Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix distance geometry stereo issues #2158

Merged
merged 10 commits into from Apr 10, 2020
Merged

Fix distance geometry stereo issues #2158

merged 10 commits into from Apr 10, 2020

Commits on Apr 5, 2020

  1. MDLFormat: Set tetrahedral stereo to unspecified for atom stereo parity 

    3. This was already the default behaviour for cis/trans stereochemistry.
    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    2d3acc1 View commit details
    Browse the repository at this point in the history

  2. OBStereoFacade: Add functions to get all stereo objects of a certain … 

    …type.
    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    6a4ab12 View commit details
    Browse the repository at this point in the history

  3. Gen3DStereoHelper: Helper class for 3D coord generation

    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    e09ce7b View commit details
    Browse the repository at this point in the history

  4. OBDistanceGeometry: 

    * Fix handling of implicit stereo references
* Fix Calculate13Angle to work for triple bonds
* Use new Gen3DStereoHelper class
    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    5288558 View commit details
    Browse the repository at this point in the history

  5. OpGen3D: Fix stereochemistry issue (check after energy minimization)

    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    4698c4c View commit details
    Browse the repository at this point in the history

  6. CisTransFrom3D: 

    * Fix issue with implicit stereo refs (L2236+L2260)
* Use torsion angles (fixes issue with non-planar geometry)
    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    211567e View commit details
    Browse the repository at this point in the history

  7. Add and enable more distance geometry roundtrip test cases. 

    (Some disabled to ensure the test runs fast enough)
    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    7772e6d View commit details
    Browse the repository at this point in the history

  8. CisTransFrom3D: Change log messages from warning to info

    @timvdm
    timvdm committed Apr 5, 2020
    Configuration menu
    Copy the full SHA
    11cfa44 View commit details
    Browse the repository at this point in the history

Commits on Apr 9, 2020

  1. OBDistanceGeometry/OpGen3D: 

    - Increase number of iterations
- Improve error handling
    @timvdm
    timvdm committed Apr 9, 2020
    Configuration menu
    Copy the full SHA
    09c2c60 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' into fix-distgeom-stereo

    @ghutchis
    ghutchis committed Apr 9, 2020
    Configuration menu
    Copy the full SHA
    431420e View commit details
    Browse the repository at this point in the history