Fixing shape support in cgtoaa module

[amjjbonvin]

Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Modified cgtoaa.cns to correctly handle a shape if present (fixing it and not including it in the morphing of the AA models onto the CG model of the complex.

Added a docking example illustrating protein-protein docking into a shape (both AA and CG)

TODO: update user manual with the information about the new docking example

[rversin]

I don't understand why some check fails here, as locally (on tintin) it doesn't fail, it actually succeeds. I don't know if need to fix a module or test script ?

[VGPReys]

I have two questions:

• *_cg.pdb: where should those files be written ? in the module (XX_topocg) directory ?
• *_cg.pdb: are those files used for backmapping ?

[rversin]

These files are used by CNS to build the topology files. They are written in the module directory (01_topocg). They are not used for backmapping.

[VGPReys]

Then let me fix this

[VGPReys]

I modified:

• the uni-tests
• some paths generation in the libaa2cg and topocg/__init__.py
• added a removal of the *_cg.pdb files (that are temporary), when debug = false

[rversin]

Thank you very much Victor for your help !