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
|
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_modify.py provides modifySlotsMixin for MWsemantics,
with modify slot methods and related helper methods.
@author: Mark
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Note: many ops_*.py files provide mixin classes for Part,
not for MWsemantics like this one.
History:
mark 2008-02-02 split this out of MWsemantics.py.
"""
from utilities import debug_flags
from utilities.debug import reload_once_per_event
class modifySlotsMixin:
"""
Mixin class to provide modify-related methods for class MWsemantics.
Has slot methods and their helper methods.
"""
def modifyAdjustSel(self):
"""
Adjust the current selection.
"""
if debug_flags.atom_debug:
print "debug: reloading sim_commandruns on each use, for development"
import simulation.sim_commandruns as sim_commandruns
reload_once_per_event(sim_commandruns)
from simulation.sim_commandruns import Minimize_CommandRun
cmdrun = Minimize_CommandRun( self, 'Sel', type = 'Adjust')
cmdrun.run()
return
def modifyAdjustAll(self):
"""
Adjust all atoms.
"""
if debug_flags.atom_debug:
print "debug: reloading sim_commandruns on each use, for development"
import simulation.sim_commandruns as sim_commandruns
reload_once_per_event(sim_commandruns)
from simulation.sim_commandruns import Minimize_CommandRun
cmdrun = Minimize_CommandRun( self, 'All', type = 'Adjust')
cmdrun.run()
return
def modifyCheckAtomTypes(self):
"""
Check Atom Types for all atoms.
"""
from simulation.sim_commandruns import CheckAtomTypes_CommandRun
cmdrun = CheckAtomTypes_CommandRun(self)
cmdrun.run()
return
def modifyHydrogenate(self):
"""
Add hydrogen atoms to each singlet in the selection.
"""
self.assy.modifyHydrogenate()
# remove hydrogen atoms from selected atoms/molecules
def modifyDehydrogenate(self):
"""
Remove all hydrogen atoms from the selection.
"""
self.assy.modifyDehydrogenate()
def modifyPassivate(self):
"""
Passivate the selection by changing surface atoms to eliminate singlets.
"""
self.assy.modifyPassivate()
def modifyDeleteBonds(self):
"""
Delete all bonds between selected and unselected atoms or chunks.
"""
self.assy.modifyDeleteBonds()
def modifyStretch(self):
"""
Stretch/expand the selected chunk(s).
"""
self.assy.Stretch()
def modifySeparate(self):
"""
Form a new chunk from the selected atoms.
"""
self.assy.modifySeparate()
def modifyMerge(self):
"""
Create a single chunk from two of more selected chunks.
"""
self.assy.merge()
self.win_update()
def makeChunkFromAtom(self):
"""
Create a new chunk from the selected atoms.
"""
self.assy.makeChunkFromSelectedAtoms()
self.win_update()
def modifyInvert(self):
"""
Invert the atoms of the selected chunk(s).
"""
self.assy.Invert()
def modifyMirror(self):
"""
Mirrors the selected chunks through a Plane (or Grid Plane).
"""
self.assy.Mirror()
def modifyAlignCommonAxis(self):
"""
Align selected chunks to the computed axis of the first chunk.
"""
self.assy.align()
self.win_update()
def modifyCenterCommonAxis(self):
"""
Same as "Align to Common Axis", except that it moves all the selected
chunks to the center of the first selected chunk after
aligning/rotating the other chunks.
"""
# This is still not fully implemented as intended. Instead of moving all the selected
# chunks to the center of the first selected chunk, I want to have them moved to the closest
# (perpendicular) point of the first chunk's axis. I've studied and understand the math involved;
# I just need to implement the code. I plan to ask Bruce for help since the two of us will get it
# done much more quickly together than me doing it alone.
# Mark 050829.
self.assy.alignmove()
self.win_update()
|
