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Ligand binding mode clustering with PyEMMA #13

Merged
merged 29 commits into from
Nov 11, 2017
Merged

Ligand binding mode clustering with PyEMMA #13

merged 29 commits into from
Nov 11, 2017

Commits on Oct 26, 2017

  1. Add content to README for Python intro.

    davidlmobley authored and davidlmobley committed Oct 26, 2017
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Commits on Nov 1, 2017

  1. Update Lecture 1 slides, add usage info

    @davidlmobley
    davidlmobley committed Nov 1, 2017
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Commits on Nov 2, 2017

  1. Update to include openforcefield in getting started

    @davidlmobley
    davidlmobley committed Nov 2, 2017
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  2. Clustering example with PyEMMA

    Nathan Lim committed Nov 2, 2017
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  3. Shrink traj file and rename

    Nathan Lim committed Nov 2, 2017
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  4. Update notebook

    Nathan Lim committed Nov 2, 2017
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Commits on Nov 3, 2017

  1. Add first pass at setting up yank hydration calculations for one of m… 

    …y molecules.
    @davidlmobley
    davidlmobley committed Nov 3, 2017
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Commits on Nov 7, 2017

  1. Tweaks/debugging.

    @davidlmobley
    davidlmobley committed Nov 7, 2017
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  2. Merge branch 'lectures' of https://github.com/MobleyLab/drug-computing … 

    …into lectures
    @davidlmobley
    davidlmobley committed Nov 7, 2017
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  3. Add draft Jupyter notebooks which I need to go through and check/upda… 

    …te, ported by Kevin Hoang.
    @davidlmobley
    davidlmobley committed Nov 7, 2017
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  4. Adjust chapter 2 to be current.

    @davidlmobley
    davidlmobley committed Nov 7, 2017
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  5. Add some prototype materials (needing generalization) for hydration f… 

    …ree energy calculations with Yank.
    @davidlmobley
    davidlmobley committed Nov 7, 2017
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  6. Merge pull request #14 from MobleyLab/chile_tutorial 

    Add some prototype materials demonstrating hydration free energy calculations in Yank
    @davidlmobley
    davidlmobley authored Nov 7, 2017
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  7. Fix broken link

    @davidlmobley
    davidlmobley committed Nov 7, 2017
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  8. Update/make current 3rd chapter of intro.

    @davidlmobley
    davidlmobley committed Nov 7, 2017
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Commits on Nov 8, 2017

  1. Add primes.py

    @davidlmobley
    davidlmobley committed Nov 8, 2017
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  2. Add test.py example

    @davidlmobley
    davidlmobley committed Nov 8, 2017
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  3. Add Chapter 4.

    @davidlmobley
    davidlmobley committed Nov 8, 2017
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  4. Add test.py updated version

    @davidlmobley
    davidlmobley committed Nov 8, 2017
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Commits on Nov 9, 2017

  1. Add program.py example

    @davidlmobley
    davidlmobley committed Nov 9, 2017
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  2. Add atom.py and test2.py examples

    @davidlmobley
    davidlmobley committed Nov 9, 2017
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  3. Finish updating Chapter 5.

    @davidlmobley
    davidlmobley committed Nov 9, 2017
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  4. Finish updating notebooks; add table of contents stuff/organize bette… 

    …r. Document in README.md.
    @davidlmobley
    davidlmobley committed Nov 9, 2017
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  5. Forgot to save a file last commit.

    @davidlmobley
    davidlmobley committed Nov 9, 2017
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Commits on Nov 10, 2017

  1. Add various slides for Lecture 1; adjust resolution and styling.

    @davidlmobley
    davidlmobley committed Nov 10, 2017
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  2. Merge pull request #12 from MobleyLab/lectures 

    Update lecture 1 slides; bring in background Python jupyter notebooks
    @davidlmobley
    davidlmobley authored Nov 10, 2017
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  3. Update Jupyter notebook for Lecture 1; add HTML version.

    @davidlmobley
    davidlmobley committed Nov 10, 2017
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  4. Merge branch 'clustering' of github.com:MobleyLab/drug-computing into… 

    … clustering
    Nathan M. Lim authored and Nathan M. Lim committed Nov 10, 2017
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  5. Add references and additional comments to code

    Nathan M. Lim authored and Nathan M. Lim committed Nov 10, 2017
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