forked from kbsezginel/nanocar-avogadro
/
connect_wheel.py
171 lines (136 loc) · 5.99 KB
/
connect_wheel.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
"""
Nanocar Avogadro 2 plug-in - Add Wheel.
Connects wheel molecule to selected atom.
Author: Kutay B. Sezginel
Date: September 2018
"""
import os
import sys
import json
import argparse
from angstrom import Molecule
import numpy as np
import periodictable
# Some globals:
debug = True
wheel_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'wheel')
wheel_list = [i.split('.')[0] for i in os.listdir(wheel_dir)]
PLUGIN_DIR = os.path.abspath(os.path.dirname(__file__))
def get_options():
"""Create user interface options."""
user_options = {}
user_options['wheel'] = {'label': 'Wheel',
'type': 'stringList',
'default': 'C60',
'values': wheel_list}
user_options['append'] = {'label': 'Append',
'type': 'boolean',
'default': True}
user_options['d'] = {'label': 'Bond Distance',
'type': 'float',
'precision': 2,
'default': 1.5,
'suffix': 'Å'}
return {'userOptions': user_options }
def connect_wheel(opts):
"""
Connect wheel molecule to selected atom position.
The wheel molecule must have a connection site (Xc) and alignmen site (Xa) to specify connectivity.
The selected wheel molecule is added to selected atom by aligning the vector of the wheel.
"""
selected = [idx for idx, atm in enumerate(opts['cjson']['atoms']['selected']) if atm]
if len(selected) == 1:
# Get chassi coordinates and bonds
coords = np.array(opts['cjson']['atoms']['coords']['3d'])
connections = opts['cjson']['bonds']['connections']['index']
atoms = [periodictable.elements[i].symbol for i in opts['cjson']['atoms']['elements']['number']]
chassi = Molecule(atoms=atoms, coordinates=np.array(coords).reshape((int(len(coords) / 3)), 3))
# Get connection site for the chassis
selected_cidx = int(selected[0] * 3)
selected_coors = coords[selected_cidx:selected_cidx + 3]
# Find atom connected to the selected atom
bond_idx = connections.index(selected[0])
if bond_idx % 2 == 0:
bond_idx += 1
else:
bond_idx -= 1
bond_idx = int(connections[bond_idx] * 3)
# Get vector btw selected atom and atom connected to it
v_chassi = selected_coors - np.array(coords[bond_idx:bond_idx + 3])
# Read wheel molecule information
wheel = read_wheel(opts['wheel'])
# Align the wheel with chassis connection vector
v_wheel = wheel.coordinates[wheel.alignment_site] - wheel.coordinates[wheel.connection_site]
wheel.align(v_wheel, v_chassi)
# Translate the wheel to match dummy coor with selected coor
v_trans = selected_coors - wheel.coordinates[wheel.connection_site]
wheel.translate(v_trans)
# Adjust bond distance
v_bond = wheel.coordinates[wheel.connection_site] - wheel.coordinates[wheel.alignment_site]
d_bond = np.linalg.norm(v_bond)
v_bond = v_bond - v_bond / d_bond * opts['d']
wheel.translate(v_bond)
# Remove dummy atoms for alignment and connection sites
wheel.coordinates = np.delete(wheel.coordinates, [wheel.connection_site, wheel.alignment_site], axis=0)
wheel.atoms = np.delete(wheel.atoms, [wheel.connection_site, wheel.alignment_site])
# Write wheel atom ids to file for grouping
# wheel_info = {'name': opts['wheel'], 'start': len(chassi.atoms), 'n_atoms': len(wheel.atoms)}
# write_wheel_list(wheel_info, refresh=opts['refresh_wheel_list'])
if not opts['append']:
wheel += chassi
wheel = mol2xyz(wheel)
else:
print('Only 1 atom should be selected!')
wheel = None
return wheel
def mol2xyz(mol):
"""Converts Angstrom Molecule to xyz string"""
mol_xyz = "%i\n%s\n" % (len(mol.atoms), mol.name)
for atom, coor in zip(mol.atoms, mol.coordinates):
mol_xyz += "%s %f %f %f\n" % (atom, coor[0], coor[1], coor[2])
return mol_xyz
def read_wheel(wheel_name):
"""Read yaml file to Molecule object"""
wheel = Molecule(read=os.path.join(wheel_dir, '%s.xyz' % wheel_name))
wheel.connection_site, = np.where(wheel.atoms == 'Xc')[0]
wheel.alignment_site, = np.where(wheel.atoms == 'Xa')[0]
return wheel
def write_wheel_list(wheel_info, refresh=False):
"""Write atom ids for the connected wheel to keep track of atom groupings"""
wheel_list_file = os.path.join(PLUGIN_DIR, 'wheel_list.json')
if os.path.exists(wheel_list_file) and not refresh:
# Read and append new wheel if we don't want to refresh
with open(wheel_list_file, 'r') as outfile:
wheels = json.load(outfile)
wheel_list = wheels + [wheel_info]
else:
wheel_list = [wheel_info]
with open(wheel_list_file, 'w') as outfile:
json.dump(wheel_list, outfile)
def run_workflow():
"""Run main function - add wheel."""
stdinStr = sys.stdin.read()
opts = json.loads(stdinStr)
result = opts['cjson']
result['append'] = opts['append']
result['moleculeFormat'] = 'xyz'
result['xyz'] = connect_wheel(opts)
return result
if __name__ == "__main__":
parser = argparse.ArgumentParser('Build Nanocar!')
parser.add_argument('--debug', action='store_true')
parser.add_argument('--print-options', action='store_true')
parser.add_argument('--run-workflow', action='store_true')
parser.add_argument('--display-name', action='store_true')
parser.add_argument('--menu-path', action='store_true')
parser.add_argument('--lang', nargs='?', default='en')
args = vars(parser.parse_args())
debug = args['debug']
if args['display_name']:
print("Connect Wheel")
if args['menu_path']:
print("&Build|Nanocar")
if args['print_options']:
print(json.dumps(get_options()))
elif args['run_workflow']:
print(json.dumps(run_workflow()))