contact map analysis module

[VGPReys]

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This closes #733 .
As a response to users request, a new analysis module is now available for user to generate contact maps of the generated structures.
The module will mainly focus on generating contact map on a per-cluster basis.
It is also possible to generate map for single structures.

Two type of graphs can be generated: heatmaps and chordcharts.

[codecov]

Codecov Report

Attention: 9 lines in your changes are missing coverage. Please review.

Comparison is base (1ea177d) 70.25% compared to head (56c6872) 72.45%.

Files	Patch %	Lines
src/haddock/modules/analysis/contactmap/contmap.py	98.68%	7 Missing ⚠️
...rc/haddock/modules/analysis/contactmap/__init__.py	95.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #731      +/-   ##
==========================================
+ Coverage   70.25%   72.45%   +2.19%     
==========================================
  Files          78       80       +2     
  Lines        6967     7547     +580     
==========================================
+ Hits         4895     5468     +573     
- Misses       2072     2079       +7     

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[rvhonorato]

Nice addition, just some small comments to be addressed and please add an integration test.

[sverhoeven]

Cool, the contacts can also be rendered in a mol viewer like

Could be part of the webapp or preprocess analysis?

Nevermind its already an issue at #733

[mgiulini]

the plot looks nice, but I wonder if this is what we want to show to the users. The majority of the contact map is dominated by intra-chain contacts, and that's what draws the attention...isn't it better to focus between inter-chain contacts so as to visualize contacts at the interface?

also, I am bit concerned about the size of the output, every contact map tsv file is 6 MB and the html is almost 5 MB..reducing the number of digits for a field (see comment) can improve things..but maybe this another argument in favour of showing only inter-chain contacts

[VGPReys]

the plot looks nice, but I wonder if this is what we want to show to the users. The majority of the contact map is dominated by intra-chain contacts, and that's what draws the attention...isn't it better to focus between inter-chain contacts so as to visualize contacts at the interface?

It as a good solution too.
I don't know what exactly is wanted here.
I felt like having plots that look like AlphaFold outputs would be simple for user to understand, as they might be used to this kind of plots.

also, I am bit concerned about the size of the output, every contact map tsv file is 6 MB and the html is almost 5 MB..
reducing the number of digits for a field (see comment) can improve things..but maybe this another argument in favour of showing only inter-chain contacts

Indeed, big issue...
Inter-chain contacts can solve this :)

Maybe a simple matplotlib plot can also be lighter.

[mgiulini]

also, I am bit concerned about the size of the output, every contact map tsv file is 6 MB and the html is almost 5 MB..
reducing the number of digits for a field (see comment) can improve things..but maybe this another argument in favour of showing only inter-chain contacts

Indeed, big issue... Inter-chain contacts can solve this :)

let's go for it then!

Maybe a simple matplotlib plot can also be lighter.

nah, being able to visualize the contacts interactively is super cool!

[amjjbonvin]

What about generating instead those circular plots (the circle being the sequence) with the contacts (intermolecular) being shown between chains. Like is being done to display crosslinks for example Joao Rodrigues wrote a library for this kind of analysis if I am correct Check https://github.com/JoaoRodrigues/interfacea <https://github.com/JoaoRodrigues/interfacea>

[rvhonorato]

Code looks good to me! 💯

[mgiulini]

added just a few comments here and there, the coordinate chart is truly beautiful!
feel free to merge as is