New module to analize water dynamics.#295
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alejob wants to merge 2 commits intoMDAnalysis:developfrom
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This module have five new analysis methods: Hydrogen Bond Lifetime (HBL) Water Orientation Relaxation (WOR) Angular Distribution (AD) Mean Square Displacement (MSD) Surivival Probability (SP)
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Hey Alejandro If you can merge develop into this branch and then push it again I think the automated testing should happen |
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I'd rather have the names as "WaterOrientationalRelaxation" rather than WOR.
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Hi Richard, I'll make the changes that you suggest and I'll push it again from my development branch to make the automatic merge. Thanks for yours suggests. |
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@alejob thanks for the contribution. In addition to @richardjgowers 's comments, see my comments on the pull request. |
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Hi Oliver, thanks for the suggestions/corrections. I'm working on both feedback, yours and from @richardjgowers. |
Documentation fixed and updated.
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This module has five new analysis methods, all focus on water dynamics:
Hydrogen Bond Lifetime (HBL), similar to an already implemented module, but focused and optimized for water
Water Orientation Relaxation (WOR)
Angular Distribution (AD)
Mean Square Displacement (MSD)
Surivival Probability (SP)
Documentation and tests has been added.
This work was developed and used in: Araya-Secchi, R., Perez-Acle, T., Kang, S. G., Huynh, T., Bernardin, A., Escalona, Y., Garate J., Martínez A., García I., Sáez J.C., & Zhou, R. (2014). Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Biophysical journal, 107(3), 599-612.
Please tell me any changes or improvements deemed necessary.