Create scenario: shape-restrained protein-small molecule

[sverhoeven]

Create a scenario page for the https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule tutorial.

It would be nice if you could

• upload a ligand as a PDB file and the scenario page would convert into a shape.
• choose between shape-restrained protocol or pharmacophore based protocol

Continuation of #29

[sverhoeven]

See haddock3 example at https://github.com/haddocking/haddock3/blob/main/examples/docking-protein-ligand-shape/docking-protein-ligand-shape-full.cfg . It has a multi model pdb file with the ensembl of ligands.

Need to figure out how to handle the ligands, for example a multi file upload and ngl viewer with toggles to hide/show

[sverhoeven]

Possible scenario:

1. User uploads
   2. pdb with protein and docked ligand
   3. a small molecule to dock in one or more conformations. Could be as pdb, sdf or smile string (smile string will need to be converted to 3D conformation(s) on server using rdkit)
2. Use selects docker ligand
3. User can specify which protein residues should be used as restraints with small molecule
4. Server will convert docker ligand to a shape
5. Server will generate pdb without selected docked ligand
6. Server will generate param/top files for small molecule
7. Server will generate restraints between shape and small molecule
8. Server will generate restraints between protein and small molecule
9. Server generates workflow and runs it

Lots of server code that haddock2.4 and @VGPReys have, will need to be made available to the webapp as a webservice.