torch-structure-manipulation
Typed, in-memory utilities for atomic structures:
AtomicStructure.from_dataframeconverts mmdf-compatible DataFrames into device-aware tensors, with positions stored in(z, y, x)array order.AtomicStructure.from_annotated_dataframeannotates bonding metadata and then constructs the structure in one step.annotate_bonding_environmentsadds template-derived bonding andprotein/rna/othermolecule annotations without reading files.classify_structure_compositionandget_scattering_provider_keysexpose aggregate composition labels and per-atom Peng provider keys respectively.- Centering, rotation, translation, atom selection, and coordinate conversion
helpers are re-exported from the package root (also available under
structure_transforms).
import mmdf
from torch_structure_manipulation import (
AtomicStructure,
annotate_bonding_environments,
center_structure,
)
# File I/O belongs to the caller; mmdf is not a runtime dependency.
atoms = mmdf.read("structure.cif")
structure = AtomicStructure.from_annotated_dataframe(atoms, include_hydrogens=False)
# Or annotate first when you still need the DataFrame:
annotated = annotate_bonding_environments(atoms)
centered = center_structure(annotated, center_point=(0.0, 0.0, 0.0), zyx=False)
structure = AtomicStructure.from_dataframe(centered)
License
This project is licensed under the BSD 3-Clause License; see LICENSE.
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