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Multiple improvements to pymcmodels #83

Merged
merged 24 commits into from
Apr 22, 2017
Merged

Multiple improvements to pymcmodels #83

merged 24 commits into from
Apr 22, 2017

Commits on Apr 17, 2017

  1. Add support for specified F_PL and its uncertainty dF_PL

    @jchodera
    jchodera committed Apr 17, 2017
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Commits on Apr 18, 2017

  1. Remove 'normal' concentration priors; use LogNormalWrapper to simplif… 

    …y lognormal priors.
    @jchodera
    jchodera committed Apr 18, 2017
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  2. Clean up LogNormalWrapper

    @jchodera
    jchodera committed Apr 18, 2017
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  3. Convert quantum yield priors to lognormal by default.

    @jchodera
    jchodera committed Apr 18, 2017
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  4. Convert fluorescence and absorbance errors to lognormal

    @jchodera
    jchodera committed Apr 18, 2017
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  5. Fix py3 issues in quickmodel

    @jchodera
    jchodera committed Apr 18, 2017
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Commits on Apr 19, 2017

  1. Fix python 3 incompatibility in platereader.py

    @jchodera
    jchodera committed Apr 19, 2017
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  2. Have quickmodel print exceptions it runs into

    @jchodera
    jchodera committed Apr 19, 2017
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  3. Adjust Metropolis step methods for new LogNormal priors; some py3 fixes

    @jchodera
    jchodera committed Apr 19, 2017
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  4. Start [L]=0 implementation

    @jchodera
    jchodera committed Apr 19, 2017
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  5. Merge branch 'improvements' of github.com:choderalab/assaytools into … 

    …improvements
    @jchodera
    jchodera committed Apr 19, 2017
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  6. Add quickmodel to continuous integration tests.

    @jchodera
    jchodera committed Apr 19, 2017
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  7. Allow ligand or protein concentrations to be zero.

    @jchodera
    jchodera committed Apr 19, 2017
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  8. Add command-line control over number of samples and thinning for quic… 

    …kmodel
    @jchodera
    jchodera committed Apr 19, 2017
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  9. Restore close to previous defaults for quickmodel

    @jchodera
    jchodera committed Apr 19, 2017
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  10. Add pymbar to requirements

    @jchodera
    jchodera committed Apr 19, 2017
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  11. Whoops! Previous behavior was actually 10000 samples, not 1000

    @jchodera
    jchodera committed Apr 19, 2017
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  12. quickmodel now plots equilibrated traces in a different shade; fix bu… 

    …g in command-line argument parsing
    @jchodera
    jchodera committed Apr 19, 2017
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  13. Fixed bug where same ligand concentration was being used for both +/-… 

    … protein rows
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    jchodera committed Apr 19, 2017
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  14. Decouple +/- protein buffer background priors

    @jchodera
    jchodera committed Apr 19, 2017
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  15. Restored Metropolis step methods with better step size guesses

    @jchodera
    jchodera committed Apr 19, 2017
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Commits on Apr 20, 2017

  1. Add AdaptiveMetropolis for correlated DeltaG and log_F_PL moves

    @jchodera
    jchodera committed Apr 20, 2017
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  2. Added tune_throughout=True

    @jchodera
    jchodera committed Apr 20, 2017
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  3. Allow Metropolis methods to tune throughout

    @jchodera
    jchodera committed Apr 20, 2017
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