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template tool doesn't actually paste template that is selected #1655

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bernstei opened this issue Mar 20, 2024 · 8 comments · Fixed by #1777
Closed

template tool doesn't actually paste template that is selected #1655

bernstei opened this issue Mar 20, 2024 · 8 comments · Fixed by #1777

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@bernstei
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bernstei commented Mar 20, 2024 •
edited
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Avogadro version: (please complete the following information from the About box):

  • Avogadrolibs: 1.99.0
  • Qt: 5.15.8

Desktop version: (please complete the following information):

  • OS: macOS
  • Version 14.4
  • Compiler N/A (application from github releases page)

Describe the bug
template tool pastes FeH$_6$ no matter what template is selected in "Template" panel

To Reproduce

  • Run Avogadro with an empty canvas
  • select template tool
  • select a template, e.g. ethylene
  • click on blank canvas

Expected behavior

The chosen template is pasted

Screenshots

Image of window after following directions in "To Reproduce"

Screenshot 2024-03-20 at 10 38 04 AM
@welcome Welcome
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welcome bot commented Mar 20, 2024

Thanks for opening your first issue here! Please try to include example files and screenshots if possible. If you're looking for support, please post on our forum: https://discuss.avogadro.cc/

@ghutchis
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This seems like more of a documentation / UI hint thing. Click on a hydrogen atom.

The template tool started with "build up metal complexes easily":

  • click to insert metal / atom with designated geometry
  • click on hydrogens to attach ligand or functional groups

@bernstei
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I agree with UI, that it needs to be more clear that this will attach a fragment to an existing atom, or replace an existing atom with a fragment. But in that case, I'd also argue that it should do nothing (or maybe give a popup error?) if you click on blank canvas space, or at least not paste a random molecule that seems to come out of nowhere (why FeH6?)

Also, putting in a single H then clicking on it with the template tool (amide selected), resulted in a crash:

-------------------------------------
Translated Report (Full Report Below)
-------------------------------------

Process:               Avogadro2 [41791]
Path:                  /Applications/Avogadro2.app/Contents/MacOS/Avogadro2
Identifier:            cc.avogadro
Version:                (1.99.0)
Code Type:             ARM-64 (Native)
Parent Process:        launchd [1]
User ID:               503

Date/Time:             2024-03-20 10:51:11.8650 -0400
OS Version:            macOS 14.4 (23E214)
Report Version:        12
Anonymous UUID:        BE9A79F9-9C83-8D45-0C6B-B901FD6A37BE

Sleep/Wake UUID:       F7E34876-D895-4B8F-87DE-49CF307BD38B

Time Awake Since Boot: 200000 seconds
Time Since Wake:       2294 seconds

System Integrity Protection: enabled

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

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Codes:       0x0000000000000001, 0x0000000000000000

Termination Reason:    Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process:   exc handler [41791]

VM Region Info: 0 is not in any region.  Bytes before following region: 4295262208
      REGION TYPE                    START - END         [ VSIZE] PRT/MAX SHRMOD  REGION DETAIL
      UNUSED SPACE AT START
--->  
      __TEXT                      100048000-10014c000    [ 1040K] r-x/r-x SM=COW  /Applications/Avogadro2.app/Contents/MacOS/Avogadro2

Thread 0 Crashed::  Dispatch queue: com.apple.main-thread
0   libAvogadroQtPlugins.1.99.0.dylib	       0x100b11f34 Avogadro::QtPlugins::TemplateTool::atomLeftClick(QMouseEvent*) + 2552
1   libAvogadroQtPlugins.1.99.0.dylib	       0x100b11f28 Avogadro::QtPlugins::TemplateTool::atomLeftClick(QMouseEvent*) + 2540
2   libAvogadroQtPlugins.1.99.0.dylib	       0x100b10df4 Avogadro::QtPlugins::TemplateTool::mousePressEvent(QMouseEvent*) + 936
3   libAvogadroQtOpenGL.1.99.0.dylib	       0x1005f5af8 Avogadro::QtOpenGL::GLWidget::mousePressEvent(QMouseEvent*) + 56
4   libQt5Widgets.5.15.8.dylib    	       0x101375e48 QWidget::event(QEvent*) + 104
5   CoreFoundation                	       0x19d4a5e44 __CFRunLoopDoSource0 + 176
6   CoreFoundation                	       0x19d4a5bb4 __CFRunLoopDoSources0 + 244
7   CoreFoundation                	       0x19d4a47a0 __CFRunLoopRun + 828
8   CoreFoundation                	       0x19d4a3e0c CFRunLoopRunSpecific + 608
9   HIToolbox                     	       0x1a7c3f000 RunCurrentEventLoopInMode + 292
10  HIToolbox                     	       0x1a7c3ec90 ReceiveNextEventCommon + 220
11  HIToolbox                     	       0x1a7c3eb94 _BlockUntilNextEventMatchingListInModeWithFilter + 76
12  AppKit                        	       0x1a0cfc970 _DPSNextEvent + 660
13  AppKit                        	       0x1a14eedec -[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 700
14  AppKit                        	       0x1a0cefcb8 -[NSApplication run] + 476
15  libqcocoa.dylib               	       0x100398a64 0x10036c000 + 182884
16  dyld                          	       0x19d03e0e0 start + 2360

Thread 1:
0   libsystem_pthread.dylib       	       0x19d3c1d20 start_wqthread + 0

Thread 2:
0   libsystem_pthread.dylib       	       0x19d3c1d20 start_wqthread + 0

Thread 3:
0   libsystem_pthread.dylib       	       0x19d3c1d20 start_wqthread + 0

Thread 4:: Qt bearer thread
0   libsystem_kernel.dylib        	       0x19d38eb70 poll + 8
1   libQt5Core.5.15.8.dylib       	       0x1020f5728 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 168
2   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 5:: QNetworkAccessManager thread
0   libsystem_kernel.dylib        	       0x19d38eb70 poll + 8
1   libQt5Core.5.15.8.dylib       	       0x1020f56d0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 80
2   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 6:: Thread (pooled)
0   libsystem_kernel.dylib        	       0x19d3899ec __psynch_cvwait + 8
1   libsystem_pthread.dylib       	       0x19d3c755c _pthread_cond_wait + 1228
2   libQt5Core.5.15.8.dylib       	       0x101fb4b20 0x101f94000 + 133920
3   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 7:: com.apple.CFSocket.private
0   libsystem_kernel.dylib        	       0x19d391358 __select + 8
1   CoreFoundation                	       0x19d4cf30c __CFSocketManager + 640
2   libsystem_pthread.dylib       	       0x19d3c6f94 _pthread_start + 136
3   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 8:: Thread (pooled)
0   libsystem_kernel.dylib        	       0x19d3899ec __psynch_cvwait + 8
1   libsystem_pthread.dylib       	       0x19d3c755c _pthread_cond_wait + 1228
2   libQt5Core.5.15.8.dylib       	       0x101fb4b20 0x101f94000 + 133920
3   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 9:: Thread (pooled)
0   libsystem_kernel.dylib        	       0x19d3899ec __psynch_cvwait + 8
1   libsystem_pthread.dylib       	       0x19d3c755c _pthread_cond_wait + 1228
2   libQt5Core.5.15.8.dylib       	       0x101fb4b20 0x101f94000 + 133920
3   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 10:: Thread (pooled)
0   libsystem_kernel.dylib        	       0x19d3899ec __psynch_cvwait + 8
1   libsystem_pthread.dylib       	       0x19d3c755c _pthread_cond_wait + 1228
2   libQt5Core.5.15.8.dylib       	       0x101fb4b20 0x101f94000 + 133920
3   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 11:
0   libsystem_pthread.dylib       	       0x19d3c1d20 start_wqthread + 0

Thread 12:: com.apple.NSEventThread
0   libsystem_kernel.dylib        	       0x19d3861f4 mach_msg2_trap + 8
1   libsystem_kernel.dylib        	       0x19d398b24 mach_msg2_internal + 80
2   libsystem_kernel.dylib        	       0x19d38ee34 mach_msg_overwrite + 476
3   libsystem_kernel.dylib        	       0x19d386578 mach_msg + 24
4   CoreFoundation                	       0x19d4a6058 __CFRunLoopServiceMachPort + 160
5   CoreFoundation                	       0x19d4a491c __CFRunLoopRun + 1208
6   CoreFoundation                	       0x19d4a3e0c CFRunLoopRunSpecific + 608
7   AppKit                        	       0x1a0e25cb4 _NSEventThread + 144
8   libsystem_pthread.dylib       	       0x19d3c6f94 _pthread_start + 136
9   libsystem_pthread.dylib       	       0x19d3c1d34 thread_start + 8

Thread 13:
0   libsystem_pthread.dylib       	       0x19d3c1d20 start_wqthread + 0

Thread 14:
0   libsystem_pthread.dylib       	       0x19d3c1d20 start_wqthread + 0


Thread 0 crashed with ARM Thread State (64-bit):
    x0: 0x000000016fdb5210   x1: 0x0000000000000000   x2: 0x0000000000000000   x3: 0x0000600002575160
    x4: 0x0000000000000000   x5: 0x0000000000000660   x6: 0x0000600002574660   x7: 0x00000000000003a0
    x8: 0x0000600002574660   x9: 0x00000000000001ff  x10: 0x0000000000001140  x11: 0x00000000b80c9829
   x12: 0x00000000000007fb  x13: 0x00000000000007fd  x14: 0x00000000b82ca08b  x15: 0x000000000000008b
   x16: 0x00000000b80c9829  x17: 0x00000000000ca000  x18: 0x0000000000000000  x19: 0x0000000000000000
   x20: 0x0000000000000000  x21: 0x00006000027e80d8  x22: 0x0000000000000001  x23: 0x00006000027e80d8
   x24: 0x00006000027e81b0  x25: 0x00006000027e81e8  x26: 0x00006000027e81e8  x27: 0x00006000027e80d0
   x28: 0x00006000014a8b40   fp: 0x000000016fdb5570   lr: 0x0000000100b11f28
    sp: 0x000000016fdb5060   pc: 0x0000000100b11f34 cpsr: 0x60001000
   far: 0x0000000000000000  esr: 0x92000006 (Data Abort) byte read Translation fault

Binary Images:
       0x10765c000 -        0x107667fff libobjc-trampolines.dylib (*) <e8a1b184-0349-3c61-a119-6543eb038317> /usr/lib/libobjc-trampolines.dylib
       0x108c20000 -        0x108c6bfff libqwebp.dylib (*) <8ad749d6-061d-363c-98af-66d5c932713f> /Applications/Avogadro2.app/Contents/PlugIns/imageformats/libqwebp.dylib
       0x103178000 -        0x10317bfff libqwbmp.dylib (*) <d63eab61-7d80-32db-ad26-98fb04a90134> /Applications/Avogadro2.app/Contents/PlugIns/imageformats/libqwbmp.dylib
       0x1041fc000 -        0x104203fff libqsvg.dylib (*) <0e08ae90-96bd-3b4d-bb52-f1a1c09632de> /Applications/Avogadro2.app/Contents/PlugIns/imageformats/libqsvg.dylib
       0x107640000 -        0x107647fff libqjpeg.dylib (*) <1b96845f-2f1b-34a3-95d3-67fd0c7bdfe9> /Applications/Avogadro2.app/Contents/PlugIns/imageformats/libqjpeg.dylib
       0x108b78000 -        0x108babfff libjpeg.9.dylib (*) <4fc900b0-7f53-34c8-a1ae-8498d1bab701> /Applications/Avogadro2.app/Contents/Frameworks/libjpeg.9.dylib
       0x10372c000 -        0x103733fff libqgif.dylib (*) <911aa0be-c20b-3790-aa5d-27cc632a1840> /Applications/Avogadro2.app/Contents/PlugIns/imageformats/libqgif.dylib
       0x1075a4000 -        0x10760ffff com.apple.AppleMetalOpenGLRenderer (1.0) <83d94df2-aca8-3695-a3a1-bf8ca16657ac> /System/Library/Extensions/AppleMetalOpenGLRenderer.bundle/Contents/MacOS/AppleMetalOpenGLRenderer
       0x107564000 -        0x107587fff libqmacstyle.dylib (*) <f5df361f-0d5d-3120-bbe8-aac07e96b9dc> /Applications/Avogadro2.app/Contents/PlugIns/styles/libqmacstyle.dylib
       0x10036c000 -        0x100467fff libqcocoa.dylib (*) <271a6c0c-dd22-3807-96e6-aceb0b152a33> /Applications/Avogadro2.app/Contents/PlugIns/platforms/libqcocoa.dylib
       0x100280000 -        0x1002bffff libQt5DBus.5.15.8.dylib (*) <b468d0a2-fea2-384e-82c1-dc4df908cc3d> /Applications/Avogadro2.app/Contents/Frameworks/libQt5DBus.5.15.8.dylib
       0x1002e4000 -        0x100307fff libQt5PrintSupport.5.15.8.dylib (*) <37a37377-c32b-3190-8a3f-5811b6d7230e> /Applications/Avogadro2.app/Contents/Frameworks/libQt5PrintSupport.5.15.8.dylib
       0x1005f0000 -        0x1005f7fff libAvogadroQtOpenGL.1.99.0.dylib (*) <f05de683-a59e-3fbb-8aba-6b1b40ba0689> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroQtOpenGL.1.99.0.dylib
       0x100a18000 -        0x100d17fff libAvogadroQtPlugins.1.99.0.dylib (*) <4c9d6db5-bbef-3d5f-bcf3-98b26c978222> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroQtPlugins.1.99.0.dylib
       0x100634000 -        0x100643fff libMoleQueueServerCore.dylib (*) <af259318-c9f0-38da-9d47-a3bd69dec687> /Applications/Avogadro2.app/Contents/Frameworks/libMoleQueueServerCore.dylib
       0x10065c000 -        0x100667fff libMoleQueueClient.dylib (*) <b2dfaa34-bfa0-31dd-9671-5611aa6f48b5> /Applications/Avogadro2.app/Contents/Frameworks/libMoleQueueClient.dylib
       0x1006ac000 -        0x1006bffff libAvogadroVtk.1.99.0.dylib (*) <3c709a90-7583-387d-a06f-5e50697d8379> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroVtk.1.99.0.dylib
       0x10060c000 -        0x10060ffff libQt5Concurrent.5.15.8.dylib (*) <eaa074a4-2bdb-3f02-a7b5-a59e6944e755> /Applications/Avogadro2.app/Contents/Frameworks/libQt5Concurrent.5.15.8.dylib
       0x1007e0000 -        0x10088bfff libQt5Network.5.15.8.dylib (*) <93795721-937c-31b0-963b-6655e689dcde> /Applications/Avogadro2.app/Contents/Frameworks/libQt5Network.5.15.8.dylib
       0x1008e4000 -        0x100957fff libAvogadroQtGui.1.99.0.dylib (*) <ab1937a1-5b21-305d-a2c8-3ab4b1bb4493> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroQtGui.1.99.0.dylib
       0x100e24000 -        0x100ebffff libAvogadroIO.1.99.0.dylib (*) <9a17f4f2-fc8a-31a7-b48c-45723913b682> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroIO.1.99.0.dylib
       0x100750000 -        0x100783fff libvtkGUISupportQt-9.2.9.2.0.dylib (*) <0c21aacb-7f4d-376d-96be-974863cda642> /Applications/Avogadro2.app/Contents/Frameworks/libvtkGUISupportQt-9.2.9.2.0.dylib
       0x1009ac000 -        0x1009d3fff libQt5OpenGL.5.15.8.dylib (*) <a0eafb30-0f57-3372-8ac0-c7dbdbc77a5f> /Applications/Avogadro2.app/Contents/Frameworks/libQt5OpenGL.5.15.8.dylib
       0x101344000 -        0x10160ffff libQt5Widgets.5.15.8.dylib (*) <e7359903-e88c-32a4-8571-03129fe25b71> /Applications/Avogadro2.app/Contents/Frameworks/libQt5Widgets.5.15.8.dylib
       0x101788000 -        0x1019f7fff libQt5Gui.5.15.8.dylib (*) <a742ecbe-93bf-3e0f-ac80-b21f6df0530d> /Applications/Avogadro2.app/Contents/Frameworks/libQt5Gui.5.15.8.dylib
       0x101f94000 -        0x102337fff libQt5Core.5.15.8.dylib (*) <e0bb6926-59d2-3e08-80a7-c092ca057d67> /Applications/Avogadro2.app/Contents/Frameworks/libQt5Core.5.15.8.dylib
       0x100f04000 -        0x100f3ffff libAvogadroRendering.1.99.0.dylib (*) <9895fb1e-9441-3a58-a624-de3012ab70c7> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroRendering.1.99.0.dylib
       0x10110c000 -        0x10125bfff libAvogadroCore.1.99.0.dylib (*) <9fce521f-2187-3045-a5c4-25c865053549> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroCore.1.99.0.dylib
       0x101008000 -        0x10106bfff libvtkRenderingVolumeOpenGL2-9.2.9.2.0.dylib (*) <3d881ebc-157c-31b3-94e0-b3631e4ead3e> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingVolumeOpenGL2-9.2.9.2.0.dylib
       0x100f68000 -        0x100f9bfff libvtkImagingMath-9.2.9.2.0.dylib (*) <032bac1e-308a-3eb7-8538-5de7998dd115> /Applications/Avogadro2.app/Contents/Frameworks/libvtkImagingMath-9.2.9.2.0.dylib
       0x101cdc000 -        0x101e3bfff libvtkChartsCore-9.2.9.2.0.dylib (*) <804adec2-c4b3-35de-a63e-81060024f3e1> /Applications/Avogadro2.app/Contents/Frameworks/libvtkChartsCore-9.2.9.2.0.dylib
       0x10067c000 -        0x100683fff libvtkViewsContext2D-9.2.9.2.0.dylib (*) <a9144073-232e-3a55-b613-dbb7938a6e4f> /Applications/Avogadro2.app/Contents/Frameworks/libvtkViewsContext2D-9.2.9.2.0.dylib
       0x10070c000 -        0x10071ffff libvtkViewsCore-9.2.9.2.0.dylib (*) <f614da7c-0bed-38ea-8c7a-1943624ded3b> /Applications/Avogadro2.app/Contents/Frameworks/libvtkViewsCore-9.2.9.2.0.dylib
       0x102654000 -        0x10279ffff libvtkInteractionWidgets-9.2.9.2.0.dylib (*) <e2dfe81c-a2ee-3914-8608-1e26ee5b1a63> /Applications/Avogadro2.app/Contents/Frameworks/libvtkInteractionWidgets-9.2.9.2.0.dylib
       0x1010a8000 -        0x1010c7fff libvtkInteractionStyle-9.2.9.2.0.dylib (*) <9430d362-47fa-34aa-ad25-9785dd2ffe1d> /Applications/Avogadro2.app/Contents/Frameworks/libvtkInteractionStyle-9.2.9.2.0.dylib
       0x102b34000 -        0x102d63fff libvtkRenderingVolume-9.2.9.2.0.dylib (*) <a413f958-ecf8-3ca2-b890-05bf7d1eb9a6> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingVolume-9.2.9.2.0.dylib
       0x1012b4000 -        0x1012dbfff libvtkRenderingContextOpenGL2-9.2.9.2.0.dylib (*) <56886719-49af-30cb-b27f-359689999607> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingContextOpenGL2-9.2.9.2.0.dylib
       0x1012fc000 -        0x10131bfff libvtkRenderingContext2D-9.2.9.2.0.dylib (*) <3d54ae87-1c03-3c2c-984c-811ddc681a0a> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingContext2D-9.2.9.2.0.dylib
       0x101bcc000 -        0x101bf3fff libvtkRenderingFreeType-9.2.9.2.0.dylib (*) <73e1eb0e-c1dc-3eed-87fb-36a6c5d5d1b1> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingFreeType-9.2.9.2.0.dylib
       0x101e9c000 -        0x101f1ffff libvtkfreetype-9.2.9.2.0.dylib (*) <c86b74b4-ec24-391a-bc76-5c11d2649b59> /Applications/Avogadro2.app/Contents/Frameworks/libvtkfreetype-9.2.9.2.0.dylib
       0x100fbc000 -        0x100fc7fff libvtkDomainsChemistryOpenGL2-9.2.9.2.0.dylib (*) <f6ecbc47-e17b-3ba8-87ec-842e7dfaff26> /Applications/Avogadro2.app/Contents/Frameworks/libvtkDomainsChemistryOpenGL2-9.2.9.2.0.dylib
       0x102898000 -        0x102a03fff libvtkRenderingOpenGL2-9.2.9.2.0.dylib (*) <84a00f10-f624-37d8-9455-46ff10f93de9> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingOpenGL2-9.2.9.2.0.dylib
       0x1006dc000 -        0x1006e3fff libvtkRenderingHyperTreeGrid-9.2.9.2.0.dylib (*) <1cb07f31-41d3-3703-8af1-5a052c3186cd> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingHyperTreeGrid-9.2.9.2.0.dylib
       0x1031f4000 -        0x1033e3fff libvtkImagingCore-9.2.9.2.0.dylib (*) <53c678ff-1fdd-390d-8de5-dd7d95938f34> /Applications/Avogadro2.app/Contents/Frameworks/libvtkImagingCore-9.2.9.2.0.dylib
       0x101b1c000 -        0x101b27fff libvtkRenderingUI-9.2.9.2.0.dylib (*) <1f62269e-fe4d-35ea-a06a-136a335bba3e> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingUI-9.2.9.2.0.dylib
       0x102508000 -        0x1025b3fff libvtkglew-9.2.9.2.0.dylib (*) <6fa5dde5-06d1-395c-b382-bb91083be983> /Applications/Avogadro2.app/Contents/Frameworks/libvtkglew-9.2.9.2.0.dylib
       0x101c7c000 -        0x101ca3fff libvtkDomainsChemistry-9.2.9.2.0.dylib (*) <1e60dab5-b1a1-346d-8142-9fe2027f5a7f> /Applications/Avogadro2.app/Contents/Frameworks/libvtkDomainsChemistry-9.2.9.2.0.dylib
       0x103458000 -        0x10355ffff libvtkRenderingCore-9.2.9.2.0.dylib (*) <7300b269-72d6-304f-a32c-b28530776e23> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingCore-9.2.9.2.0.dylib
       0x102f90000 -        0x10300ffff libvtkFiltersSources-9.2.9.2.0.dylib (*) <8f9dc4ae-2e42-3067-b4cf-d65a3bbf5ca3> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersSources-9.2.9.2.0.dylib
       0x103aa4000 -        0x103d57fff libvtkFiltersGeneral-9.2.9.2.0.dylib (*) <d89480db-29f2-3549-bee6-71ae77357e4f> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersGeneral-9.2.9.2.0.dylib
       0x104858000 -        0x104df7fff libvtkFiltersCore-9.2.9.2.0.dylib (*) <76009a49-eb8b-3b28-9be3-93581e7cba70> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersCore-9.2.9.2.0.dylib
       0x103060000 -        0x1030bffff libvtkIOLegacy-9.2.9.2.0.dylib (*) <75151c5b-a9a8-3963-b53e-11baf19c991c> /Applications/Avogadro2.app/Contents/Frameworks/libvtkIOLegacy-9.2.9.2.0.dylib
       0x101b40000 -        0x101b53fff libvtkIOXMLParser-9.2.9.2.0.dylib (*) <c25212c3-1ae0-39d9-801d-98d1603c4019> /Applications/Avogadro2.app/Contents/Frameworks/libvtkIOXMLParser-9.2.9.2.0.dylib
       0x102484000 -        0x1024bffff libvtkIOCore-9.2.9.2.0.dylib (*) <96aea8df-f68a-3d64-ac2d-07c95f2a291d> /Applications/Avogadro2.app/Contents/Frameworks/libvtkIOCore-9.2.9.2.0.dylib
       0x103744000 -        0x1037bffff libvtkCommonExecutionModel-9.2.9.2.0.dylib (*) <f89c84a7-c551-35db-8e0d-106801953836> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonExecutionModel-9.2.9.2.0.dylib
       0x1051a4000 -        0x1054ebfff libvtkCommonDataModel-9.2.9.2.0.dylib (*) <032e3760-4484-3c9a-81b4-d49073e4dc13> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonDataModel-9.2.9.2.0.dylib
       0x101f44000 -        0x101f63fff libvtkCommonTransforms-9.2.9.2.0.dylib (*) <492e3962-ee20-3430-8e6e-182479a30306> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonTransforms-9.2.9.2.0.dylib
       0x1056c0000 -        0x1058a7fff libvtkCommonMisc-9.2.9.2.0.dylib (*) <5d7c4e9c-4133-313b-9fb6-bcb1ea33bde4> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonMisc-9.2.9.2.0.dylib
       0x101b9c000 -        0x101bb3fff libvtkCommonMath-9.2.9.2.0.dylib (*) <a20b4ac3-6ebe-33a6-882e-cd07bce7741f> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonMath-9.2.9.2.0.dylib
       0x106604000 -        0x106b23fff libvtkCommonCore-9.2.9.2.0.dylib (*) <95870d28-86de-3a9b-a6c6-bdd65562d71e> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonCore-9.2.9.2.0.dylib
       0x102ac4000 -        0x102af3fff libvtksys-9.2.9.2.0.dylib (*) <95d9fea5-9217-37f5-bd37-e0fb74ccfad1> /Applications/Avogadro2.app/Contents/Frameworks/libvtksys-9.2.9.2.0.dylib
       0x100620000 -        0x100623fff libvtkkissfft-9.2.9.2.0.dylib (*) <5954a95d-4eee-3897-b627-0b40fc2d0f6e> /Applications/Avogadro2.app/Contents/Frameworks/libvtkkissfft-9.2.9.2.0.dylib
       0x103628000 -        0x103693fff libGLEW.2.2.0.dylib (*) <6226c90a-76b2-3c0d-acf8-36f44abea956> /Applications/Avogadro2.app/Contents/Frameworks/libGLEW.2.2.0.dylib
       0x101b6c000 -        0x101b7ffff libz.1.2.13.dylib (*) <7980eb91-76ae-3db4-9494-5d493132a9c7> /Applications/Avogadro2.app/Contents/Frameworks/libz.1.2.13.dylib
       0x103980000 -        0x103a3bfff libc++.1.0.dylib (*) <d9229d7d-8f7e-3e8f-a88e-15125158bcae> /Applications/Avogadro2.app/Contents/Frameworks/libc++.1.0.dylib
       0x102604000 -        0x10262ffff libpng16.16.dylib (*) <65ae0218-f865-3615-a66d-cebd5ef18965> /Applications/Avogadro2.app/Contents/Frameworks/libpng16.16.dylib
       0x104218000 -        0x1043f7fff libicui18n.70.1.dylib (*) <0b278e7a-d470-318e-884b-ca84d968a2aa> /Applications/Avogadro2.app/Contents/Frameworks/libicui18n.70.1.dylib
       0x104510000 -        0x104667fff libicuuc.70.1.dylib (*) <6129977b-c912-3603-8284-c7081ac287d2> /Applications/Avogadro2.app/Contents/Frameworks/libicuuc.70.1.dylib
       0x108c8c000 -        0x10a8a7fff libicudata.70.1.dylib (*) <f88edc5c-053b-3f63-9fa1-05b2a44fbb18> /Applications/Avogadro2.app/Contents/Frameworks/libicudata.70.1.dylib
       0x103860000 -        0x1038fbfff libzstd.1.5.2.dylib (*) <8bf2a8a0-69e3-3788-bf85-d24c9ae8373d> /Applications/Avogadro2.app/Contents/Frameworks/libzstd.1.5.2.dylib
       0x102410000 -        0x10241bfff libAvogadroCalc.1.99.0.dylib (*) <6fbc21c9-b8c0-3c9d-abdb-4ef37650752f> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroCalc.1.99.0.dylib
       0x105eec000 -        0x10617bfff libopenbabel.7.0.0.dylib (*) <294d7935-5926-3d86-b815-8fc55fb32a2d> /Applications/Avogadro2.app/Contents/Frameworks/libopenbabel.7.0.0.dylib
       0x1030fc000 -        0x103123fff libQt5Svg.5.15.8.dylib (*) <c57f4a8b-9933-3114-ab17-d846fd4c7427> /Applications/Avogadro2.app/Contents/Frameworks/libQt5Svg.5.15.8.dylib
       0x103914000 -        0x10394bfff libAvogadroMoleQueue.1.99.0.dylib (*) <ec90719c-7522-311b-a153-969111cb10a5> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroMoleQueue.1.99.0.dylib
       0x103f20000 -        0x103f6bfff libAvogadroQuantumIO.1.99.0.dylib (*) <01fdc2e8-90ec-3803-a4ee-f7617f73dde3> /Applications/Avogadro2.app/Contents/Frameworks/libAvogadroQuantumIO.1.99.0.dylib
       0x10406c000 -        0x10411bfff libarchive.19.dylib (*) <9bb4eacf-3e88-34b1-a89e-36cd05ba7501> /Applications/Avogadro2.app/Contents/Frameworks/libarchive.19.dylib
       0x102430000 -        0x102447fff libmsym.0.2.4.dylib (*) <6e065d27-3de1-31b6-9f22-0dead42140a9> /Applications/Avogadro2.app/Contents/Frameworks/libmsym.0.2.4.dylib
       0x106200000 -        0x106313fff libvtkFiltersExtraction-9.2.9.2.0.dylib (*) <5da602d3-e256-31ef-9ca9-740bbf8b6b21> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersExtraction-9.2.9.2.0.dylib
       0x10318c000 -        0x1031abfff libvtkCommonSystem-9.2.9.2.0.dylib (*) <23e6c0e7-0e87-392f-bfa7-2717211bb73b> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonSystem-9.2.9.2.0.dylib
       0x105bd8000 -        0x105c7ffff libvtkFiltersHybrid-9.2.9.2.0.dylib (*) <b54b0b21-ec5d-3dc2-a51c-cf264f662f55> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersHybrid-9.2.9.2.0.dylib
       0x103f98000 -        0x103fbffff libvtkFiltersHyperTree-9.2.9.2.0.dylib (*) <a52fbd65-208c-3efd-a455-bb8a79186cf2> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersHyperTree-9.2.9.2.0.dylib
       0x105cc8000 -        0x105d5bfff libvtkFiltersGeometry-9.2.9.2.0.dylib (*) <8b37d661-508a-3154-b4cf-a28f01f598ed> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersGeometry-9.2.9.2.0.dylib
       0x103fe4000 -        0x104017fff libvtkImagingSources-9.2.9.2.0.dylib (*) <49d4d821-ec1a-3c3f-a5d7-454ed452fb10> /Applications/Avogadro2.app/Contents/Frameworks/libvtkImagingSources-9.2.9.2.0.dylib
       0x1036ec000 -        0x10370ffff libvtkpugixml-9.2.9.2.0.dylib (*) <4f689ad2-c20a-3111-ae06-b9ef7f230bf2> /Applications/Avogadro2.app/Contents/Frameworks/libvtkpugixml-9.2.9.2.0.dylib
       0x102458000 -        0x102467fff libvtkCommonColor-9.2.9.2.0.dylib (*) <29610653-6888-3f6d-96ee-3087953cebfb> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonColor-9.2.9.2.0.dylib
       0x104034000 -        0x104047fff libvtkCommonComputationalGeometry-9.2.9.2.0.dylib (*) <90f85ba1-c81d-3ce5-bb82-cc99d2a60b5b> /Applications/Avogadro2.app/Contents/Frameworks/libvtkCommonComputationalGeometry-9.2.9.2.0.dylib
       0x104140000 -        0x104157fff libvtkfmt-9.2.9.2.0.dylib (*) <cf485205-a796-3ae0-a132-c62feb81eb41> /Applications/Avogadro2.app/Contents/Frameworks/libvtkfmt-9.2.9.2.0.dylib
       0x105dd8000 -        0x105e6bfff libvtkFiltersModeling-9.2.9.2.0.dylib (*) <38087b92-970a-3b88-abde-7218ca81d150> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersModeling-9.2.9.2.0.dylib
       0x10314c000 -        0x10315bfff libvtkFiltersTexture-9.2.9.2.0.dylib (*) <259ace51-2de1-39a8-aeb8-a0d681220ef0> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersTexture-9.2.9.2.0.dylib
       0x1063d0000 -        0x106473fff libvtkImagingGeneral-9.2.9.2.0.dylib (*) <b469706f-89d1-3279-8ebd-37b77bbbac53> /Applications/Avogadro2.app/Contents/Frameworks/libvtkImagingGeneral-9.2.9.2.0.dylib
       0x104798000 -        0x1047f7fff libvtkImagingHybrid-9.2.9.2.0.dylib (*) <90151770-981d-3be9-8607-a775b63069e2> /Applications/Avogadro2.app/Contents/Frameworks/libvtkImagingHybrid-9.2.9.2.0.dylib
       0x107030000 -        0x1070affff libvtkRenderingAnnotation-9.2.9.2.0.dylib (*) <7d864bfd-1c76-3f32-b5d5-679f74c93e8b> /Applications/Avogadro2.app/Contents/Frameworks/libvtkRenderingAnnotation-9.2.9.2.0.dylib
       0x1046ec000 -        0x104727fff libvtkImagingColor-9.2.9.2.0.dylib (*) <91f30752-95c4-3b93-871b-93f85116df1b> /Applications/Avogadro2.app/Contents/Frameworks/libvtkImagingColor-9.2.9.2.0.dylib
       0x107294000 -        0x1073c3fff libvtkIOImage-9.2.9.2.0.dylib (*) <b5596ffd-4186-396c-8fc8-fba2d7de17bb> /Applications/Avogadro2.app/Contents/Frameworks/libvtkIOImage-9.2.9.2.0.dylib
       0x104170000 -        0x104183fff libvtkDICOMParser-9.2.9.2.0.dylib (*) <3cf234f6-4c4e-395b-bcbb-7d0ecaa62756> /Applications/Avogadro2.app/Contents/Frameworks/libvtkDICOMParser-9.2.9.2.0.dylib
       0x106554000 -        0x1065cbfff libvtkmetaio-9.2.9.2.0.dylib (*) <360d8ee1-e70c-3b80-9e60-18985077b071> /Applications/Avogadro2.app/Contents/Frameworks/libvtkmetaio-9.2.9.2.0.dylib
       0x104748000 -        0x104777fff libvtkpng-9.2.9.2.0.dylib (*) <369d93e8-5b09-3bae-b5a3-661da5f4ccdc> /Applications/Avogadro2.app/Contents/Frameworks/libvtkpng-9.2.9.2.0.dylib
       0x1064ac000 -        0x106503fff libvtktiff-9.2.9.2.0.dylib (*) <cb37c254-4a34-3b7b-98d0-589ce4502811> /Applications/Avogadro2.app/Contents/Frameworks/libvtktiff-9.2.9.2.0.dylib
       0x107108000 -        0x107153fff libvtkjpeg-9.2.9.2.0.dylib (*) <ed9b6ccd-073e-3dbe-9375-de1f2286844a> /Applications/Avogadro2.app/Contents/Frameworks/libvtkjpeg-9.2.9.2.0.dylib
       0x107420000 -        0x1074c3fff libvtkFiltersStatistics-9.2.9.2.0.dylib (*) <ddcaedd5-4728-39c1-97a9-32f510356c54> /Applications/Avogadro2.app/Contents/Frameworks/libvtkFiltersStatistics-9.2.9.2.0.dylib
       0x107678000 -        0x107743fff libvtkParallelDIY-9.2.9.2.0.dylib (*) <8a879631-4123-338d-884f-4dfa8ba0f189> /Applications/Avogadro2.app/Contents/Frameworks/libvtkParallelDIY-9.2.9.2.0.dylib
       0x107168000 -        0x1071a7fff libvtkParallelCore-9.2.9.2.0.dylib (*) <22223b9a-230a-3935-8449-32abd1e36bb6> /Applications/Avogadro2.app/Contents/Frameworks/libvtkParallelCore-9.2.9.2.0.dylib
       0x1077cc000 -        0x107847fff libvtkIOXML-9.2.9.2.0.dylib (*) <13c9a20b-9a8f-3f60-9748-b5bfecf519c3> /Applications/Avogadro2.app/Contents/Frameworks/libvtkIOXML-9.2.9.2.0.dylib
       0x1031cc000 -        0x1031dbfff libvtkdoubleconversion-9.2.9.2.0.dylib (*) <c2c49076-8b74-3708-abbf-1eb4e50a210d> /Applications/Avogadro2.app/Contents/Frameworks/libvtkdoubleconversion-9.2.9.2.0.dylib
       0x1041cc000 -        0x1041ebfff libvtklz4-9.2.9.2.0.dylib (*) <de8ac615-dfa9-33dc-9fca-110a32ee5da5> /Applications/Avogadro2.app/Contents/Frameworks/libvtklz4-9.2.9.2.0.dylib
       0x1071d0000 -        0x1071f3fff libvtklzma-9.2.9.2.0.dylib (*) <81f13b4a-e758-35b3-859e-c02d4bec6daf> /Applications/Avogadro2.app/Contents/Frameworks/libvtklzma-9.2.9.2.0.dylib
       0x107208000 -        0x107227fff libvtkexpat-9.2.9.2.0.dylib (*) <cba87202-19c6-3896-8a0c-bd2d2c475026> /Applications/Avogadro2.app/Contents/Frameworks/libvtkexpat-9.2.9.2.0.dylib
       0x1078ac000 -        0x107933fff libvtkInfovisCore-9.2.9.2.0.dylib (*) <d8251cb2-0901-30e2-82db-383293bfd77e> /Applications/Avogadro2.app/Contents/Frameworks/libvtkInfovisCore-9.2.9.2.0.dylib
       0x10419c000 -        0x1041bbfff liblz4.1.9.4.dylib (*) <fab75602-2a38-3cbd-827a-7e04e6c34176> /Applications/Avogadro2.app/Contents/Frameworks/liblz4.1.9.4.dylib
       0x100048000 -        0x10014bfff cc.avogadro (*) <60acc3cb-0338-3464-ad65-c55ce4de1c4d> /Applications/Avogadro2.app/Contents/MacOS/Avogadro2
       0x19d428000 -        0x19d900fff com.apple.CoreFoundation (6.9) <33908a83-098f-3437-973e-fb848c4f39df> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
       0x1a7c0c000 -        0x1a7ecffff com.apple.HIToolbox (2.1.1) <c315e2a3-3fd1-3a2b-b205-b8b492b0f506> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
       0x1a0cc2000 -        0x1a1ffefff com.apple.AppKit (6.9) <8b85317d-d56a-3370-8b78-da6c1d0fb53c> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
       0x19d038000 -        0x19d0c09db dyld (*) <8e1e5ee2-f89a-33a7-bb0a-74bdc06b7828> /usr/lib/dyld
               0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ???
       0x19d3c0000 -        0x19d3ccfff libsystem_pthread.dylib (*) <45239f06-cc53-36d0-9933-7776ac7ea2fa> /usr/lib/system/libsystem_pthread.dylib
       0x19d385000 -        0x19d3bfffb libsystem_kernel.dylib (*) <1889ce0a-52e7-3122-8907-81af920ac472> /usr/lib/system/libsystem_kernel.dylib

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@bernstei
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Putting in a CH4 and clicking on one of the hydrogens with the template tool worked nicely.

@ghutchis
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Thanks for the single-H report. I'll hunt down that crash. I think the problem is that it's trying to find the atom the hydrogen is attached to.

@bernstei
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Makes sense. Thanks.

@matterhorn103
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But in that case, I'd also argue that it should do nothing (or maybe give a popup error?) if you click on blank canvas space, or at least not paste a random molecule that seems to come out of nowhere (why FeH6?)

I tested it a little myself and the reason that FeH6 appeared in your case is because that was what was currently selected under the "Centers" tab. Equally, if you change to e.g. nickel, then go back to the ligands or groups tab, then click empty space, a nickel atom will appear.

I agree with @bernstei that from a UX perspective new metal centres shouldn't be created when the Ligands or Groups tabs are open, only when the Centers tab is the currently selected one. If Ligands or Groups are selected and one clicks on empty space rather than a H atom, nothing should appear at all.

@matterhorn103
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I've also put some changes in the docs to try and make it as clear as possible that the ligands and groups work by replacing existing H atoms and they can't be placed into empty space.

@ghutchis ghutchis linked a pull request Nov 11, 2024 that will close this issue
Update the template tool to place ligands or functional groups #1777
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Update the template tool to place ligands or functional groups ghutchis/avogadrolibs
3 participants
@ghutchis @bernstei @matterhorn103