Add modules that could add/delete molecules within a workflow

[amjjbonvin]

Desired feature/enhancement

Create new modules to add or delete a component during a workflow.

Description

Currently the number of molecules is defined in the start section of a workflow config file and can not be changed during the workflow execution. It would be nice to have two new modules:

1. one to add a molecule to the current status of the workflow (e.g. moladd). The idea would be to create a new step in which the new molecule is added to the current PDBs, making sure there is no overlap in chain/segID, and an updated io file is created. Adding a topoaa module after that step would build the new topology and from there on the workflow can continue with the expanded complex. Most likely this would only allow for single models to be added.

2. one to delete a current molecule from the current models (e.g. moldel).

Motivation

Possible application examples would be:

1. Run a pre-sampling workflow (e.g. for glycans or for peptide cyclisation), then add a protein and perform docking, all within the same workflow.

2. Following some shape-restrained docking, delete the shape from the current models to be able to continue the workflow differently (e.g. add an openmm step).

In all cases, a topoaa step would be required after adding or deleting a component.

[VGPReys]

Great idea.
Could as well be part of the getting rid of topoaa as first module PR #921

[VGPReys]

I guess should be discussed next Friday during the meeting.