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starting docstring
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StephMcCallum committed Dec 27, 2024
1 parent 53a80d5 commit e2f8633
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26 changes: 26 additions & 0 deletions grits/finegrain.py
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Expand Up @@ -21,6 +21,32 @@ def backmap_snapshot_to_compound(
ref_distance=None,
energy_minimize=False,
):
"""Backmap a fine-grained snapshot onto a coarse one.
Creates a fine-grained compound from a coarse one using the given parameters.
Parameters
----------
snapshot : one frame of gsd trajectory
bead_mapping (string) : SMILES string of fine-grain monomer
bond_head_index (list of int) : index of polymer reaction, choose head to orient chain
bond_tail_index (list of int) : index of polymer reaction, choose tail to orient chain
library_key (string) : string key to dictionary, reactant_dict, with known bead_mapping, bond_head_index, and bond_tail_index
ref_distance (float) : distance between monomers
energy_minimize (bool) : Option to run a mbuild energy minimization.
Returns
-------
:py:class:`mbuild.Compound`
The atomistic structure mapped onto the coarse-grained one.
"""
# TODO
# assert all 3 dicts have the same keys
if (
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