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Create smiles string input #11

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Merged
BTSpeake merged 2 commits into from
Feb 10, 2026
Merged

Create smiles string input #11

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bf6b90f
Create SMILES string structure input widget
BTSpeake Feb 10, 2026
21d3098
Add rdkit to python package requirements to support SMILES string inputs
BTSpeake Feb 10, 2026
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1 change: 1 addition & 0 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ install_requires =
aiida-core
aiidalab-widgets-base
aiida-chemshell>=0.1.5
rdkit

python_requires = >=3.10

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19 changes: 17 additions & 2 deletions src/aiidalab_chemshell/wizards/structure.py
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Expand Up @@ -65,11 +65,18 @@ def __init__(self, model: StructureInputModel, **kwargs):
)
ipw.dlink((self.database_widget, "data_object"), (self.model, "structure_file"))

self.tabs.children = [self.file_input_widget, self.database_widget]
for i, title in enumerate(["Upload File", "AiiDA Database"]):
self.smiles_widget = awb.SmilesWidget(title="SMILES")

self.tabs.children = [
self.file_input_widget,
self.database_widget,
self.smiles_widget,
]
for i, title in enumerate(["Upload File", "AiiDA Database", "SMILES String"]):
self.tabs.set_title(i, title)

self.model.observe(self._on_file_upload, "structure_file")
self.smiles_widget.observe(self._on_smiles_generation, "structure")

def render(self):
"""Render the wizard's contents if not already rendered."""
Expand Down Expand Up @@ -116,6 +123,14 @@ def _on_file_upload(self, change=None):
self._update_children()
return

def _on_smiles_generation(self, change=None):
"""When SMILES string is inputted."""
self.viewer = awb.viewers.StructureDataViewer(
structure=self.smiles_widget.structure
)
self._update_children()
return

def _get_ase_object_from_file(self, fname: str, content: bytes) -> ase.Atoms | None:
suffix = "".join(Path(fname).suffixes)
with NamedTemporaryFile(suffix=suffix) as tmpf:
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