13726590978

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

Build # 13726590978

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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

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/CodeEntropy/poseidon/extractData/outputFiles.py

#!/usr/bin/env python

# import math
# import sys

# import numpy as np

# from CodeEntropy.poseidon.extractData.generalFunctions import (
#     calcAngleWithNearestNonlike,
# )


def moleculeObjectPopulation(all_data, allMoleculeList, frame, dimensions):
    """
    For all molecules in the system, populate a list with required
    info for further analysis across any trajectory frame.
    """

    for x in range(0, len(all_data)):
        atom = all_data[x]
        if atom.mass > 1.1:
            nearestInfo = []
            if atom.nearestAnyNonlike is not None:
                nearestInfo = [
                    atom.nearestAnyNonlike[0].atom_name,
                    atom.nearestAnyNonlike[0].resname,
                    atom.nearestAnyNonlike[0].resid,
                    round(atom.nearestAnyNonlike[1], 3),  # dist
                ]

            allMoleculeList.append(
                [
                    frame,  # 0
                    atom.atom_name,  # 1
                    atom.atom_num,  # 2
                    atom.resname,  # 3
                    atom.resid,  # 4
                    atom.bondedUA_H,  # 5
                    atom.molecule_atomNums,  # 6
                    nearestInfo,  # 7
                    atom.hydrationShellRAD_solute,  # 8
                    atom.RAD_shell_ranked,  # 9
                    atom.MweightedForces,  # 10
                    atom.MweightedTorques,  # 11
                    atom.UA_PKenergy,  # 12
                    atom.UAweightedForces,  # 13
                    atom.UAweightedTorques,  # 14
                    atom.dihedral_phi_type,  # 15
                    atom.molecule_UA_Fs,  # 16
                    atom.molecule_UA_Ts,  # 17
                    atom.RAD_nAtoms,  # 18
                ]
            )

        else:
            continue

    return allMoleculeList


def pdbGenerate(all_data, fileName, dimensions):
    """
    Output a pdb file to visualise different waters in system.
    Might have to also make an equivalent .csv file so that
    we have an easier time analysing the files.
    But append to one global file rather than each frame,
    so need a column of frame number for analysis later.
    pdb file pure for producing images with vmd,
    but could create these later anyway?
    Then we can choose our beta column?
    """

    data = open(fileName + "_solProx_dist.pdb", "w")
    # solute resid, int(dist) from solute resid

    data3 = open(fileName + "_RADHBlengths.pdb", "w")
    # Nc, N_acceptors/N_donors

    data6 = open(fileName + "_solProx_RAD.pdb", "w")
    # solute resid, int(dist) from solute resid

    file_list = [data, data3, data6]

    for x in range(0, len(all_data)):
        atom = all_data[x]

        try:
            a = int(atom.nearestAnyNonlike[0].resid)
        except TypeError:
            a = 0
        try:
            b = int(atom.nearestAnyNonlike[1])
        except TypeError:
            b = 0
        try:
            e = len(atom.RAD)
        except TypeError:
            e = 0
        try:
            As = len(atom.RAD_shell_ranked[1])
            Ds = len(atom.RAD_shell_ranked[2])
            DAhh_type = "%s%s" % (Ds, As)
            f = str(DAhh_type)
        except TypeError:
            f = "00"
        try:
            i = int(atom.hydrationShellRAD_solute)
        except (TypeError, ValueError):
            i = 0

        data.write(
            "\n".join(
                [
                    "{:6s}{:5d} {:^4s}{:1s}{:3s}"
                    " {:1s}{:4d}{:1s}   {:8.3f}{:8.3f}{:8.3f}"
                    "{:6.0f}{:6.0f}          {:>2s}{:2s}".format(
                        "ATOM",
                        int(str(atom.atom_num)[0:5]),
                        atom.atom_name,
                        " ",
                        atom.resname[0:3],
                        "A",
                        int(str(atom.resid)[0:4]),
                        " ",
                        float(atom.coords[0]),
                        float(atom.coords[1]),
                        float(atom.coords[2]),
                        a,
                        b,
                        " ",
                        " ",
                    )
                ]
            )
            + "\n"
        )

        data3.write(
            "\n".join(
                [
                    "{:6s}{:5d} {:^4s}{:1s}{:3s}"
                    " {:1s}{:4d}{:1s}   {:8.3f}{:8.3f}{:8.3f}"
                    "{:6.0f}    {:2s}          {:>2s}{:2s}".format(
                        "ATOM",
                        int(str(atom.atom_num)[0:5]),
                        atom.atom_name,
                        " ",
                        atom.resname[0:3],
                        "A",
                        int(str(atom.resid)[0:4]),
                        " ",
                        float(atom.coords[0]),
                        float(atom.coords[1]),
                        float(atom.coords[2]),
                        e,
                        f,
                        " ",
                        " ",
                    )
                ]
            )
            + "\n"
        )

        data6.write(
            "\n".join(
                [
                    "{:6s}{:5d} {:^4s}{:1s}{:3s}"
                    " {:1s}{:4d}{:1s}   {:8.3f}{:8.3f}{:8.3f}"
                    "{:6.0f}{:6.0f}          {:>2s}{:2s}".format(
                        "ATOM",
                        int(str(atom.atom_num)[0:5]),
                        atom.atom_name,
                        " ",
                        atom.resname[0:3],
                        "A",
                        int(str(atom.resid)[0:4]),
                        " ",
                        float(atom.coords[0]),
                        float(atom.coords[1]),
                        float(atom.coords[2]),
                        a,
                        i,
                        " ",
                        " ",
                    )
                ]
            )
            + "\n"
        )

    for d in file_list:
        d.close()

1	#!/usr/bin/env python
2
3	# import math
4	# import sys
5
6	# import numpy as np
7
8	# from CodeEntropy.poseidon.extractData.generalFunctions import (
9	# calcAngleWithNearestNonlike,
10	# )
11
12
13	def moleculeObjectPopulation(all_data, allMoleculeList, frame, dimensions):	×
14	"""
15	For all molecules in the system, populate a list with required
16	info for further analysis across any trajectory frame.
17	"""
18
19	for x in range(0, len(all_data)):	×
20	atom = all_data[x]	×
21	if atom.mass > 1.1:	×
22	nearestInfo = []	×
NEW 23	if atom.nearestAnyNonlike is not None:	×
24	nearestInfo = [	×
25	atom.nearestAnyNonlike[0].atom_name,
26	atom.nearestAnyNonlike[0].resname,
27	atom.nearestAnyNonlike[0].resid,
28	round(atom.nearestAnyNonlike[1], 3), # dist
29	]
30
NEW 31	allMoleculeList.append(	×
32	[
33	frame, # 0
34	atom.atom_name, # 1
35	atom.atom_num, # 2
36	atom.resname, # 3
37	atom.resid, # 4
38	atom.bondedUA_H, # 5
39	atom.molecule_atomNums, # 6
40	nearestInfo, # 7
41	atom.hydrationShellRAD_solute, # 8
42	atom.RAD_shell_ranked, # 9
43	atom.MweightedForces, # 10
44	atom.MweightedTorques, # 11
45	atom.UA_PKenergy, # 12
46	atom.UAweightedForces, # 13
47	atom.UAweightedTorques, # 14
48	atom.dihedral_phi_type, # 15
49	atom.molecule_UA_Fs, # 16
50	atom.molecule_UA_Ts, # 17
51	atom.RAD_nAtoms, # 18
52	]
53	)
54
55	else:
56	continue	×
57
58	return allMoleculeList	×
59
60
61	def pdbGenerate(all_data, fileName, dimensions):	×
62	"""
63	Output a pdb file to visualise different waters in system.
64	Might have to also make an equivalent .csv file so that
65	we have an easier time analysing the files.
66	But append to one global file rather than each frame,
67	so need a column of frame number for analysis later.
68	pdb file pure for producing images with vmd,
69	but could create these later anyway?
70	Then we can choose our beta column?
71	"""
72
NEW 73	data = open(fileName + "_solProx_dist.pdb", "w")	×
74	# solute resid, int(dist) from solute resid
75
NEW 76	data3 = open(fileName + "_RADHBlengths.pdb", "w")	×
77	# Nc, N_acceptors/N_donors
78
NEW 79	data6 = open(fileName + "_solProx_RAD.pdb", "w")	×
80	# solute resid, int(dist) from solute resid
81
82	file_list = [data, data3, data6]	×
83
84	for x in range(0, len(all_data)):	×
85	atom = all_data[x]	×
86
87	try:	×
88	a = int(atom.nearestAnyNonlike[0].resid)	×
89	except TypeError:	×
90	a = 0	×
91	try:	×
92	b = int(atom.nearestAnyNonlike[1])	×
93	except TypeError:	×
94	b = 0	×
95	try:	×
96	e = len(atom.RAD)	×
97	except TypeError:	×
98	e = 0	×
99	try:	×
100	As = len(atom.RAD_shell_ranked[1])	×
101	Ds = len(atom.RAD_shell_ranked[2])	×
NEW 102	DAhh_type = "%s%s" % (Ds, As)	×
103	f = str(DAhh_type)	×
104	except TypeError:	×
NEW 105	f = "00"	×
106	try:	×
107	i = int(atom.hydrationShellRAD_solute)	×
108	except (TypeError, ValueError):	×
109	i = 0	×
110
NEW 111	data.write(	×
112	"\n".join(
113	[
114	"{:6s}{:5d} {:^4s}{:1s}{:3s}"
115	" {:1s}{:4d}{:1s} {:8.3f}{:8.3f}{:8.3f}"
116	"{:6.0f}{:6.0f} {:>2s}{:2s}".format(
117	"ATOM",
118	int(str(atom.atom_num)[0:5]),
119	atom.atom_name,
120	" ",
121	atom.resname[0:3],
122	"A",
123	int(str(atom.resid)[0:4]),
124	" ",
125	float(atom.coords[0]),
126	float(atom.coords[1]),
127	float(atom.coords[2]),
128	a,
129	b,
130	" ",
131	" ",
132	)
133	]
134	)
135	+ "\n"
136	)
137
NEW 138	data3.write(	×
139	"\n".join(
140	[
141	"{:6s}{:5d} {:^4s}{:1s}{:3s}"
142	" {:1s}{:4d}{:1s} {:8.3f}{:8.3f}{:8.3f}"
143	"{:6.0f} {:2s} {:>2s}{:2s}".format(
144	"ATOM",
145	int(str(atom.atom_num)[0:5]),
146	atom.atom_name,
147	" ",
148	atom.resname[0:3],
149	"A",
150	int(str(atom.resid)[0:4]),
151	" ",
152	float(atom.coords[0]),
153	float(atom.coords[1]),
154	float(atom.coords[2]),
155	e,
156	f,
157	" ",
158	" ",
159	)
160	]
161	)
162	+ "\n"
163	)
164
NEW 165	data6.write(	×
166	"\n".join(
167	[
168	"{:6s}{:5d} {:^4s}{:1s}{:3s}"
169	" {:1s}{:4d}{:1s} {:8.3f}{:8.3f}{:8.3f}"
170	"{:6.0f}{:6.0f} {:>2s}{:2s}".format(
171	"ATOM",
172	int(str(atom.atom_num)[0:5]),
173	atom.atom_name,
174	" ",
175	atom.resname[0:3],
176	"A",
177	int(str(atom.resid)[0:4]),
178	" ",
179	float(atom.coords[0]),
180	float(atom.coords[1]),
181	float(atom.coords[2]),
182	a,
183	i,
184	" ",
185	" ",
186	)
187	]
188	)
189	+ "\n"
190	)
191
192	for d in file_list:	×
193	d.close()	×

CCPBioSim / CodeEntropy / 13726590978

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