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%)

53 of 3071 relevant lines covered (1.73%)

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0.0

/CodeEntropy/poseidon/extractData/mainClass.py

#!/usr/bin/env python


class atom_info(object):
    """
    Class for all information attributed to atoms and molecules in the system.
    """

    def __init__(
        self,
        atom_num,
        atom_name,
        mass,
        charge,
        resid,
        resname,
        bonded_to_atom_num,
        dihedral_list,
    ):  # order important

        self.atom_num = atom_num
        self.atom_name = atom_name
        self.resid = resid
        self.resname = resname
        self.mass = mass
        self.charge = charge
        self.bonded_to_atom_num = bonded_to_atom_num
        self.dihedral_list = dihedral_list
        # list of lists of atom nums in dihedrals, not including Hs

        self.molecule_atomNums = None  # list of bonded UA atom nums
        self.bonded_to_resids = None  # list of resids residue is bonded to

        self.coords = None
        self.forces = None
        self.nearest_sorted_array = None  # list of (atom_nums, distances)
        # from nearest to furthest within a set cutoff distance,
        # not including Hs
        self.nearest_all_atom_array = None  # list containing sorted by
        # dist (atom_num, dist) for all atoms, including Hs
        self.PKenergy = None
        self.UA_PKenergy = None

        self.bondedUA_H = None  # [num_bondedUAs, num_bonded Hs]
        self.nearest_atom = None  # HB acceptor all atom info
        self.nearest_Hs = []  # HB
        self.dist = None  # HB distance between donor and acceptor
        self.broken = None  # HB
        self.RAD = None  # list of atoms.all_info
        self.RAD_dist = None  # list of (atoms.all_info, dist from ref)

        self.UAweightedForces = None
        self.UAweightedTorques = None
        self.MweightedForces = None
        self.MweightedTorques = None
        self.molecule_UA_Fs = None
        self.molecule_UA_Ts = None
        self.WMprincipalAxis = None

        self.dihedral_phi_type = None  # unique dihedral angles, in degrees
        self.nearestAnyNonlike = None  # tuple (atom.all_info, dist)
        self.RAD_shell_ranked = None  # list of 3 tuple
        # RAD shell ranked, acceptors ranked, donors ranked by RAD
        self.RAD_nAtoms = None
        self.hydrationShellRAD_solute = None  # nearest solute molecule centric

    def __repr__(self):  # return the output below if whole object is printed
        return "%s %s %s %s %s %s %s" % (
            self.atom_num,
            self.atom_name,
            self.mass,
            self.charge,
            self.resid,
            self.resname,
            self.bonded_to_atom_num,
        )


def clearClass(all_data):
    """
    For variables in the class, clear after each frame is analysed.
    """

    def reset(self):
        """
        reset attributes in a class. Except those from topology.
        This prevents memory overload from each frame.
        """
        dic = vars(self)
        noEdit = [
            "atom_num",
            "atom_name",
            "resid",
            "resname",
            "mass",
            "charge",
            "bonded_to_atom_num",
            "nearest_Hs",
            "molecule_atomNums",
            "bonded_to_resids",
            "dihedral_list",
            "bondedUA_H",
        ]
        for i in dic.keys():
            if i not in noEdit:
                dic[i] = None
            else:
                continue
        dic["nearest_Hs"] = []

    # clear all objects from previous frame
    for x in range(0, len(all_data)):
        atom = all_data[x]
        reset(atom)

1	#!/usr/bin/env python
2
3
4	class atom_info(object):	×
5	"""
6	Class for all information attributed to atoms and molecules in the system.
7	"""
8
NEW 9	def __init__(	×
10	self,
11	atom_num,
12	atom_name,
13	mass,
14	charge,
15	resid,
16	resname,
17	bonded_to_atom_num,
18	dihedral_list,
19	): # order important
20
21	self.atom_num = atom_num	×
22	self.atom_name = atom_name	×
23	self.resid = resid	×
24	self.resname = resname	×
25	self.mass = mass	×
26	self.charge = charge	×
27	self.bonded_to_atom_num = bonded_to_atom_num	×
NEW 28	self.dihedral_list = dihedral_list	×
29	# list of lists of atom nums in dihedrals, not including Hs
30
NEW 31	self.molecule_atomNums = None # list of bonded UA atom nums	×
NEW 32	self.bonded_to_resids = None # list of resids residue is bonded to	×
33
34	self.coords = None	×
35	self.forces = None	×
NEW 36	self.nearest_sorted_array = None # list of (atom_nums, distances)	×
37	# from nearest to furthest within a set cutoff distance,
38	# not including Hs
NEW 39	self.nearest_all_atom_array = None # list containing sorted by	×
40	# dist (atom_num, dist) for all atoms, including Hs
41	self.PKenergy = None	×
42	self.UA_PKenergy = None	×
43
NEW 44	self.bondedUA_H = None # [num_bondedUAs, num_bonded Hs]	×
NEW 45	self.nearest_atom = None # HB acceptor all atom info	×
NEW 46	self.nearest_Hs = [] # HB	×
NEW 47	self.dist = None # HB distance between donor and acceptor	×
NEW 48	self.broken = None # HB	×
NEW 49	self.RAD = None # list of atoms.all_info	×
NEW 50	self.RAD_dist = None # list of (atoms.all_info, dist from ref)	×
51
52	self.UAweightedForces = None	×
53	self.UAweightedTorques = None	×
54	self.MweightedForces = None	×
55	self.MweightedTorques = None	×
56	self.molecule_UA_Fs = None	×
57	self.molecule_UA_Ts = None	×
58	self.WMprincipalAxis = None	×
59
NEW 60	self.dihedral_phi_type = None # unique dihedral angles, in degrees	×
NEW 61	self.nearestAnyNonlike = None # tuple (atom.all_info, dist)	×
NEW 62	self.RAD_shell_ranked = None # list of 3 tuple	×
63	# RAD shell ranked, acceptors ranked, donors ranked by RAD
64	self.RAD_nAtoms = None	×
NEW 65	self.hydrationShellRAD_solute = None # nearest solute molecule centric	×
66
NEW 67	def __repr__(self): # return the output below if whole object is printed	×
NEW 68	return "%s %s %s %s %s %s %s" % (	×
69	self.atom_num,
70	self.atom_name,
71	self.mass,
72	self.charge,
73	self.resid,
74	self.resname,
75	self.bonded_to_atom_num,
76	)
77
78
79	def clearClass(all_data):	×
80	"""
81	For variables in the class, clear after each frame is analysed.
82	"""
83
84	def reset(self):	×
85	"""
86	reset attributes in a class. Except those from topology.
87	This prevents memory overload from each frame.
88	"""
89	dic = vars(self)	×
NEW 90	noEdit = [	×
91	"atom_num",
92	"atom_name",
93	"resid",
94	"resname",
95	"mass",
96	"charge",
97	"bonded_to_atom_num",
98	"nearest_Hs",
99	"molecule_atomNums",
100	"bonded_to_resids",
101	"dihedral_list",
102	"bondedUA_H",
103	]
104	for i in dic.keys():	×
105	if i not in noEdit:	×
106	dic[i] = None	×
107	else:
108	continue	×
NEW 109	dic["nearest_Hs"] = []	×
110
111	# clear all objects from previous frame
112	for x in range(0, len(all_data)):	×
113	atom = all_data[x]	×
114	reset(atom)	×

CCPBioSim / CodeEntropy / 13726590978

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