Swapaa seg fault (in Ring::aromatic)

[tic20@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-07-27)
Description
Swapaa is occasionally causing segmentation faults when mutating to/from PHE (and probably other aromatic residues). To replicate:

open 3io0
swapaa :159 ILE
swapaa :159 PHE

... and repeat until crash (usually first or second time, *possibly* more often when atoms are displayed, but that might be my imagination). I've caught two different tracebacks with GDB (copied below).

Traceback 1:
Program received signal SIGSEGV, Segmentation fault.
0x00007fffb71200b8 in atomstruct::Ring::aromatic() const ()
   from /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/atomic/lib/libatomstruct.so
Missing separate debuginfos, use: debuginfo-install ucsf-chimerax-daily-2019.07.27-1.el7.x86_64
(gdb) bt
#0  0x00007fffb71200b8 in atomstruct::Ring::aromatic() const ()
    at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/atomic/lib/libatomstruct.so
#1  0x00007fff2cb18452 in find_aro_amines(PyObject*, PyObject*) (args=<optimized out>) at _cg/cg.cpp:1384
#2  0x00007ffff790937a in PyCFunction_Call (kwargs=<optimized out>, args=0x7fff2d24f3b0, func=0x7fff440610a0) at Objects/call.c:772
#3  0x00007ffff790937a in PyCFunction_Call (func=0x7fff440610a0, args=0x7fff2d24f3b0, kwargs=<optimized out>) at Objects/call.c:788
#4  0x00007ffff78dfeaf in _PyEval_EvalFrameDefault (kwdict=0x0, callargs=0x7fff2d24f3b0, func=0x7fff440610a0) at Python/ceval.c:4641
#5  0x00007ffff78dfeaf in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:3191
#6  0x00007ffff79f188e in _PyEval_EvalCodeWithName (_co=0x7fffb66c4780, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=4, kwnames=0x0, kwargs=0x7fff2d1a9c08, kwcount=0, kwstep=1, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x7fffb66bae90, qualname=0x7fffb66bae90) at Python/ceval.c:3930
#7  0x00007ffff7906cc5 in _PyFunction_FastCallKeywords (func=<optimized out>, stack=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:433


Traceback 2:
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7ffef2884700 (LWP 10926)]
0x00007fff38ef4f32 in find_5ring_planar_NR2 (symmetric=true, a=0x57ff910, 
    this=<optimized out>) at _cg/cg.cpp:903
903	_cg/cg.cpp: No such file or directory.
Missing separate debuginfos, use: debuginfo-install ucsf-chimerax-daily-2019.07.27-1.el7.x86_64
(gdb) bt
#0  0x00007fff38ef4f32 in initiate_find_5ring_planar_NR2(std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, bool, std::vector<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> >, std::allocator<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> > > >*, std::mutex*) (symmetric=true, a=0x57ff910, this=<optimized out>) at _cg/cg.cpp:903
#1  0x00007fff38ef4f32 in initiate_find_5ring_planar_NR2(std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, bool, std::vector<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> >, std::allocator<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> > > >*, std::mutex*) (start=..., end=..., symmetric=true, groups=0x7fffffff9810, groups_mutex=0x7fffffff9850) at _cg/cg.cpp:1112
#2  0x00007fffe6f61070 in  () at /lib64/libstdc++.so.6
#3  0x00007ffff7055dd5 in start_thread () at /lib64/libpthread.so.0
#4  0x00007ffff759eead in clone () at /lib64/libc.so.6
(gdb) 
#0  0x00007fff38ef4f32 in initiate_find_5ring_planar_NR2(std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, bool, std::vector<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> >, std::allocator<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> > > >*, std::mutex*) (symmetric=true, a=0x57ff910, this=<optimized out>) at _cg/cg.cpp:903
#1  0x00007fff38ef4f32 in initiate_find_5ring_planar_NR2(std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, std::vector<atomstruct::Atom*, std::allocator<atomstruct::Atom*> >::const_iterator, bool, std::vector<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> >, std::allocator<std::vector<atomstruct::Atom const*, std::allocator<atomstruct::Atom const*> > > >*, std::mutex*) (start=..., end=..., symmetric=true, groups=0x7fffffff9810, groups_mutex=0x7fffffff9850) at _cg/cg.cpp:1112


OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Rings weren't being marked as "dirty" when atoms/bonds deleted.