Further small updates to examples, quickmodel, and pymcmodels #113
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jchodera
reviewed
Jun 22, 2017
| # log_F_PL is highly correlated with DeltaG | ||
| mcmc.use_step_method(pymc.AdaptiveMetropolis, [pymc_model.log_F_PL, pymc_model.DeltaG], scales={ pymc_model.log_F_PL : 0.1, pymc_model.DeltaG : 0.1 }) | ||
| # Uncomment below to use log_F_PL highly correlated with DeltaG to improve sampling somewhat. | ||
| #mcmc.use_step_method(pymc.AdaptiveMetropolis, [pymc_model.log_F_PL, pymc_model.DeltaG], scales={ pymc_model.log_F_PL : 0.1, pymc_model.DeltaG : 0.1 }) |
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I think we have to add back Metropolis methods for log_F_PL and DeltaG.
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That would be something like
mcmc.use_step_method(pymc.Metropolis, getattr(pymc_model, 'log_F_PL'), proposal_sd=0.1, proposal_distribution='Normal')
mcmc.use_step_method(pymc.Metropolis, getattr(pymc_model, 'DeltaG'), proposal_sd=0.1, proposal_distribution='Normal')There was a problem hiding this comment.
Aren't they still there? https://github.com/choderalab/assaytools/blob/master/AssayTools/pymcmodels.py#L771-L772
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Yes, those exact lines were never removed and are still at lines 771-2.
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All these changes are done! You can now define Mergeable when checks pass. |
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Woohoo! |
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In this PR I hope to tackle a few small updates:
env PYTHONPATH="./"quickmodelto be slightly more flexible, currently it seems to stop at 4 ligands, which is not how our 384-well plates are organizedAdaptiveMetropolisin pymcmodelsquickmodel