Premature tool-added trigger

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-5.13.0-40-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.4rc202205060510 (2022-05-06 05:10:33 UTC)
Description
At the moment the session 'add tool instance' trigger is fired at the end of the base class `ToolInstance.__init__()` method, before all of the derived-class specialisations are applied. So my code to automatically add a few ISOLDE-specific callbacks to the Ramachandran plot tool fails. Of course I can trivially avoid the issue by delaying to the next 'frame drawn' event... but I think it might be more sensible if the `Tools` class were to do that?

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.4rc202205060510 (2022-05-06)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde demo crystal_intro

> set selectionWidth 4

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description | UniProt  
A | predicted microcompartment protein | A5N734_CLOK5  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description | UniProt  
1.2/A | predicted microcompartment protein | A5N734_CLOK5  
  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.303, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0569,0.0569, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.602, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
shown at level 0.366, step 1, values float32  

> ui tool show "Ramachandran Plot"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/home/tic20/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 2190, in
_register_ramaplot_callbacks  
rplot = tool.tool_window  
AttributeError: 'Rama_ToolUI' object has no attribute 'tool_window'  
  
Error processing trigger "add tool instance":  
AttributeError: 'Rama_ToolUI' object has no attribute 'tool_window'  
  
File "/home/tic20/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 2190, in
_register_ramaplot_callbacks  
rplot = tool.tool_window  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 510.47.03
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision T5600
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi        11Gi        45Gi       119Mi       5.9Gi        50Gi
	Swap:         4.9Gi          0B       4.9Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation GP102 [TITAN Xp] [10de:11df]	
	Kernel driver in use: nvidia

Installed Packages:
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    appdirs: 1.4.4
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[pett]

The problem with the suggested fix is that tools can be started while no frames are being drawn (e.g. Rapid Access is showing). Maybe QTimer.singleShot(0, file_trigger) instead?