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SciPy conference proceedings: MDAnalysis paper
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Analysis chapter #7

Closed kain88-de closed 8 years ago

kain88-de commented 8 years ago

This is a start for the analysis module section. A little bit of work left but it would be nice to hear if this goes into the right direction.

kain88-de commented 8 years ago

@orbeckst do you remember where the q1q2 analysis first showed up? I only know the original MDAnalysis paper

kain88-de commented 8 years ago

Included @richardjgowers suggestions

orbeckst commented 8 years ago

On 24 May, 2016, at 08:24, kain88-de notifications@github.com wrote:

@orbeckst do you remember where the q1q2 analysis first showed up? I only know the original MDAnalysis paper

I got it from Mark Delarue’s MinActionPath paper [1 and they don’t reference anyone else for it]. I think I also collected a few references in the issue report for the remodelling of the contacts analysis class – didn’t you add them to the docs anyway?

[1] J. Franklin, P. Koehl, S. Doniach, and M. Delarue. MinActionPath: maximum likelihood trajectory for large- scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Res., 35 (Web Server issue):W477–W482, 2007. doi: 10.1093/nar/gkm342. URL http://nar.oxfordjournals. org/cgi/content/abstract/35/suppl_2/W477.

Oliver Beckstein * orbeckst@gmx.net skype: orbeckst * orbeckst@gmail.com

kain88-de commented 8 years ago

That is the paper I added and as far as I remember the only one you listed in the PR. But I'll have a look again.

orbeckst commented 8 years ago

Fine with me, I'd merge but you need to fix the conflicts first.

kain88-de commented 8 years ago

I rebased this against the 2016 branch. I feel like I should add bit more information though, I think the text is still hard to understand for someone who isn't a coredev.

kain88-de commented 8 years ago

@orbeckst

I'm happy now with the first paragraph. I added a note why we need to unify the API and added citations for all used analysis algorithms from the docs if specified.

For the second paragraph I'm going into to more detail what the contacts class does and what a native contact is. That is already better then previously but I think could be improved still.

I'm good to have this merged. I can still make small PR's if I want more changes.

orbeckst commented 8 years ago

Only small changes, see above.

orbeckst commented 8 years ago

It would be good to have references for the analysis algorithms or quantitites that are calculated — can be text books, e.g., for persistence length.

kain88-de commented 8 years ago

I included suggestions. I don't have good references for the persistence length or RDF's. @richardjgowers implemented those and should know some good values (I think)