Atoms.transform trigger

[Tristan Croll]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005292300 (2020-05-29 23:00:06 UTC)
Description
Would it be possible for the `Atoms.transform(Place)` method to fire a trigger distinct from 'coords changed', providing the atoms and the transform applied as data? One useful application of this in ISOLDE would be the (not entirely rare) situation where it makes sense to shift a particular chain (or ligand) from one symmetry-related position to another. This could be simply to create a more biologically relevant asymmetric unit, or to correct the geometry at an interface (since ISOLDE's simulations aren't symmetry aware, and probably won't be for quite some time). In either case, any restraints created by ISOLDE need to find out about the move and update intelligently to avoid creating a woeful mess.

OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir7,2
      Processor Name: Intel Core i5
      Processor Speed: 1.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 188.0.0.0.0
      SMC Version (system): 2.27f2

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G95)
      Kernel Version: Darwin 18.7.0
      Time since boot: 89 days 9:30

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tom Goddard]

There is a MODEL_POSITION_CHANGED trigger in core/models.py that seems to be what you need.

[Tristan Croll]

Are you sure? Atoms.transform() changes the coordinates of the actual atoms (and updates the ANISOU terms accordingly) - it doesn’t change the model’s position.
 

[Tom Goddard]

Oh, I didn't know the Atoms.transform() method existed. Eric added that so I'll let him deal with it.

[Tristan Croll]

Actually, I wrote it, and Eric merged it. :) The rationale was to have a transform method that keeps ANISOUs consistent.

 

 

[Eric Pettersen]

Okay, pushed an (untested) code change. Let me know if there's anything wrong with it.

--Eric