From cb7c2b99d4f05a51bd6f561f3addb3d3eeb7d7e7 Mon Sep 17 00:00:00 2001
From: semantic-release <semantic-release>
Date: Wed, 2 Jul 2025 13:27:01 +0000
Subject: [PATCH] 2.4.8

Automatically generated by python-semantic-release
---
 pyproject.toml                            |  2 +-
 scripts/tool_benchmark/chimerax_family.py | 16 ++++++++++++++++
 scripts/tool_benchmark/pymol_family.py    | 18 +++++++++++++++++-
 src/flatprot/__init__.py                  |  2 +-
 uv.lock                                   |  2 +-
 5 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1b9a538..b7fffb4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "FlatProt"
-version = "2.4.7"
+version = "2.4.8"
 description = "Python package for creating simplified 2D protein visualizations. Specialized on showing differences and similarities between proteins of the same protein family."
 readme = "README.md"
 license = "Apache-2.0"
diff --git a/scripts/tool_benchmark/chimerax_family.py b/scripts/tool_benchmark/chimerax_family.py
index e842e4f..03a1ed0 100644
--- a/scripts/tool_benchmark/chimerax_family.py
+++ b/scripts/tool_benchmark/chimerax_family.py
@@ -29,6 +29,12 @@ def parse_args() -> argparse.Namespace:
         nargs="+",
         help="Paths to the input structure files (e.g., .cif)",
     )
+    parser.add_argument(
+        "--opacity",
+        type=float,
+        default=1.0,
+        help="Opacity level for the visualization (0.0-1.0). Default is 1.0 (fully opaque).",
+    )
     return parser.parse_args()
 
 
@@ -65,6 +71,16 @@ def main() -> None:
     # Apply visual style
     run(session, "hide ribbons")
     run(session, "show cartoon")
+    run(session, "color gray")  # Color everything gray first
+    run(session, "color helix red")  # Then color helices red
+    run(session, "color strand blue")  # Then color strands blue
+    if args.opacity < 1.0:
+        transparency_percent = (1.0 - args.opacity) * 100
+        # Apply transparency to all models
+        run(
+            session,
+            f"transparency #{','.join([str(m.id[0]) for m in model_ids])} {transparency_percent:.0f}",
+        )
     run(session, "view orient")
     run(session, "set bgColor white")
 
diff --git a/scripts/tool_benchmark/pymol_family.py b/scripts/tool_benchmark/pymol_family.py
index d7dfc79..9e64a25 100644
--- a/scripts/tool_benchmark/pymol_family.py
+++ b/scripts/tool_benchmark/pymol_family.py
@@ -19,6 +19,7 @@
 def main(
     output_file: Path,
     structure_files: List[Path],
+    opacity: float = 1.0,
 ) -> None:
     """Load multiple structures, align them, and save a PNG image using PyMOL.
 
@@ -31,6 +32,8 @@ def main(
         Path to save the output PNG image.
     structure_files
         Paths to the input structure files. At least one must be provided.
+    opacity
+        Opacity level for the visualization (0.0-1.0). Default is 1.0 (fully opaque).
     """
     if not structure_files:
         print("Error: No structure files provided.", file=sys.stderr)
@@ -49,6 +52,13 @@ def main(
 
     # Style the scene
     cmd.do("as cartoon")
+    cmd.do("color gray")  # Color everything gray first
+    cmd.do("color red, ss h")  # Then color helices red
+    cmd.do("color blue, ss s")  # Then color sheets blue
+    if opacity < 1.0:
+        # Apply transparency to all objects
+        cmd.set("cartoon_transparency", 1.0 - opacity, "all")
+        cmd.set("transparency", 1.0 - opacity, "all")
     cmd.bg_color("white")
 
     # Ensure output directory exists
@@ -73,13 +83,19 @@ def main(
         nargs="+",
         help="One or more paths to input structure files (e.g., CIF, PDB).",
     )
+    parser.add_argument(
+        "--opacity",
+        type=float,
+        default=1.0,
+        help="Opacity level for the visualization (0.0-1.0). Default is 1.0 (fully opaque).",
+    )
     try:
         args = parser.parse_args()
         for f in args.structure_files:
             if not f.exists():
                 print(f"Error: structure file not found: {f}", file=sys.stderr)
                 cmd.quit(1)
-        main(args.output_file, args.structure_files)
+        main(args.output_file, args.structure_files, args.opacity)
     except Exception as e:
         print(f"An error occurred: {e}", file=sys.stderr)
         cmd.quit(1)
diff --git a/src/flatprot/__init__.py b/src/flatprot/__init__.py
index 75cef64..c1d83e0 100644
--- a/src/flatprot/__init__.py
+++ b/src/flatprot/__init__.py
@@ -1,4 +1,4 @@
 # Copyright 2024 Rostlab.
 # SPDX-License-Identifier: Apache-2.0
-__version__ = "2.4.7"
+__version__ = "2.4.8"
 __app_name__ = "flatprot"
diff --git a/uv.lock b/uv.lock
index c04c662..bca0c99 100644
--- a/uv.lock
+++ b/uv.lock
@@ -548,7 +548,7 @@ wheels = [
 
 [[package]]
 name = "flatprot"
-version = "2.4.7"
+version = "2.4.8"
 source = { editable = "." }
 dependencies = [
     { name = "cairosvg" },