When running the example notebook with the production data specified, we get an error producing an HTML table of the target set:
from plbenchmark import targets
from IPython.core.display import HTML
targets.set_data_dir('../protein-ligand-benchmark/data/')
# it is initialized from the `plbenchmark/sample_data/targets.yml` file
target_set = targets.TargetSet()
# to see which targets are available, one can get a list of names
target_set.get_names()
HTML(target_set.get_html(columns=['name', 'fullname', 'pdb', 'references', 'numLigands', 'minDG', 'maxDG', 'associated_sets']))
we get:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-5-9831143c195f> in <module>
----> 1 HTML(target_set.get_html(columns=['name', 'fullname', 'pdb', 'references', 'numLigands', 'minDG', 'maxDG', 'associated_sets']))
~/Projects/openff/protein-ligand/protein-ligand-benchmark/plbenchmark/targets.py in get_html(self, columns)
348 :return: HTML string
349 """
--> 350 df = self.get_dataframe(columns=columns)
351 html_string = df.to_html()
352 html_string = html_string.replace("REP1", '<a target="_blank" href="')
~/Projects/openff/protein-ligand/protein-ligand-benchmark/plbenchmark/targets.py in get_dataframe(self, columns)
324 dfs = []
325 for key in self.keys():
--> 326 self[key].add_ligand_data()
327 self[key].find_links()
328 dfs.append(self[key].get_dataframe())
~/Projects/openff/protein-ligand/protein-ligand-benchmark/plbenchmark/targets.py in add_ligand_data(self)
111 :return: None
112 """
--> 113 lgs = self.get_ligand_set()
114 self.ligand_data = pd.Series({"numLigands": len(lgs)})
115 affinities = []
~/Projects/openff/protein-ligand/protein-ligand-benchmark/plbenchmark/targets.py in get_ligand_set(self)
102 """
103 if self._ligands is None:
--> 104 self._ligands = ligands.LigandSet(self._name)
105 return self._ligands
106
~/Projects/openff/protein-ligand/protein-ligand-benchmark/plbenchmark/ligands.py in __init__(self, target, *arg, **kw)
254 data = yaml.full_load(file)
255 for name, d in data.items():
--> 256 lig = Ligand(d, target)
257 lig.derive_observables(derived_type="dg")
258 # l.find_links()
~/Projects/openff/protein-ligand/protein-ligand-benchmark/plbenchmark/ligands.py in __init__(self, d, target)
57 unit = utils.unit_registry(self._data[("measurement", "unit")])
58 self._data[("measurement", "error")] = (
---> 59 self._data[("measurement", "error")] * unit
60 )
61 self._data[("measurement", "value")] = (
TypeError: unsupported operand type(s) for *: 'NoneType' and 'Quantity'
When running the example notebook with the production data specified, we get an error producing an HTML table of the target set:
we get: