From 69deaba61873fc719585e697bb49f00db335075d Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 18 Jun 2025 12:00:26 -0700 Subject: [PATCH 1/2] update docs to show default as element_change=True --- openfecli/commands/plan_rbfe_network.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openfecli/commands/plan_rbfe_network.py b/openfecli/commands/plan_rbfe_network.py index 951cde2c1..240df42b3 100644 --- a/openfecli/commands/plan_rbfe_network.py +++ b/openfecli/commands/plan_rbfe_network.py @@ -168,7 +168,7 @@ 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 + 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. From 184624f4313466cd9bad8cb19bd12b8e2c88be19 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> Date: Mon, 23 Jun 2025 10:13:04 -0700 Subject: [PATCH 2/2] Update openfecli/commands/plan_rbfe_network.py Co-authored-by: Irfan Alibay --- openfecli/commands/plan_rbfe_network.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openfecli/commands/plan_rbfe_network.py b/openfecli/commands/plan_rbfe_network.py index 240df42b3..c7b5d12e2 100644 --- a/openfecli/commands/plan_rbfe_network.py +++ b/openfecli/commands/plan_rbfe_network.py @@ -167,7 +167,7 @@ def plan_rbfe_network( By default, this tool makes the following choices: - * Atom mappings performed by LOMAP, with settings max3d=1.0 and + * 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