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update docs to show default as element_change=True #1380

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Merged
atravitz merged 3 commits into from
Jun 23, 2025
Merged

update docs to show default as element_change=True #1380

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69deaba
update docs to show default as element_change=True
atravitz Jun 18, 2025
161ba1a
Merge branch 'main' into update_element_change_doc
atravitz Jun 18, 2025
184624f
Update openfecli/commands/plan_rbfe_network.py
atravitz Jun 23, 2025
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4 changes: 2 additions & 2 deletions openfecli/commands/plan_rbfe_network.py
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Expand Up @@ -167,8 +167,8 @@ def plan_rbfe_network(

By default, this tool makes the following choices:

* Atom mappings performed by LOMAP, with settings max3d=1.0 and
element_change=False
* Atom mappings performed by LOMAP, with settings max3d=1.0, threed=True, shift=False and
element_change=True
* Minimal spanning network as the network planner, with LOMAP default
score as the weight function
* Water as solvent, with NaCl counter ions at 0.15 M concentration.
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