodeEntropy/poseidon/analysis/classes.py

#!/usr/bin/env python


from collections import defaultdict


# create nested dict in one go
def nested_dict():
    return defaultdict(nested_dict)


class variables_dicts(object):
    """
    Main class containing dicts for all
    thermodynamic (Energy and Entropy) calculations per proximity
    shell in the system.
    """

    def __init__(self, initiate):

        self.initiate = None

        # dict with variables named rather than ordered
        self.allVariables_dict = nested_dict()  # *

        # get info about weight of bias in biased simulations
        self.weighting_list = None
        self.weighting_chunks = None

        # For Sor population
        self.RADshell_Sor_dict = nested_dict()  # for S_or, pijs
        self.Sor_reference_dict = nested_dict()

        # For Svib / E population
        self.RADshell_dict = nested_dict()
        # FT decomposed to prox or dist
        self.WM_FT_shell_dict = nested_dict()

        # dicts for dihedrals
        self.initiate = None
        # bin dihs into 30 degrees bin, uses p ln p (not matrix)
        self.adaptive_dih_dict = nested_dict()

        # contacts between resids with central molecule resid using RAD
        self.resid_contact_matrix_dict = nested_dict()

1	#!/usr/bin/env python
2
3
4	from collections import defaultdict	×
5
6
7	# create nested dict in one go
NEW 8	def nested_dict():	×
NEW 9	return defaultdict(nested_dict)	×
10
11
12	class variables_dicts(object):	×
13	"""
14	Main class containing dicts for all
15	thermodynamic (Energy and Entropy) calculations per proximity
16	shell in the system.
17	"""
18
19	def __init__(self, initiate):	×
20
21	self.initiate = None	×
22
23	# dict with variables named rather than ordered
NEW 24	self.allVariables_dict = nested_dict() # *	×
25
26	# get info about weight of bias in biased simulations
27	self.weighting_list = None	×
28	self.weighting_chunks = None	×
29
30	# For Sor population
NEW 31	self.RADshell_Sor_dict = nested_dict() # for S_or, pijs	×
32	self.Sor_reference_dict = nested_dict()	×
33
34	# For Svib / E population
35	self.RADshell_dict = nested_dict()	×
36	# FT decomposed to prox or dist
37	self.WM_FT_shell_dict = nested_dict()	×
38
39	# dicts for dihedrals
40	self.initiate = None	×
41	# bin dihs into 30 degrees bin, uses p ln p (not matrix)
42	self.adaptive_dih_dict = nested_dict()	×
43
44	# contacts between resids with central molecule resid using RAD
45	self.resid_contact_matrix_dict = nested_dict()	×

CCPBioSim / CodeEntropy / 13726590978

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