From 1891033a617f59eabc1f3627d79184ec5b97b827 Mon Sep 17 00:00:00 2001
From: gadorlhiac <gadorlhiac@gmail.com>
Date: Mon, 13 May 2024 12:26:07 -0700
Subject: [PATCH] SKL Outline for Phenix EMMA Task

---
 lute/io/models/sfx_solve.py | 45 +++++++++++++++++++++++++++++++++++++
 lute/managed_tasks.py       |  5 +++++
 2 files changed, 50 insertions(+)

diff --git a/lute/io/models/sfx_solve.py b/lute/io/models/sfx_solve.py
index a6435947..5806f97e 100644
--- a/lute/io/models/sfx_solve.py
+++ b/lute/io/models/sfx_solve.py
@@ -348,3 +348,48 @@ def validate_instructions_file(cls, in_file: str, values: Dict[str, Any]) -> str
                 prefix: str = shelxc_cmd.split()[1]
                 return f"{prefix}_fa"
         return in_file
+
+
+class RunPhenixEMMA(ThirdPartyParameters):
+    """Phenix's Euclidian Model Matching.
+
+    Superimposes two structure solutions to derive a consensus.
+
+    More information is availble at:
+    https://phenix-online.org/documentation/reference/emma.html
+    """
+
+    executable: str = Field(
+        "/sdf/group/lcls/ds/tools/phenix/phenix-1.16-3549/build/bin/phenix.emma",
+        description="Phenix EMMA program for model comparison.",
+        flag_type="",
+    )
+    unit_cell: Optional[str] = Field(
+        description=(
+            "Unit cell parameters listed as a comma-separated list.\n"
+            "Listed as: a,b,c,al,be,ga"
+        ),
+        flag_type="--",
+    )
+    space_group: Optional[str] = Field(
+        description="Space group symbol, e.g. P212121.",
+        flag_type="--",
+    )
+    symmetry_file: Optional[str] = Field(
+        description="External file with symmetry information.",
+        rename_param="symmetry",
+        flag_type="--",
+    )
+    tolerance: Optional[float] = Field(
+        description="Match tolerance for comparison.", flag_type="--"
+    )
+    diffraction_index_equivalent: Optional[bool] = Field(
+        description="Use only if models are diffraction-index equivalent.",
+        flag_type="--",
+    )
+    reference_coords: str = Field(
+        "", description="Reference coordinates to compare with.", flag_type=""
+    )
+    other_coords: str = Field(
+        "", description="Other coordinates to compare with.", flag_type=""
+    )
diff --git a/lute/managed_tasks.py b/lute/managed_tasks.py
index 4764a0c7..28096132 100644
--- a/lute/managed_tasks.py
+++ b/lute/managed_tasks.py
@@ -40,3 +40,8 @@
 SHELXDEditor: Executor = Executor("EditSHELXDInstructions")
 SHELXDRunner: Executor = Executor("RunSHELXD")
 SHELXDRunner.shell_source("/sdf/group/lcls/ds/tools/ccp4-8.0/bin/ccp4.setup-sh")
+
+PhenixEMMARunner: Executor = Executor("RunPhenixEMMA")
+PhenixEMMARunner.shell_source(
+    "/sdf/group/lcls/ds/tools/phenix/phenix-1.16-3549/phenix_env.sh"
+)