Survival probability: Intermittency, Step, Residues, Overlapping SP Selection Example#2226

Merged

orbeckst merged 20 commits intoMDAnalysis:developfrom bieniekmateusz:survival_probability

Apr 6, 2019

+264-52

Commits on Mar 21, 2019

Added skipping frames that are not used in the Survival Probability analysis. Before, all frames were loaded (and selection was always applied). Now, the frames which are not used are not loaded, t…
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Use the same code for loading the frames regardless of whether the step
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A test case that checks if all frames are loaded. This is the
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Refactoring with the simpler "return_value" when possible with the mock
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Better "verbose" message - avoid polluting.
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The SP value of entire residues can be calculated, regardless
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Intermittency added with a simple implementation. Intermittency is taken
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Refactored intermittency: fewer nested blocks, giving the user access
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Minor updates to the documentation.
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New test cases for the step+intermittency relation. - not finished
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The relationship between the intermittency and the window "step"
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Corrected documentation / proofreading.
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An example covering the case with multiple references for the SP
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Commits on Apr 3, 2019

Commits on Apr 4, 2019

Merge branch 'survival_probability' of https://github.com/bieniekmateusz/mdanalysis into bieniekmateusz-survival_probability
orbeckst
committed

Commits on Apr 5, 2019