Deleting atoms causes crash in atomstruct::Atom.remove_bond()

[Tom Goddard]

Opening 1grl and then deleting chain A with command "delete /a" causes a crash as it tries to delete the 17th atom.

I haven't checked in the "delete" command yet since we have a demo on Monday, but will check it in after that.

The pointers to the deleted atoms look fine, here are the 16 atoms that delete before the crash

0 0x7f8a27162210
1 0x7f8a27162350
2 0x7f8a27162410
3 0x7f8a271625b0
4 0x7f8a271626f0
5 0x7f8a271628b0
6 0x7f8a27162ab0
7 0x7f8a27162be0
8 0x7f8a27162d00
9 0x7f8a27163040
10 0x7f8a27163100
11 0x7f8a271631c0
12 0x7f8a27162990
13 0x7f8a27163580
14 0x7f8a271636a0
15 0x7f8a271637c0
Segmentation fault: 11

Here's the crash dump:

Process: Chimera2 [89328]
Path: /Users/USER/*/Chimera2.app/Contents/MacOS/Chimera2
Identifier: edu.ucsf.cgl.Chimera2
Version: 2.0.0 (2.0.0.0)
Code Type: X86-64 (Native)
Parent Process: bash [68484]
Responsible: Emacs-10.7 [68473]
User ID: 501

Date/Time: 2015-05-29 19:01:54.845 -0700
OS Version: Mac OS X 10.10.3 (14D136)
Report Version: 11
Anonymous UUID: ADCA02F2-9A59-6574-CF8F-380125498A20

Time Awake Since Boot: 2700000 seconds

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00007ff7dfc00000

VM Regions Near 0x7ff7dfc00000:

MALLOC_TINY 00007ff7dfb00000-00007ff7dfc00000 [ 1024K] rw-/rwx SM=COW

-->

STACK GUARD 00007fff53694000-00007fff56e43000 [ 55.7M] ---/rwx SM=NUL stack guard for thread 0

Application Specific Information:
Performing @selector(controlAction:) from sender wxNSComboBox 0x7ff7d96a7c00

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_platform.dylib 0x00007fff838ee331 _platform_memmove$VARIANT$Ivybridge + 49
1 libmolc.dylib 0x0000000109fbeef0 basegeom::Connectible<atomstruct::Bond, atomstruct::Atom>::remove_connection(atomstruct::Bond*) + 1792 (algorithm:1894)
2 libmolc.dylib 0x0000000109fbdb98 atomstruct::Atom::remove_bond(atomstruct::Bond*) + 40 (Atom.h:101)
3 libmolc.dylib 0x0000000109fbc951 atomstruct::AtomicStructure::delete_bond(atomstruct::Bond*) + 97 (AtomicStructure.h:153)
4 libmolc.dylib 0x0000000109fb6b69 atomstruct::AtomicStructure::delete_atom(atomstruct::Atom*) + 457 (AtomicStructure.h:144)
5 libmolc.dylib 0x0000000109fb2a7d atom_delete + 285 (molc.cpp:90)
6 _ctypes.so 0x0000000109a71697 ffi_call_unix64 + 79 (darwin64.S:79)
7 _ctypes.so 0x0000000109a71ef8 ffi_call + 872 (x86-ffi64.c:581)
8 _ctypes.so 0x0000000109a6d05b _ctypes_callproc + 891 (callproc.c:811)
9 _ctypes.so 0x0000000109a672f1 PyCFuncPtr_call + 1057 (_ctypes.c:3848)
10 org.python.python 0x000000010857fbc7 PyObject_Call + 103 (abstract.c:2040)
11 org.python.python 0x00000001086355ae PyEval_EvalFrameEx + 20958 (ceval.c:4466)
12 org.python.python 0x0000000108638fc2 fast_function + 210 (ceval.c:4334)
13 org.python.python 0x0000000108635314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
14 org.python.python 0x0000000108630267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
15 org.python.python 0x00000001085a513d function_call + 381 (funcobject.c:632)
16 org.python.python 0x000000010857fbc7 PyObject_Call + 103 (abstract.c:2040)
17 org.python.python 0x000000010863601f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
18 org.python.python 0x0000000108630267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
19 org.python.python 0x000000010863902c fast_function + 316 (ceval.c:4348)
20 org.python.python 0x0000000108635314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
21 org.python.python 0x0000000108630267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
22 org.python.python 0x00000001085a513d function_call + 381 (funcobject.c:632)
23 org.python.python 0x000000010857fbc7 PyObject_Call + 103 (abstract.c:2040)
24 org.python.python 0x00000001085931bd method_call + 141 (classobject.c:347)
25 org.python.python 0x000000010857fbc7 PyObject_Call + 103 (abstract.c:2040)
26 org.python.python 0x000000010863865d PyEval_CallObjectWithKeywords + 93 (ceval.c:4114)
27 _core.so 0x000000010a5c21fc wxPyCallback::EventThunker(wxEvent&) + 284 (sip_corewxEvtHandler.cpp:70)
28 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b601dba wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 186
29 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b601b2b wxEvtHandler::ProcessEventLocally(wxEvent&) + 59
30 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b601a3e wxEvtHandler::ProcessEvent(wxEvent&) + 190
31 _core.so 0x000000010a5157ea sipwxComboBox::ProcessEvent(wxEvent&) + 154 (sip_corewxComboBox.cpp:439)
32 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b601e5f wxEvtHandler::SafelyProcessEvent(wxEvent&) + 15
33 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b704f86 wxNSTextFieldControl::controlAction(NSView*, void*, void*) + 166
34 libsystem_trace.dylib 0x00007fff8a7d5cd7 _os_activity_initiate + 75
35 com.apple.AppKit 0x00007fff8f5b6fb1 -[NSApplication sendAction:to:from:] + 452
36 com.apple.AppKit 0x00007fff8f5cca46 -[NSControl sendAction:to:] + 86
37 com.apple.AppKit 0x00007fff8f6096df -[NSTextField textDidEndEditing:] + 853
38 com.apple.CoreFoundation 0x00007fff81c2345c CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER + 12
39 com.apple.CoreFoundation 0x00007fff81b13634 _CFXNotificationPost + 3140
40 com.apple.Foundation 0x00007fff8c6449d1 -[NSNotificationCenter postNotificationName:object:userInfo:] + 66
41 com.apple.AppKit 0x00007fff8f714947 -[NSTextView(NSPrivate) _giveUpFirstResponder:] + 423
42 com.apple.AppKit 0x00007fff8f790912 -[NSTextView(NSKeyBindingCommands) insertNewline:] + 239
43 com.apple.AppKit 0x00007fff8f65d001 -[NSTextView doCommandBySelector:] + 195
44 com.apple.AppKit 0x00007fff8f65cf11 -[NSTextInputContext(NSInputContext_WithCompletion) doCommandBySelector:completionHandler:] + 118
45 com.apple.AppKit 0x00007fff8f642d33 -[NSKeyBindingManager(NSKeyBindingManager_MultiClients) interpretEventAsCommand:forClient:] + 1899
46 com.apple.AppKit 0x00007fff8fc09292 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke972 + 335
47 com.apple.AppKit 0x00007fff8f644d0f -[NSTextInputContext(NSInputContext_WithCompletion) hasMarkedTextWithCompletionHandler:] + 76
48 com.apple.AppKit 0x00007fff8f65ce13 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke_3 + 95
49 com.apple.AppKit 0x00007fff8f655fe8 -[NSTextInputContext tryHandleEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 101
50 com.apple.AppKit 0x00007fff8fc09094 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke960 + 321
51 com.apple.HIToolbox 0x00007fff8dc33d4f TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_5 + 70
52 com.apple.HIToolbox 0x00007fff8dc32c45 _ZL23DispatchEventToHandlersP14EventTargetRecP14OpaqueEventRefP14HandlerCallRec_block_invoke + 108
53 com.apple.AppKit 0x00007fff8f645716 55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke174 + 2387
54 com.apple.AppKit 0x00007fff8f644d0f -[NSTextInputContext(NSInputContext_WithCompletion) hasMarkedTextWithCompletionHandler:] + 76
55 com.apple.AppKit 0x00007fff8f644cb0 55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke_2 + 95
56 com.apple.AppKit 0x00007fff8f644c28 -[NSTextInputContext tryHandleTSMEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 101
57 com.apple.AppKit 0x00007fff8f6448e5 -[NSTextInputContext handleTSMEvent:completionHandler:] + 3122
58 com.apple.AppKit 0x00007fff8f643c3e _NSTSMEventHandler + 324
59 com.apple.HIToolbox 0x00007fff8dbccb6c DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1260
60 com.apple.HIToolbox 0x00007fff8dbcbfae SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 386
61 com.apple.HIToolbox 0x00007fff8dbcbe22 SendEventToEventTargetWithOptions + 43
62 com.apple.HIToolbox 0x00007fff8dc3026c SendTSMEvent_WithCompletionHandler + 417
63 com.apple.HIToolbox 0x00007fff8dc3076c SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler_block_invoke + 400
64 com.apple.HIToolbox 0x00007fff8dc305a6 SendFilterTextEvent_WithCompletionHandler_block_invoke + 189
65 com.apple.HIToolbox 0x00007fff8dc302c0 SendTSMEvent_WithCompletionHandler + 501
66 com.apple.HIToolbox 0x00007fff8dc3008f SendFilterTextEvent_WithCompletionHandler + 236
67 com.apple.HIToolbox 0x00007fff8dc2fd51 SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler + 295
68 com.apple.HIToolbox 0x00007fff8dc2fae9 utDeliverTSMEvent_WithCompletionHandler_block_invoke_2 + 296
69 com.apple.HIToolbox 0x00007fff8dc2f988 utDeliverTSMEvent_WithCompletionHandler_block_invoke + 437
70 com.apple.HIToolbox 0x00007fff8dc2f7cd TSMKeyEvent_WithCompletionHandler + 701
71 com.apple.HIToolbox 0x00007fff8dc2f4d0 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_4 + 251
72 com.apple.HIToolbox 0x00007fff8dc2f386 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_3 + 330
73 com.apple.HIToolbox 0x00007fff8dc2f112 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_2 + 259
74 com.apple.HIToolbox 0x00007fff8dc2ef25 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke + 251
75 com.apple.HIToolbox 0x00007fff8dc1376f TSMProcessRawKeyEventWithOptionsAndCompletionHandler + 3068
76 com.apple.AppKit 0x00007fff8fc08ea6 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke949 + 131
77 com.apple.AppKit 0x00007fff8f642462 -[NSTextInputContext tryTSMProcessRawKeyEvent:dispatchCondition:setupForDispatch:furtherCondition:dispatchWork:continuation:] + 127
78 com.apple.AppKit 0x00007fff8f642195 -[NSTextInputContext _handleEvent:options:completionHandler:] + 1266
79 com.apple.AppKit 0x00007fff8f641c5e -[NSTextInputContext handleEvent:] + 109
80 com.apple.AppKit 0x00007fff8f641b64 -[NSView interpretKeyEvents:] + 207
81 com.apple.AppKit 0x00007fff8f64197a -[NSTextView keyDown:] + 695
82 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b701eee -[wxNSTextFieldEditor keyDown:] + 110
83 com.apple.AppKit 0x00007fff8fb3111b -[NSWindow _reallySendEvent:isDelayedEvent:] + 5452
84 com.apple.AppKit 0x00007fff8f4c2d76 -[NSWindow sendEvent:] + 470
85 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b6fa7c6 -[wxNSWindow sendEvent:] + 118
86 com.apple.AppKit 0x00007fff8f4bf9b1 -[NSApplication sendEvent:] + 4199
87 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b60ff36 -[wxNSApplication sendEvent:] + 134
88 com.apple.AppKit 0x00007fff8f3e8c68 -[NSApplication run] + 711
89 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b6eeec3 wxGUIEventLoop::OSXDoRun() + 115
90 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b5ccc14 wxCFEventLoop::DoRun() + 52
91 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b4f7b45 wxEventLoopBase::Run() + 165
92 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010b4bbee1 wxAppConsoleBase::MainLoop() + 209
93 _core.so 0x000000010a83eee5 wxPyApp::MainLoop() + 181 (sip_corewxPyApp.cpp:316)
94 _core.so 0x000000010a84265d meth_wxPyApp_MainLoop(_object*, _object*) + 205 (sip_corewxPyApp.cpp:1794)
95 org.python.python 0x0000000108635913 PyEval_EvalFrameEx + 21827 (ceval.c:4237)
96 org.python.python 0x0000000108638fc2 fast_function + 210 (ceval.c:4334)
97 org.python.python 0x0000000108635314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
98 org.python.python 0x0000000108638fc2 fast_function + 210 (ceval.c:4334)
99 org.python.python 0x0000000108635314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
100 org.python.python 0x0000000108630267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
101 org.python.python 0x000000010863902c fast_function + 316 (ceval.c:4348)
102 org.python.python 0x0000000108635314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
103 org.python.python 0x0000000108630267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
104 org.python.python 0x000000010862f84f PyEval_EvalCode + 63 (ceval.c:775)
105 org.python.python 0x000000010864fab5 PyImport_ImportFrozenModuleObject + 469 (import.c:869)
106 org.python.python 0x000000010864fba2 PyImport_ImportFrozenModule + 34 (import.c:1291)
107 org.python.python 0x000000010864945e Py_FrozenMain + 430 (frozenmain.c:84)
108 libdyld.dylib 0x00007fff8c2f45c9 start + 1

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff87db4232 kevent64 + 10
1 libdispatch.dylib 0x00007fff8750ca6a _dispatch_mgr_thread + 52

Thread 2:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 3:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 4:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 5:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 6:
0 libsystem_kernel.dylib 0x00007fff87dae4de mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff87dad64f mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff81b75eb4 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff81b7537b CFRunLoopRun + 1371
4 com.apple.CoreFoundation 0x00007fff81b74bd8 CFRunLoopRunSpecific + 296
5 com.apple.AppKit 0x00007fff8f4bb66b _NSEventThread + 137
6 libsystem_pthread.dylib 0x00007fff8cda6268 _pthread_body + 131
7 libsystem_pthread.dylib 0x00007fff8cda61e5 _pthread_start + 176
8 libsystem_pthread.dylib 0x00007fff8cda441d thread_start + 13

Thread 7:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 8:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 9:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 10:
0 libsystem_kernel.dylib 0x00007fff87db394a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8cda440d start_wqthread + 13

Thread 11:

Thread 12:: OGL Profiler
0 libsystem_kernel.dylib 0x00007fff87dae4de mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff87dad64f mach_msg + 55
2 com.apple.opengl 0x00007fff8decba79 glcDebugListener + 336
3 libsystem_pthread.dylib 0x00007fff8cda6268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8cda61e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8cda441d thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):

rax: 0x00007ff7df7ebd88 rbx: 0x00007fff5768eb58 rcx: 0xffffffffffbebd88 rdx: 0xfffffffffffffff8
rdi: 0x00007ff7dfbffff8 rsi: 0x00007ff7dfc00000 rbp: 0x00007fff5768eaa0 rsp: 0x00007fff5768eaa0

r8: 0x00007ff7df7ebd80 r9: 0x0000000000000008 r10: 0x00007ff7df7ebd88 r11: 0xfffffffffffffff8

r12: 0x00007ff7dbf03c70 r13: 0x00007ff7dbf03c70 r14: 0x00007ff7df7ebd60 r15: 0x00007ff7df7ebd60
rip: 0x00007fff838ee331 rfl: 0x0000000000010282 cr2: 0x00007ff7dfc00000

Logical CPU: 2
Error Code: 0x00000004
Trap Number: 14

Binary Images:

0x10856c000 - 0x10856cff7 +edu.ucsf.cgl.Chimera2 (2.0.0 - 2.0.0.0) <BA3B1610-2D5F-38F1-B2C6-8E9624DE4AB8> /Users/USER/*/Chimera2.app/Contents/MacOS/Chimera2
0x108573000 - 0x108702ff7 +org.python.python (3.4.3, [c] 2001-2015 Python Software Foundation. - 3.4.3) <B05216B6-F925-3443-8EDD-E303D42E94A4> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/Python
0x108af2000 - 0x108af3fff +_heapq.so (0) <C9A206E4-A401-3B7E-8740-A5BAE8839184> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_heapq.so
0x108b37000 - 0x108b3bff7 +_struct.so (0) <3D108042-4157-3FBA-B318-08C56E80698D> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_struct.so
0x108ba4000 - 0x108ba6fff +time.so (0) <307B7F4F-645D-3C3D-BFEF-0A5C4F6D390A> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/time.so
0x108bae000 - 0x108baffff +_posixsubprocess.so (0) <EEFDE49E-4BFF-3D97-8F06-8946F073B3C5> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_posixsubprocess.so
0x108bb3000 - 0x108bb5ff7 +select.so (0) <A4E82A09-6F63-3DA7-A7EB-30597FC4AD82> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/select.so
0x108bfb000 - 0x108bffff7 +math.so (0) <C7AC55D2-554C-352B-A739-ABAA213F73A7> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/math.so
0x108c46000 - 0x108c49ff7 +binascii.so (0) <F71A29DE-1EBF-3BD4-B753-8BF4C0D4CA31> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/binascii.so
0x108c4d000 - 0x108c5ffff +libz.1.dylib (0) <36544000-4EE5-3392-957E-4D2B77C70B5B> /Users/USER/*/libz.1.dylib
0x108c63000 - 0x108c6eff7 +_datetime.so (0) <9AE5EAA1-6686-32CE-B810-0D97535BD444> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_datetime.so
0x108cb9000 - 0x108ce2fff +pyexpat.so (0) <32E313AD-F9E6-3744-BE64-6687CE52F33A> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/pyexpat.so
0x108d74000 - 0x108d74ff7 +_opcode.so (0) <7BA2D27A-F922-37C5-A54B-3EAAA737E552> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_opcode.so
0x108db7000 - 0x108dc8ff7 +_pickle.so (0) <BDBBFEF4-FC06-34C6-9F1B-A1ED83285598> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_pickle.so
0x108dd4000 - 0x108ddafff +_geometry.so (0) <ED57222B-4D45-36D9-8BAB-754E7332B31E> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/chimera/core/geometry/_geometry.so
0x108de0000 - 0x108e45ff7 +libarrays.dylib (0) <2FA87925-A92A-3B87-BC09-E6720E1F0C1F> /Users/USER/*/libarrays.dylib
0x108e93000 - 0x108e96fff +zlib.so (0) <3BCE3DFF-1B10-3484-A468-1117E5D76A7E> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/zlib.so
0x108e9b000 - 0x108e9cff7 +_bz2.so (0) <BDA4B442-81D6-3254-A1B1-E9A5C1E53E8D> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_bz2.so
0x108f60000 - 0x108f60fff +grp.so (0) <F6F2336F-6A42-319F-93D3-08C0AA807410> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/grp.so
0x108fa3000 - 0x108fa3ff7 +_bisect.so (0) <B8DDB08B-CC89-3354-B123-15061E0E63C6> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_bisect.so
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0x7fff90718000 - 0x7fff90725ff3 com.apple.ProtocolBuffer (1 - 228.0.1) <3429EB06-9F0E-355F-B9AB-F72879177398> /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer
0x7fff90726000 - 0x7fff9072cff7 com.apple.XPCService (2.0 - 1) <AA4A5393-1F5D-3465-A417-0414B95DC052> /System/Library/PrivateFrameworks/XPCService.framework/Versions/A/XPCService
0x7fff90730000 - 0x7fff90734fff libCoreVMClient.dylib (79.1) <201EF6DF-5074-3CB7-A361-398CF957A264> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff907d5000 - 0x7fff907efff7 com.apple.Kerberos (3.0 - 1) <7760E0C2-A222-3709-B2A6-B692D900CEB1> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
0x7fff907f0000 - 0x7fff90811fff com.apple.framework.Apple80211 (10.3 - 1030.71.6) <D3862426-2586-3DF7-BA75-9A184FCD74C4> /System/Library/PrivateFrameworks/Apple80211.framework/Versions/A/Apple80211
0x7fff908fd000 - 0x7fff90917ff7 libextension.dylib (55.2) <3BB019CA-199A-36AC-AA22-14B562138545> /usr/lib/libextension.dylib
0x7fff9092e000 - 0x7fff9097fff7 com.apple.AppleVAFramework (5.0.31 - 5.0.31) <FED294D2-13CB-381D-98D0-BDA909AACA32> /System/Library/PrivateFrameworks/AppleVA.framework/Versions/A/AppleVA
0x7fff90b13000 - 0x7fff90c43fff com.apple.UIFoundation (1.0 - 1) <466BDFA8-0B9F-3AB0-989D-F9779422926A> /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff90c44000 - 0x7fff90c53fff com.apple.LangAnalysis (1.7.0 - 1.7.0) <D1E527E4-C561-352F-9457-E8C50232793C> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
0x7fff90ede000 - 0x7fff90ef3ffb libCGInterfaces.dylib (294.1) <1A6AADE6-09EC-3054-85F9-E6A3607EBA70> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x7fff90ef4000 - 0x7fff90fd8fff libcrypto.0.9.8.dylib (52.20.2) <977DA067-2588-3BF8-A7B2-F08FC6E9088F> /usr/lib/libcrypto.0.9.8.dylib
0x7fff90fd9000 - 0x7fff90fdbff7 libsystem_coreservices.dylib (9) <41B7C578-5A53-31C8-A96F-C73E030B0938> /usr/lib/system/libsystem_coreservices.dylib
0x7fff90fdc000 - 0x7fff913b3fe7 com.apple.CoreAUC (211.1.0 - 211.1.0) <12645629-E065-388E-A6B5-094A240578CE> /System/Library/PrivateFrameworks/CoreAUC.framework/Versions/A/CoreAUC
0x7fff9142e000 - 0x7fff914c2fff com.apple.ink.framework (10.9 - 213) <8E029630-1530-3734-A446-13353F0E7AC5> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
0x7fff9153a000 - 0x7fff91542ff3 com.apple.CoreServices.FSEvents (1210.20.1 - 1210.20.1) <84F79D3E-7B5E-3C93-8479-35794A3F125E> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/FSEvents
0x7fff91543000 - 0x7fff91568ff7 libPng.dylib (1237) <CFBF1344-36AB-3AAE-B2EB-9FC1369F967F> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
0x7fff91569000 - 0x7fff915dbfff com.apple.framework.IOKit (2.0.2 - 1050.20.2) <09C0518C-90DF-3FC3-96D6-34D35F72C8EF> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
0x7fff915e1000 - 0x7fff915e9ffb libcopyfile.dylib (118.1.2) <0C68D3A6-ACDD-3EF3-991A-CC82C32AB836> /usr/lib/system/libcopyfile.dylib

External Modification Summary:

Calls made by other processes targeting this process:

task_for_pid: 1
thread_create: 0
thread_set_state: 0

Calls made by this process:

task_for_pid: 0
thread_create: 0
thread_set_state: 0

Calls made by all processes on this machine:

task_for_pid: 6801127
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=294.6M resident=164.5M(56%) swapped_out_or_unallocated=130.1M(44%)
Writable regions: Total=225.4M written=52.9M(23%) resident=94.0M(42%) swapped_out=0K(0%) unallocated=131.4M(58%)

REGION TYPE VIRTUAL
=========== =======
Activity Tracing 2048K
CG backing stores 4280K
CG image 164K
CG raster data 1072K
CG shared images 272K
CoreAnimation 52K
CoreImage 8K
CoreServices 3668K
CoreUI image data 60K
Dispatch continuations 16.0M
Foundation 4K
IOKit 13.0M
Kernel Alloc Once 8K
MALLOC 155.6M
MALLOC (admin) 32K
MALLOC_LARGE (reserved) 256K reserved VM address space (unallocated)
Memory Tag 242 12K
OpenCL 16K
OpenGL GLSL 256K
STACK GUARD 55.7M
Stack 13.5M
Stack (reserved) 520K reserved VM address space (unallocated)
VM_ALLOCATE 18.3M
DATA 34.4M
GLSLBUILTINS 2588K
IMAGE 528K
LINKEDIT 86.5M
TEXT 208.1M
UNICODE 552K
mapped file 69.4M
shared memory 68K
=========== =======
TOTAL 686.6M
TOTAL, minus reserved VM space 685.8M

Model: iMac13,2, BootROM IM131.010A.B05, 4 processors, Intel Core i7, 3.4 GHz, 32 GB, SMC 2.11f16
Graphics: NVIDIA GeForce GTX 680MX, NVIDIA GeForce GTX 680MX, PCIe, 2048 MB
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 0/DIMM1, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 1/DIMM1, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xF4), Broadcom BCM43xx 1.0 (7.15.166.24.3)
Bluetooth: Version 4.3.4f4 15601, 3 services, 27 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: Wi-Fi, AirPort, en1
Serial ATA Device: APPLE HDD ST3000DM001, 3 TB
Serial ATA Device: APPLE SSD SM128E, 121.33 GB
USB Device: Kinesis Keyboard Hub
USB Device: Keyboard Hub
USB Device: Composite Device
USB Device: Composite Device
USB Device: Hub
USB Device: Rift DK2
USB Device: Rift DK2
USB Device: FaceTime HD Camera (Built-in)
USB Device: Hub
USB Device: Camera DK2
USB Device: Hub
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: iMac, Apple Inc., 23.4

[Eric Pettersen]

Needed to iterate through a _copy_ of the atom's bond list as I remove bonds!