Safeguard against accidental multi-residue swapaa

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
I've messed myself up a few times in the past by accidentally running swapaa on a selection encompassing multiple residues rather than just the single residue I wanted. Since there is no undo for steps that add or remove atoms, that can be pretty disastrous. I wonder if it would be worth adding an optional argument (multiResidue?) that defaults to false, and if true raises a UserError if more than one residue is selected?

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

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description  
A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> show

> select :120-158

272 atoms, 274 bonds, 39 residues, 1 model selected  

> swapaa sel ALA

Using Dunbrack library  
Swapping /A ARG 120 to ALA  
  
Swapping /A VAL 121 to ALA  
  
Swapping /A GLY 122 to ALA  
  
Swapping /A ALA 123 to ALA  
  
Swapping /A PRO 124 to ALA  
  
Swapping /A ALA 125 to ALA  
  
Swapping /A GLN 126 to ALA  
  
Swapping /A MET 127 to ALA  
  
Swapping /A MET 128 to ALA  
  
Swapping /A ALA 129 to ALA  
  
Swapping /A ALA 130 to ALA  
  
Swapping /A ASP 131 to ALA  
  
Swapping /A GLU 132 to ALA  
  
Swapping /A ALA 133 to ALA  
  
Swapping /A VAL 134 to ALA  
  
Swapping /A LYS 135 to ALA  
  
Swapping /A GLY 136 to ALA  
  
Swapping /A THR 137 to ALA  
  
Swapping /A ASN 138 to ALA  
  
Swapping /A THR 139 to ALA  
  
Swapping /A GLU 140 to ALA  
  
Swapping /A VAL 141 to ALA  
  
Swapping /A ALA 142 to ALA  
  
Swapping /A THR 143 to ALA  
  
Swapping /A ILE 144 to ALA  
  
Swapping /A GLU 145 to ALA  
  
Swapping /A LEU 146 to ALA  
  
Swapping /A PRO 147 to ALA  
  
Swapping /A ARG 148 to ALA  
  
Swapping /A ASP 149 to ALA  
  
Swapping /A THR 150 to ALA  
  
Swapping /A LYS 151 to ALA  
  
Swapping /A GLY 152 to ALA  
  
Swapping /A GLY 153 to ALA  
  
Swapping /A ALA 154 to ALA  
  
Swapping /A GLY 155 to ALA  
  
Swapping /A HIS 156 to ALA  
  
Swapping /A GLY 157 to ALA  
  
Swapping /A ILE 158 to ALA  
  

> usage swapaa

swapaa residues resType [angleSlop a number] [bfactor a number] [criteria
criteria] [density a density map specifier] [distSlop a number]
[hbondAllowance a number] [ignoreOtherModels true or false] [rotLib rotLib]
[log true or false] [preserve preserve] [relax true or false] [retain true or
false] [scoreMethod scoreMethod] [overlapCutoff a number]  
— Swap amino acid side chain(s)  
resType: a text string  
criteria: some an integer ≥ 0 or a text string  
rotLib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode  
preserve: a number ≥ 0  
scoreMethod: one of num or sum

swapaa interactive residues resType [rotLib rotLib] [log true or false]  
— Show possible side-chain rotamers  
resType: a text string  
rotLib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode

swapaa mousemode residues restype  
— Replace residue with specified amino acid  
restype: one of ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS,
MET, PHE, PRO, SER, THR, TRP, TYR, or VAL  




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
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:            62G        6.5G         39G        263M         16G         55G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
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    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
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    ChimeraX-ShowAttr: 1.0
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    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
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[Eric Pettersen]

In this situation, I could raise a confirmation dialog in GUI mode (and not a script) and just go ahead in non-GUI mode.

[Eric Pettersen]

swapaa now asks for confirmation before swapping multiple residues

[Tristan Croll]

Would it be possible for swapaa mousemode to do the same? I just did a mis-type (didn't notice that the previous command hadn't properly cleared, and typed "sel #1" in the middle of it... somehow "sel :410sel #1; view sel; swapaa mouse sel ASP" was still parsed and caused the whole model to be selected; ChimeraX is now hung while it presumably works through converting 3,736 residues to ASP (on a model with an hour or two of unsaved - albeit fairly easy to repeat - work).

[Eric Pettersen]

Tom implemented the "swapaa mousemode" command. The relevant diff to the "regular" swapaa command was:

--- a/src/bundles/swap_res/src/cmd.py
+++ b/src/bundles/swap_res/src/cmd.py
@@ -21,6 +21,13 @@ def swap_aa(session, residues, res_type, *, angle_slop=None, bfactor=None, crite

residues = _check_residues(residues)

+ if len(residues) > 2 and session.ui.is_gui and not session.in_script:
+ from chimerax.ui.ask import ask
+ if ask(session, "Really swap side chains for %d residues?" % len(residues),
+ title="Confirm Swap") == "no":
+ from chimerax.core.errors import CancelOperation
+ raise CancelOperation("Swap %d side chains cancelled" % len(residues))
+

if type(criteria) == str:

for c in criteria:

if c not in "dchp":