has attribute 'in_units_of'

[Dariuscty]

Hello, I prepare the environment as envs/environment-0.3.0-v3.yaml, but I meet the problem as

how can I deal with it?

[ijpulidos]

Hi, thanks for the feedback.

When is this happening exactly? Can you share the code that is causing this to happen?

That said, we should probably update the environment file since there has been some new releases for the dependencies that should be reflected in this file.

[Dariuscty]

in this two line code
ligand_positions = ligand_positions.in_units_of(unit.nanometers)
complex_positions = unit.Quantity(np.zeros([n_atoms_total, 3]), unit=unit.nanometers)

[ijpulidos]

I see, this probably comes from a difference between versions of the openff-toolkit. Basically, before version 0.11 the conformers would be of type openmm.unit.quantity.Quantity, but since version 0.11 the conformers are of type openff.units.units.Quantity.

The scripts in this repo expect an older (and now unsupported) version of the toolkit, which is 0.10.6. We should probably adapt the scripts here to be able to use the recent and supported versions of the toolkit.

As a workaround for the snippet of code you shared you could do something like the following

ligand_positions = ligand_positions.to_openmm().in_units_of(unit.nanometers)
complex_positions = unit.Quantity(np.zeros([n_atoms_total, 3]), unit=unit.nanometers)

which is just adding to_openmm to pass from the openff units to openmm units. And the rest of the code should work.