From 46925c8804e63615f4d733c07b1447744067a8f6 Mon Sep 17 00:00:00 2001
From: Jannis de Riz <jannis.deriz@gmail.com>
Date: Thu, 12 Feb 2026 20:08:42 +0100
Subject: [PATCH 1/2] feat: Add an `interface` option to `cartesian_ddg`/
 options_rosetta.py for defining the interface via a string AB_HL in line with
 other apps, overriding the `interface_ddg` jump number.

---
 source/src/apps/public/ddg/cartesian_ddg.cc | 12 ++++++++++++
 source/src/basic/options/options_rosetta.py |  1 +
 2 files changed, 13 insertions(+)

diff --git a/source/src/apps/public/ddg/cartesian_ddg.cc b/source/src/apps/public/ddg/cartesian_ddg.cc
index 3f7f2369195..cff8a936ab4 100644
--- a/source/src/apps/public/ddg/cartesian_ddg.cc
+++ b/source/src/apps/public/ddg/cartesian_ddg.cc
@@ -41,6 +41,8 @@
 #include <protocols/toolbox/pose_manipulation/pose_manipulation.hh>
 #include <protocols/ddg/CartesianddG.hh>
 #include <protocols/membrane/AddMembraneMover.hh>
+#include <protocols/docking/types.hh>
+#include <protocols/docking/util.hh>
 
 //Auto Headers
 #include <core/import_pose/import_pose.hh>
@@ -315,6 +317,16 @@ main( int argc, char * argv [] )
 			//interface mode? setting = jump number to use for interface
 			Size interface_ddg = option[ OptionKeys::ddg::interface_ddg ].value();
 
+			if ( option[ OptionKeys::ddg::interface ].user() ) {
+				std::string interface_str = option[ OptionKeys::ddg::interface ].value();
+				protocols::docking::DockJumps movable_jumps;
+				protocols::docking::setup_foldtree( pose, interface_str, movable_jumps );
+				if ( movable_jumps.size() > 0 ) {
+					interface_ddg = movable_jumps[1];
+					TR << "Setting interface jump to " << interface_ddg << " from string " << interface_str << std::endl;
+				}
+			}
+
 			//fd try to be smart .. look for interchain jump
 			if ( interface_ddg > pose.num_jump() ) {
 				for ( int i=1; i<=(int)pose.fold_tree().num_jump(); ++i ) {
diff --git a/source/src/basic/options/options_rosetta.py b/source/src/basic/options/options_rosetta.py
index 6a11697e848..f6ea793c753 100755
--- a/source/src/basic/options/options_rosetta.py
+++ b/source/src/basic/options/options_rosetta.py
@@ -5424,6 +5424,7 @@
 		Option('initial_repack','Boolean',default='false'),
 #		Option('rb_file','String'),
 		Option('interface_ddg','Integer',default='0', desc='Calculate ddGs across an interface? Uses jump # specified for determining interface.'),
+		Option('interface', 'String', default='', desc="Interface definition (e.g. 'AB_HL' for chains A,B vs H,L). Overrides interface_ddg jump number if specified." ),
 		Option('ens_variation', 'Real', default='0.5'),
 		Option('sc_min_only','Boolean',default='true'),
 		Option('rna_all_prot_sc_min_only','Boolean',default='false'),

From c46612a2ccdbd8e0ee49cc39f63c67e3884fbfcb Mon Sep 17 00:00:00 2001
From: Rocco Moretti <rmorettiase@gmail.com>
Date: Tue, 7 Jul 2026 17:07:12 -0500
Subject: [PATCH 2/2] Fix compilation post-merge.

---
 source/src/apps/public/ddg/cartesian_ddg.cc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/source/src/apps/public/ddg/cartesian_ddg.cc b/source/src/apps/public/ddg/cartesian_ddg.cc
index cff8a936ab4..da27d701748 100644
--- a/source/src/apps/public/ddg/cartesian_ddg.cc
+++ b/source/src/apps/public/ddg/cartesian_ddg.cc
@@ -19,6 +19,7 @@
 #include <core/pack/task/TaskFactory.hh>
 #include <core/pose/Pose.hh>
 #include <core/pose/PDBInfo.hh>
+#include <core/pose/DockingPartners.hh>
 
 #include <basic/options/util.hh>
 #include <basic/options/keys/OptionKeys.hh>
@@ -320,7 +321,7 @@ main( int argc, char * argv [] )
 			if ( option[ OptionKeys::ddg::interface ].user() ) {
 				std::string interface_str = option[ OptionKeys::ddg::interface ].value();
 				protocols::docking::DockJumps movable_jumps;
-				protocols::docking::setup_foldtree( pose, interface_str, movable_jumps );
+				protocols::docking::setup_foldtree( pose, core::pose::DockingPartners::docking_partners_from_string(interface_str), movable_jumps );
 				if ( movable_jumps.size() > 0 ) {
 					interface_ddg = movable_jumps[1];
 					TR << "Setting interface jump to " << interface_ddg << " from string " << interface_str << std::endl;