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choderalab / pymbar-examples

Examples of applications of pymbar to various problems in simulation and experiment
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a pull request on alchemical-free-energy #10

Closed FEPanalysis closed 9 years ago

FEPanalysis commented 9 years ago

Michael,

Please look into the alchemical-free-energy/ directory and let me know whether you like the format.

mrshirts commented 9 years ago

Travelling with poor internets, so will look when I come back on Tuesday. Is pull request 10 following 9, or are they independent?

mrshirts commented 9 years ago

One quick but very important comment. There should not be two separate analysis scripts -- that defeats the purpose of having modularized code. There should be one script, that has all the common code, and calls on analysis_gromacs.py and analysis_sire.py modules for program specific functionality.

FEPanalysis commented 9 years ago

Despite residing in separate directories they are the same; only the default settings -- like prefix, suffix, etc. -- differ.

mrshirts commented 9 years ago

Then there should be only one file, with instructions on how to call it in two different ways for the two different modes of action. As it is, it's code duplication in almost pure form. A code repository doesn't need two copies of the same code.