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Contacts #84

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merged 6 commits into from
Oct 6, 2020
Merged

Contacts #84

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48db63f
add rtd
lilyminium Jun 18, 2020
726fbcf
update contacts
lilyminium Jun 29, 2020
9125b45
updated rst intro
lilyminium Jun 29, 2020
60897be
review fixes
lilyminium Sep 25, 2020
a075627
Merge github.com:lilyminium/UserGuide into contacts
lilyminium Sep 25, 2020
1cbdbec
Merge branch 'master' into contacts
lilyminium Oct 6, 2020
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3 changes: 2 additions & 1 deletion doc/source/examples/analysis/distances_and_contacts/README.rst
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Expand Up @@ -7,14 +7,15 @@ Distances and contacts
The :mod:`MDAnalysis.analysis.distances` module provides functions to rapidly compute distances. These largely take in coordinate arrays.



.. toctree::
:maxdepth: 1

/examples/analysis/distances_and_contacts/distances_between_atomgroups
/examples/analysis/distances_and_contacts/distances_between_selections
/examples/analysis/distances_and_contacts/distances_within_selection

Residues can be determined to be in contact if atoms from the two residues are within a certain distance. Analysing the fraction of contacts retained by a protein over at trajectory, as compared to the number of contacts in a reference frame or structure, can give insight into folding processes and domain movements.

:mod:`MDAnalysis.analysis.contacts` contains functions and a class to analyse the fraction of native contacts over a trajectory.

.. toctree::
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125 changes: 107 additions & 18 deletions doc/source/examples/analysis/distances_and_contacts/contacts_custom.ipynb
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5,947 changes: 5,882 additions & 65 deletions doc/source/examples/analysis/distances_and_contacts/contacts_native_fraction.ipynb
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64 changes: 39 additions & 25 deletions doc/source/examples/analysis/distances_and_contacts/contacts_q1q2.ipynb
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41 changes: 28 additions & 13 deletions doc/source/examples/analysis/distances_and_contacts/contacts_within_cutoff.ipynb
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6 changes: 3 additions & 3 deletions doc/source/examples/analysis/structure/dihedrals.ipynb
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],
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