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

Refactor align #1136

Closed
wants to merge 14 commits into from
Closed

Refactor align #1136

wants to merge 14 commits into from

Commits on Jan 27, 2017

  1. refactor rms.py:rmsd 

    simplify weights handling
    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    12b65f3 View commit details
    Browse the repository at this point in the history

  2. Add weights kwarg to alignto 

    This new general weights kwarg can take an mass argument or arbitrary weights to
allow new fitting algorithms.
    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    69a6dbf View commit details
    Browse the repository at this point in the history

  3. introduce weights kwargs also for AlignTrj

    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    729d8bc View commit details
    Browse the repository at this point in the history

  4. RMSD uses new weights kwarg, fixes bug as well 

    This also fixes a centering bug. Previous the center of mass was used
independent of the used weights. Now we center with the chosen weights. This
means results might change!
    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    be6dd77 View commit details
    Browse the repository at this point in the history

  5. correct test results! 

    The old results have been wrong due to a centering bug in the RMSD code
    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    4f8c5be View commit details
    Browse the repository at this point in the history

  6. convert RMSF to AnalysisBase

    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    758b43d View commit details
    Browse the repository at this point in the history

  7. fix docs from using deprecated method

    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    9959db7 View commit details
    Browse the repository at this point in the history

  8. add deprecation warnings

    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    49eb5a5 View commit details
    Browse the repository at this point in the history

  9. update CHANGELOG

    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    0c19152 View commit details
    Browse the repository at this point in the history

  10. add deprecation tests

    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    9477de7 View commit details
    Browse the repository at this point in the history

  11. Change encore function expect conf distance 

    This changes the methods in encore to the new arbitrary weights system. The last
one conf_distance_matrix does need more refactoring work to simplify the code
before I change it as well.
    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    0299873 View commit details
    Browse the repository at this point in the history

  12. fix docs and default parameters

    @kain88-de
    kain88-de committed Jan 27, 2017
    Configuration menu
    Copy the full SHA
    cffa207 View commit details
    Browse the repository at this point in the history

Commits on Feb 4, 2017

  1. update confdistmatrix.py to new weights 

    This replaces the old mass only weights with general weights
    @kain88-de
    kain88-de committed Feb 4, 2017
    Configuration menu
    Copy the full SHA
    11d4d46 View commit details
    Browse the repository at this point in the history

  2. update tests to new kwargs

    @kain88-de
    kain88-de committed Feb 4, 2017
    Configuration menu
    Copy the full SHA
    937c523 View commit details
    Browse the repository at this point in the history