T019: AttributeError: 'numpy.ndarray' object has no attribute 'unit'

[dominiquesydow]

T019 fails with the traceback below.

Actions to be taken after running T019 locally:

• Change openmm import because of Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
• openmmforcefields install fails under MacOS/M1 with

  $ mamba install -q -y -c conda-forge openmmforcefields
  Could not solve for environment specs
  Encountered problems while solving:
    - nothing provides ambertools >=20.0 needed by openmmforcefields-0.10.0-pyhd8ed1ab_0
  The environment can't be solved, aborting the operation
  

  Can be fixed with a CONDA_SUBDIR=osx-64 in front of the conda command
• Change atom.unit to atom.units

____ teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 12 ____
[gw0] linux -- Python 3.9.15 /usr/share/miniconda/envs/teachopencadd/bin/python
Notebook cell execution failed
Cell 12: Cell execution caused an exception

Input:
omm_ligand = rdkit_to_openmm(rdkit_ligand, ligand_name)

Traceback:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
File /usr/share/miniconda/envs/teachopencadd/lib/python3.9/site-packages/pint/facets/numpy/quantity.py:228, in NumpyQuantity.__getattr__(self, item)
    227 try:
--> 228     return getattr(self._magnitude,item)
    229 except AttributeError:

AttributeError: 'numpy.ndarray' object has no attribute 'unit'

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
Cell In[13], line 1
----> 1 omm_ligand = rdkit_to_openmm(rdkit_ligand,ligand_name)

Cell In[12], line 41, in rdkit_to_openmm(rdkit_mol, name)
     39 # convert units from Ångström to Nanometers
     40 for atom in mol_positions:
---> 41     coords = atom / atom.unit
     42     atom = (coords / 10.0) * unit.nanometers  # since openmm works in nm
     44 # combine topology and positions in modeller object

File /usr/share/miniconda/envs/teachopencadd/lib/python3.9/site-packages/pint/facets/numpy/quantity.py:230, in NumpyQuantity.__getattr__(self, item)
    228     return getattr(self._magnitude, item)
    229 except AttributeError:
--> 230     raise AttributeError(
    231         "Neither Quantity object nor its magnitude ({}) "
    232         "has attribute '{}'".format(self._magnitude, item)
    233     )

AttributeError: Neither Quantity object nor its magnitude ([14.734 33.5[59](https://github.com/volkamerlab/teachopencadd/actions/runs/3793382330/jobs/6450440241#step:8:60) 13.1[61](https://github.com/volkamerlab/teachopencadd/actions/runs/3793382330/jobs/6450440241#step:8:62)]) has attribute 'unit'