Re-implement rigid body docking

[rvhonorato]

This PR re-implements the rigid body docking feature as the rigidbody module in the new architecture. Its cns/ folder contains only the protocols that are needed for it.

[amjjbonvin]

Probably indeed CNS scripts in this pull - but we can clean later. E.g. build missing is only used when creating the topology / start structures. Should be part of a separate module (e.g. gentop)

[rvhonorato]

Probably indeed CNS scripts in this pull - but we can clean later. E.g. build missing is only used when creating the topology / start structures. Should be part of a separate module (e.g. gentop)

Yes the issue about it is #42 and the topology is already its own module.

[joaomcteixeira]

Please give me some time to inspect this PR

[joaomcteixeira]

Just looking very quickly now:
Why are you uploading again the trans_vector_# files if they are already on data/toppar/initial_positions ?

[rvhonorato]

Quick screenshot of a superimposition of 100 models to show that the module is working and using restraints:

[rvhonorato]

Why are you uploading again the trans_vector_# files if they are already on data/toppar/initial_positions ?

These are also CNS scripts, so I copied them to this module's cns/

[joaomcteixeira]

This block before was inside the for loop. Now it is outside. Is this intended?

[rvhonorato]

yes, before it was generating the topology for the models into an assembly, now it does both the models from the assembly and different inputs.

[joaomcteixeira]

Is is able to continue from a half-run run? If you tested it and it works, perfect.

[joaomcteixeira]

Following today's conversation, rigidbody/cns has now 98 CNS scripts. Some script names there point to very general purposes, for example the centroids_*.cns family. My question is whether these are really SPECIFIC for rigid body docking, or we can already think of placing them in a module-independent cns dedicated folder.

[amjjbonvin]

Probably best if I take a look - cannot think so many are required just for the rigid body docking

[rvhonorato]

Following today's conversation, rigidbody/cns has now 98 CNS scripts.

45 + translation vectors (approximately). Keep in mind there are nested dependencies, the first level account for ~32

[joaomcteixeira]

Can't the nested dependencies by pulled from another folder? Maybe via a bridge python file?

[rvhonorato]

Its cns/ folder contains only the protocols that are needed for it.

What I mean with the nested dependencies is that: cns scripts can call another cns scripts that can call another cns script that can call another cns script

[rvhonorato]

Probably best if I take a look - cannot think so many are required just for the rigid body docking

There are not 98, I replied to it in a comment above.

[joaomcteixeira]

@rvhonorato plase have a look at https://github.com/rvhonorato/haddock3/pull/2 before merging.

As we discussed today, we have a roadmap to change some things here. But if you prefer to merge as it is now and than work on what we discussed with @amjjbonvin, perfect for me.