New functions to calculate state lifetimes by counting frames#173
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New functions to calculate state lifetimes by counting frames#173
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Refactor the function `mdtools.numpy_helper_functions.group_by`: * Use a stable sort when sorting the keys and values with respect to the keys. A stable sort keeps the relative order of equal elements. * Always check the input arguments. The `debug` argument is now without use. * Add examples to the docstring.
Create a new function `mdtools.dtrj.lifetimes` that calculates the lifetimes averaged over all compounds and all states by simply counting the number of frames a given compound stays in a given state.
Create a new function `mdtools.dtrj.lifetimes_per_state` that calculates the lifetime of each state in a discrete trajectory by simply counting the number of frames a given compound stays in a given state.
Add more information about how to calculate lifetimes from remain probabilities to the docstring of the function `mdtools.dtrj.remain_prob`.
Correct wrong comment in the Examples section of the docstring of the function `mdtools.dtrj.remain_prob_discrete`.
Extend the functionality of the function `mdtools.dtrj.lifetimes_per_states`: * Add a new argument `return_cmp_ix` that allows the user to return the compound indices associated with the returned lifetimes. * Add a new argument `discard_neg_start` that allows the user to discard lifetimes of negative states (like in the functions `mdtools.dtrj.remain_prob` and `mdtools.dtrj.remain_prob_discrete`). * Add a new argument `discard_all_neg` that allows the user to discard the lifetimes of all negative states and of all states that are followed by a negative state (like in the functions `mdtools.dtrj.remain_prob` and `mdtools.dtrj.remain_prob_discrete`).
Extend the functionality of the function `mdtools.dtrj.lifetimes`: * Add a new argument `return_states` that allows the user to return the state indices associated with the returned lifetimes. * Add a new argument `discard_neg_start` that allows the user to discard lifetimes of negative states (like in the functions `mdtools.dtrj.remain_prob` and `mdtools.dtrj.remain_prob_discrete`). * Add a new argument `discard_all_neg` that allows the user to discard the lifetimes of all negative states and of all states that are followed by a negative state (like in the functions `mdtools.dtrj.remain_prob` and `mdtools.dtrj.remain_prob_discrete`).
Replace the main body of the function `mdtools.dtrj.lifetimes_per_state` by a call of the function `mdtools.dtrj.lifetimes`.
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New functions to calculate state lifetimes by counting frames
Type of change
Proposed changes
New features
mdtools.dtrj.lifetimesthat calculates the lifetimes for all compounds in all states of a discrete trajectory by simply counting the number of frames a given compound stays in a given state.mdtools.dtrj.lifetimes_per_statethat calculates the lifetime of each state in a discrete trajectory by simply counting the number of frames a given compound stays in a given state.Cod refactoring
mdtools.numpy_helper_functions.group_by:debugargument is now without use.Documentation update
Add more information about how to calculate lifetimes from remain probabilities to the docstring of the function
mdtools.dtrj.remain_prob.Correct a wrong comment in the Examples section of the docstring of the function
mdtools.dtrj.remain_prob_discrete.PR checklist