Description
Describe the bug
When using the Molecule.from_dict method, molecule_dict["conformers"][0] cannot be a numpy array.
To Reproduce
import numpy as np
from openff.toolkit import Molecule
test = {'atoms': [{'atomic_number': 17,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 7,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 16,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 7,
'formal_charge': 0,
'is_aromatic': True,
'stereochemistry': None},
{'atomic_number': 16,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 7,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 7,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': True,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': True,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': True,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': True,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': True,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 6,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 29,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': 'R'},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None},
{'atomic_number': 1,
'formal_charge': 0,
'is_aromatic': False,
'stereochemistry': None}],
'bonds': [{'atom1': 0,
'atom2': 20,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 1,
'atom2': 4,
'bond_order': 2,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 1,
'atom2': 2,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 4,
'atom2': 7,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 20,
'atom2': 2,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 20,
'atom2': 3,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 20,
'atom2': 8,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 2,
'atom2': 11,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 7,
'atom2': 9,
'bond_order': 2,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 3,
'atom2': 18,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 11,
'atom2': 9,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 11,
'atom2': 12,
'bond_order': 2,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 8,
'atom2': 12,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 8,
'atom2': 10,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 18,
'atom2': 10,
'bond_order': 2,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 18,
'atom2': 6,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 12,
'atom2': 13,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 6,
'atom2': 19,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 14,
'atom2': 13,
'bond_order': 2,
'is_aromatic': True,
'stereochemistry': None},
{'atom1': 14,
'atom2': 15,
'bond_order': 1,
'is_aromatic': True,
'stereochemistry': None},
{'atom1': 13,
'atom2': 5,
'bond_order': 1,
'is_aromatic': True,
'stereochemistry': None},
{'atom1': 15,
'atom2': 16,
'bond_order': 2,
'is_aromatic': True,
'stereochemistry': None},
{'atom1': 5,
'atom2': 17,
'bond_order': 2,
'is_aromatic': True,
'stereochemistry': None},
{'atom1': 16,
'atom2': 17,
'bond_order': 1,
'is_aromatic': True,
'stereochemistry': None},
{'atom1': 1,
'atom2': 21,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 4,
'atom2': 22,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 7,
'atom2': 23,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 9,
'atom2': 24,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 14,
'atom2': 25,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 15,
'atom2': 26,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 16,
'atom2': 27,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 17,
'atom2': 28,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 19,
'atom2': 29,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 19,
'atom2': 30,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None},
{'atom1': 19,
'atom2': 31,
'bond_order': 1,
'is_aromatic': False,
'stereochemistry': None}],
'conformers': [np.array([[1.032, -1.316, -2.215],
[-0.521, -3.197, 0.611],
[-0.433, -1.89, 0.232],
[2.289, -0.98, 0.702],
[-1.7, -3.715, 1.009],
[-3.487, 1.084, 0.136],
[3.983, 1.697, 0.757],
[-2.855, -2.905, 1.036],
[0.18, 0.5, -0.023],
[-2.777, -1.592, 0.714],
[1.312, 1.288, 0.12],
[-1.525, -1.028, 0.346],
[-1.197, 0.293, 0.106],
[-2.189, 1.365, -0.001],
[-1.77, 2.681, -0.246],
[-2.719, 3.678, -0.344],
[-4.061, 3.339, -0.194],
[-4.408, 2.023, 0.046],
[2.498, 0.788, 0.494],
[3.492, 3.401, 0.372],
[0.716, -1.001, -0.41],
[0.359, -3.823, 0.588],
[-1.761, -4.752, 1.307],
[-3.805, -3.334, 1.315],
[-3.664, -0.975, 0.736],
[-0.721, 2.911, -0.357],
[-2.427, 4.701, -0.532],
[-4.825, 4.098, -0.266],
[-5.449, 1.761, 0.161],
[4.347, 4.064, 0.502],
[3.145, 3.454, -0.66],
[2.689, 3.708, 1.041]])],
'conformers_unit': 'angstrom',
'hierarchy_schemes': {},
'name': 'data_0TE',
'partial_charges': None,
'properties': {}}
test["conformers"][0] = np.array(test["conformers"][0])
mol = Molecule.from_dict(
test,
)
Output
UnboundLocalError Traceback (most recent call last)
Cell In[64], [line 13](vscode-notebook-cell:?execution_count=64&line=13)
[11](vscode-notebook-cell:?execution_count=64&line=11) print(test)
[12](vscode-notebook-cell:?execution_count=64&line=12) test["conformers"][0] = np.array(test["conformers"][0])
---> [13](vscode-notebook-cell:?execution_count=64&line=13) mol = Molecule.from_dict(
[14](vscode-notebook-cell:?execution_count=64&line=14) test,
[15](vscode-notebook-cell:?execution_count=64&line=15) )
File ~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1252, in FrozenMolecule.from_dict(cls, molecule_dict)
[1250](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1250) # This implementation is a compromise to let this remain as a classmethod
[1251](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1251) mol = cls()
-> [1252](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1252) mol._initialize_from_dict(molecule_dict)
[1253](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1253) return mol
File ~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1291, in FrozenMolecule._initialize_from_dict(self, molecule_dict)
[1288](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1288) else:
[1289](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1289) from openff.toolkit.utils.utils import deserialize_numpy
-> [1291](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1291) self._conformers = [
[1292](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1292) Quantity(
[1293](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1293) deserialize_numpy(ser_conf, (self.n_atoms, 3)),
[1294](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1294) unit.Unit(molecule_dict["conformers_unit"]),
[1295](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1295) )
[1296](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1296) for ser_conf in molecule_dict["conformers"]
[1297](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/topology/molecule.py:1297) ]
...
[442](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/utils/utils.py:442) np_array = np.frombuffer(serialized_np, dtype=dt)
--> [443](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/utils/utils.py:443) np_array = np_array.reshape(shape)
[444](https://file+.vscode-resource.vscode-cdn.net/Users/jenniferclark/OMSF/OpenFF/Organometallics/Datasets/DS1-CCD/~/bin/openff-toolkit/openff/toolkit/utils/utils.py:444) return np_array
UnboundLocalError: cannot access local variable 'np_array' where it is not associated with a value
Computing environment (please complete the following information):
- Operating system: MacOS
- Output of running
conda list:
List of packages in environment: "/Users/jenniferclark/.local/share/mamba/envs/qca"
Name Version Build Channel
──────────────────────────────────────────────────────────────────────────────────────────────────────────
alabaster 1.0.0 pyhd8ed1ab_1 conda-forge
ambertools 23.6 cuda_None_nompi_py311h486627a_105 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
anyio 4.8.0 pyhd8ed1ab_0 conda-forge
appnope 0.1.4 pyhd8ed1ab_1 conda-forge
apsw 3.47.0.0 py311hde754ab_0 conda-forge
argcomplete 3.5.2 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_1 conda-forge
argon2-cffi-bindings 21.2.0 py311h460d6c5_5 conda-forge
arpack 3.9.1 nompi_h1f29f7c_102 conda-forge
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-lru 2.0.4 pyhd8ed1ab_1 conda-forge
attrs 24.3.0 pyh71513ae_0 conda-forge
autodoc-pydantic 2.1.0 pyh3cfb1c2_1 conda-forge
babel 2.16.0 pyhd8ed1ab_1 conda-forge
basis_set_exchange 0.10 pyhd8ed1ab_1 conda-forge
beautifulsoup4 4.12.3 pyha770c72_1 conda-forge
bleach 6.2.0 pyhd8ed1ab_3 conda-forge
blosc 1.21.6 h7dd00d9_1 conda-forge
brotli 1.1.0 hd74edd7_2 conda-forge
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brotli-python 1.1.0 py311h3f08180_2 conda-forge
bson 0.5.9 pyhd8ed1ab_1 conda-forge
bzip2 1.0.8 h99b78c6_7 conda-forge
c-ares 1.34.4 h5505292_0 conda-forge
c-blosc2 2.15.2 h9cbb436_1 conda-forge
ca-certificates 2024.12.14 hf0a4a13_0 conda-forge
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cairo 1.18.2 h6a3b0d2_1 conda-forge
certifi 2024.12.14 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py311h3a79f62_0 conda-forge
chardet 5.2.0 py311h267d04e_2 conda-forge
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click 8.1.8 pyh707e725_0 conda-forge
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pip 24.3.1 pyh8b19718_2 conda-forge
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pydantic 2.10.4 pyh3cfb1c2_0 conda-forge
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pygments 2.18.0 pyhd8ed1ab_1 conda-forge
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pyobjc-core 10.3.2 py311hab620ed_0 conda-forge
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python 3.11.11 hc22306f_1_cpython conda-forge
python-constraint 1.4.0 pyhff2d567_1 conda-forge
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python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.2 pyhd8ed1ab_1 conda-forge
python_abi 3.11 5_cp311 conda-forge
pytorch 2.5.1 cpu_generic_py311_h0ba074a_8 conda-forge
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pyyaml 6.0.2 py311h460d6c5_1 conda-forge
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qcaide 1.0.0+10.g2054cf4.dirty pypi_0 pypi
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requests 2.32.3 pyhd8ed1ab_1 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
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sphinx 8.1.3 pyhd8ed1ab_1 conda-forge
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tk 8.6.13 h5083fa2_1 conda-forge
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
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tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
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types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
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unicodedata2 15.1.0 py311hae2e1ce_1 conda-forge
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webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
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widgetsnbextension 4.0.13 pyhd8ed1ab_1 conda-forge
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xorg-libice 1.1.2 h5505292_0 conda-forge
xorg-libsm 1.2.5 h5505292_0 conda-forge
xorg-libx11 1.8.10 h6a5fb8c_1 conda-forge
xorg-libxau 1.0.12 h5505292_0 conda-forge
xorg-libxdmcp 1.1.5 hd74edd7_0 conda-forge
xorg-libxext 1.3.6 hd74edd7_0 conda-forge
xorg-libxt 1.3.1 h5505292_0 conda-forge
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zeromq 4.3.5 hc1bb282_7 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
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zlib-ng 2.2.3 h13dfb9a_0 conda-forge
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zstd 1.5.6 hb46c0d2_0 conda-forge
Additional context
removing np.array() from the conformers key (so a list of lists) will allow the example to run as expected.