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Do not rebond in view_in_agui
we use gjf file format
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spdkit/__init__.py

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -341,11 +341,9 @@ def view_in_agui(mols: Union[Molecule, List[Molecule]], sleep=5):
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with tempfile.TemporaryDirectory() as td:
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# the molecule file for visualization in jmol
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molfile = os.path.join(td, "spdkit.mol2")
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for m in mols:
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m.rebond(ignore_pbc=True)
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molfile = os.path.join(td, "spdkit.gjf")
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io.write(molfile, mols)
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# open jmol script
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# open agui script
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p = subprocess.Popen(
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["agui", molfile], stdout=subprocess.PIPE, stderr=subprocess.PIPE
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)

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