Create blank collections when importing only water

[mattwthompson]

Description

Fixes #1132

Checklist

• Add tests
• Lint
• Update docstrings

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.72%. Comparing base (d283069) to head (01b437c).
Report is 5 commits behind head on main.

Additional details and impacted files

[pbuslaev]

I think the change is good, though my minor bit is about the place, where empty collections are created.

[pbuslaev]

In my personal opinion it is a bit more logical to create those empty collections earlier, when all the collections are created. Those collections are anyway created, since _fill_in_rigid_water_bonds is anyway called, but now, _fill_in_rigid_water_bonds has sort of two tasks, which are not logically connected.

[mattwthompson]

I think of this as a sort of special case since it's only hit when the entire system lacks bonds and the collections are created elsewhere in dedicated private methods. I agree it shouldn't make a difference

The only problematic case I can think of is a system that constrained angles but not constrained bonds, which is weird and certainly outside what I think of as a normal treatment of rigid water

[pbuslaev]

Ok, I see you point. I think the PR is good. Thanks a lot for a prompt fix.