Loading a specific PDB file crashes Avogadro

[fxcoudert]

Avogadro version:

• Avogadrolibs: 1.99.0
• Qt: 5.15.8

Desktop version: (please complete the following information):

• OS: macOS 14.3.1 (arm64)
• Version: 1.99.0

Describe the bug Loading a specific PDB file crashes Avogadro

To Reproduce Steps to reproduce the behavior:

1. Download PDB file at https://gist.github.com/fxcoudert/6ea151fc53e446572d990aaa69468558
2. Drag-and-drop it into Avogadro
3. Observe crash

Expected behavior That PDB file loads fine with various software. At the very least, it should give an error but not crash.

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[fxcoudert]

If the crash happens during a drop event, the backtrace of the active thread is:

Thread 0::  Dispatch queue: com.apple.main-thread
0   CoreFoundation                         0x18549a804 __CFStringHash + 884
1   CoreFoundation                         0x1854c9d10 -[__NSDictionaryM setObject:forKey:] + 292
2   CoreFoundation                         0x1854f72ec -[NSMutableDictionary addEntriesFromDictionary:] + 216
3   AppKit                                 0x188cbcef8 -[NSAppearance _callCoreUIWithBlock:options:requireBezelTintColor:] + 412
4   AppKit                                 0x188cf630c -[NSCompositeAppearance _callCoreUIWithBlock:options:requireBezelTintColor:] + 288
5   AppKit                                 0x188d0bbb8 -[NSAppearance _createOrUpdateLayer:options:] + 100
6   AppKit                                 0x1899097c0 -[NSTitlebarContainerView _configureLayer:forDividerStyle:widgetHeight:] + 288
7   AppKit                                 0x189909dd4 -[NSTitlebarContainerView _updateDividerLayerForController:animated:] + 1012
8   AppKit                                 0x188d0aa10 -[NSTitlebarContainerView observeValueForKeyPath:ofObject:change:context:] + 340
9   Foundation                             0x1865efcf4 NSKeyValueNotifyObserver + 252
10  Foundation                             0x18669fee0 NSKeyValueDidChange + 360
11  Foundation                             0x1865e2e68 -[NSObject(NSKeyValueObservingPrivate) _changeValueForKeys:count:maybeOldValuesDict:maybeNewValuesDict:usingBlock:] + 680
12  Foundation                             0x18660c458 -[NSObject(NSKeyValueObservingPrivate) _changeValueForKey:key:key:usingBlock:] + 64
13  Foundation                             0x18662d97c _NSSetRectValueAndNotify + 324
14  AppKit                                 0x189aaab38 -[NSWindowSectionContentController _updateSectionState] + 336
15  AppKit                                 0x18987c62c -[NSWindowSectionController setWindow:] + 164
16  AppKit                                 0x1899082a4 -[NSTitlebarContainerView viewDidMoveToWindow] + 48
17  AppKit                                 0x188d009d8 -[NSView _setWindow:] + 1788
18  AppKit                                 0x188d080e4 -[NSView addSubview:] + 212
19  AppKit                                 0x188d0dbbc -[NSFrameView addSubview:] + 52
20  AppKit                                 0x188d0db70 -[NSThemeFrame addSubview:] + 456
21  AppKit                                 0x188d0d590 -[NSView addSubview:positioned:relativeTo:] + 372
22  AppKit                                 0x188d0d398 -[NSThemeFrame addSubview:positioned:relativeTo:] + 52
23  AppKit                                 0x188d0d34c -[NSThemeFrame _addKnownSubview:positioned:relativeTo:] + 44
24  AppKit                                 0x188d03ef0 __49-[NSThemeFrame _floatTitlebarAndToolbarFromInit:]_block_invoke + 324
25  AppKit                                 0x188d03ccc +[NSAnimationContext runAnimationGroup:] + 56
26  AppKit                                 0x188d03b78 -[NSThemeFrame _floatTitlebarAndToolbarFromInit:] + 120
27  AppKit                                 0x188cffed4 -[NSThemeFrame initWithFrame:styleMask:owner:] + 212
28  AppKit                                 0x188cfdf74 -[NSWindow _commonInitFrame:styleMask:backing:defer:] + 524
29  AppKit                                 0x188cfda20 -[NSWindow _initContent:styleMask:backing:defer:contentView:] + 796
30  AppKit                                 0x188e566b0 -[NSPanel _initContent:styleMask:backing:defer:contentView:] + 48
31  AppKit                                 0x188cfd6f8 -[NSWindow initWithContentRect:styleMask:backing:defer:] + 48
32  AppKit                                 0x188e56664 -[NSPanel initWithContentRect:styleMask:backing:defer:] + 48
33  AppKit                                 0x188f57bb0 -[NSWindow initWithContentRect:styleMask:backing:defer:screen:] + 24
34  libqcocoa.dylib                        0x100ff69f4 0x100fcc000 + 174580
35  Avogadro2                              0x100ccc938 Avogadro::MainWindow::dropEvent(QDropEvent*) + 360
36  libQt5Widgets.5.15.8.dylib             0x101fd5e48 QWidget::event(QEvent*) + 104
37  HIServices                             0x18b88da7c CallReceiveMessageCollectionWithMessage + 116
38  HIServices                             0x18b887b18 DoMultipartDropMessage + 104
39  HIServices                             0x18b8878d0 DoDropMessage + 56
40  HIServices                             0x18b88b664 CoreDragMessageHandler + 924
41  CoreFoundation                         0x1855ac718 __CFMessagePortPerform + 596
42  CoreFoundation                         0x18550ff6c __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE1_PERFORM_FUNCTION__ + 60
43  CoreFoundation                         0x18550fe8c __CFRunLoopDoSource1 + 520
44  CoreFoundation                         0x18550e858 __CFRunLoopRun + 2244
45  CoreFoundation                         0x18550d93c CFRunLoopRunSpecific + 608
46  HIToolbox                              0x18fad6448 RunCurrentEventLoopInMode + 292
47  HIToolbox                              0x18fad6284 ReceiveNextEventCommon + 648
48  HIToolbox                              0x18fad5fdc _BlockUntilNextEventMatchingListInModeWithFilter + 76
49  AppKit                                 0x188ceced0 _DPSNextEvent + 660
50  AppKit                                 0x1894d7eec -[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 716
51  AppKit                                 0x188ce037c -[NSApplication run] + 476
52  libqcocoa.dylib                        0x100ff8a64 0x100fcc000 + 182884
53  dyld                                   0x1850b10e0 start + 2360

If the crash occurs with the File > Open menu, the backtrace is the following:

Thread 0::  Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib                 0x1853f1808 semaphore_timedwait_trap + 8
1   SkyLight                               0x18aead57c SLSTransactionWait + 224
2   SkyLight                               0x18ae08e78 SLSConnectionSynchronizeSLSCATransaction + 48
3   SkyLight                               0x18ac03b40 SLSWindowIsOrderedIn + 48
4   AppKit                                 0x188ee44a4 -[_NSCGSWindowOrdering isWindowOrderedIn:] + 108
5   AppKit                                 0x188f57c00 -[NSWindow _fromScreenCommonCode:] + 52
6   AppKit                                 0x188f57bbc -[NSWindow initWithContentRect:styleMask:backing:defer:screen:] + 36
7   libqcocoa.dylib                        0x1024369f4 0x10240c000 + 174580
8   Avogadro2                              0x10210fb64 Avogadro::MainWindow::importFile() + 616
9   libQt5Core.5.15.8.dylib                0x104179424 0x104034000 + 1332260
10  CoreFoundation                         0x18550f970 __CFRunLoopDoSource0 + 176
11  CoreFoundation                         0x18550f740 __CFRunLoopDoSources0 + 340
12  CoreFoundation                         0x18550e2d0 __CFRunLoopRun + 828
13  CoreFoundation                         0x18550d93c CFRunLoopRunSpecific + 608
14  HIToolbox                              0x18fad6448 RunCurrentEventLoopInMode + 292
15  HIToolbox                              0x18fad6284 ReceiveNextEventCommon + 648
16  HIToolbox                              0x18fad5fdc _BlockUntilNextEventMatchingListInModeWithFilter + 76
17  AppKit                                 0x188ceced0 _DPSNextEvent + 660
18  AppKit                                 0x1894d7eec -[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 716
19  AppKit                                 0x188ce037c -[NSApplication run] + 476
20  libqcocoa.dylib                        0x102438a64 0x10240c000 + 182884
21  dyld                                   0x1850b10e0 start + 2360

[ghutchis]

Because we do file loading in a separate thread, backtraces are unfortunately not very useful.

I have a better trace from the command-line. Since we're using our own code, the PDB reader isn't quite as battle-tested as the Open Babel code.

[fxcoudert]

the PDB reader isn't quite as battle-tested as the Open Babel code

I had a look and there's at least one weird thing: it assumes all SE atoms are sulfur, which means it's mistyping selenium atoms.

https://github.com/OpenChemistry/avogadrolibs/blob/7061aac5d761406c98229d4f7b19132b89c3136c/avogadro/io/pdbformat.cpp#L147

I tested with a simple PDB file with a selenium atom, which VMD and Mercury read fine, but Avogadro transforms the selenium into sulfur.

$ cat test.pdb      
HETATM    1  SE  HOH     1       0.013   0.831  -0.083  1.00  0.00           SE 
HETATM    2  H   HOH     0       0.941   0.844   0.163  1.00  0.00           H  
HETATM    3  H   HOH     0      -0.250  -0.068  -0.293  1.00  0.00           H  
END

I've also looked at openbabel and it definitely trusts the element field: https://github.com/openbabel/openbabel/blob/32cf131444c1555c749b356dab44fb9fe275271f/src/formats/pdbformat.cpp#L932

[ghutchis]

It's one thing if the SE is in the atom name, but SE in the element column is reliable.

https://github.com/OpenChemistry/avogadrolibs/pull/1643

[github-actions[bot]]

Here are the build results macOS.dmg Avogadro2.AppImage Win64.exe Artifacts will only be retained for 90 days.

[github-actions[bot]]

Here are the build results Avogadro2.AppImage macOS.dmg Win64.exe Artifacts will only be retained for 90 days.