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Fixed an issue where creating an object array would unpack a Molecule into Atoms #94

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merged 2 commits into from
Mar 19, 2020
Merged

Fixed an issue where creating an object array would unpack a Molecule into Atoms #94

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db4783d
Fixed an issue where creating an object array would unpack a Molecule…
Mar 19, 2020
df643f9
Update multi_ligand.py
Mar 19, 2020
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18 changes: 9 additions & 9 deletions CAT/multi_ligand.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,8 @@ def init_multi_ligand(qd_df):
if workflow.mol_format is not None:
path = workflow.path
mol_format = workflow.mol_format
mol_to_file(qd_df[columns].values.ravel(), path, mol_format=mol_format)
mol_ar_flat = qd_df[columns].values.ravel()
mol_to_file(mol_ar_flat, path, mol_format=mol_format)


@overload
Expand Down Expand Up @@ -79,14 +80,13 @@ def multi_lig(qd_series, ligands, dummy=None, f=None, **kwargs):
raise TypeError("'f' and 'dummy' cannot be both 'None'")


def _multi_lig_dummy(qd_series, ligands, path, dummy, allignment) -> List[List[Molecule]]:
def _multi_lig_dummy(qd_series, ligands, path, dummy, allignment) -> np.ndarray:
"""Gogogo."""
ret_list = []
for qd in qd_series:
ret = []
ret_list.append(ret)
ret = np.empty((len(ligands), len(qd_series)), dtype=object)
for i, qd in enumerate(qd_series):
qd = qd.copy()

for ligand, atnum in zip(ligands, dummy):
for j, (ligand, atnum) in enumerate(zip(ligands, dummy)):
try:
atoms = [at for at in qd if at.atnum == atnum]
assert atoms
Expand All @@ -102,8 +102,8 @@ def _multi_lig_dummy(qd_series, ligands, path, dummy, allignment) -> List[List[M
qd = ligand_to_qd(qd, ligand, path=path,
allignment=allignment,
idx_subset=qd.properties.indices)
ret.append(qd)
return np.array(ret_list, dtype=object).T
ret[j, i] = qd
return ret


def _multi_lig_f(qd_series, ligands, path, f, **kwargs):
Expand Down