Latest devel does not run setup demo about biosimspace HOT 3 CLOSED

This is now fixed. The problem was introduced when closing issue #46, i.e. adding a molecule to a list of molecules now extends the list, rather than creating a System object. (Previously, any multi-molecule data structure was converted to a System.) I've updated _solvent.py to reflect the changes.

I'll also have to update the binding_freenrg.py script used for the D3R2018 challenge as it will no longer work, i.e. the line...

system = merged + protein + waters

...will no longer create a system, but a list of molecules instead. We'll probably need to rethink this, as there is currently no way for the user to create a system from a list of molecules. (The System object is deliberately hidden from the user and is only used internally.)

from biosimspace.

Thank you!

from biosimspace.

No problem.

To get around the other issue I'll create a MoleculeList object that is subclassed from a regular Python list. I can then add a toSystem method that converts the MoleculeList to a system. Just noting here so I don't forget :-)

from biosimspace.