Add basic LigPlot for server and fix paper DOIs (#47)

* Add basic LigPlot for server and fix paper DOIs

Author: abhishektiwari

hbat/server/components/results_panel.py

@@ -28,6 +28,7 @@
 )
 from ...visualization.chain_graph import render_chain_for_web
 from ...visualization import export_interactions_to_pymol
+from ...visualization.ligplot import LigplotGenerator
 from ...visualization.pymol3d import (
     generate_carbonyl_interaction_viewer_js,
     generate_halogen_bond_viewer_js,
@@ -1491,6 +1492,33 @@ def build_water_bridges_data(selected_value):
                 .classes("w-full mb-4")
             )
 
+            # Ligplot visualization (2D structure with highlighted atoms)
+            ligplot_container = ui.html().classes("w-full mb-4")
+
+            def update_ligplot(ligand_res):
+                """Update ligplot when ligand selection changes."""
+                try:
+                    ligand_name = ligand_res.split(":")[1]
+                    gen = LigplotGenerator(
+                        ligand_name, self.analyzer, residue_id=ligand_res
+                    )
+                    html = gen.generate_svg(width=400, height=300)
+                    ligplot_container.content = html
+                except Exception as e:
+                    ligplot_container.content = (
+                        f"<p>Could not generate ligplot: {str(e)}</p>"
+                    )
+
+            # Initial ligplot
+            if first_ligand:
+                update_ligplot(first_ligand)
+
+            # Update ligplot when selection changes
+            def on_ligand_change(selected_value):
+                update_ligplot(selected_value.value)
+
+            selected_ligand.on_value_change(on_ligand_change)
+
             # Action buttons for regular interactions
             def show_all_interactions_viewer(selected_ligand_res):
                 """Show 3D viewer dialog with all regular interactions for selected ligand."""

hbat/server/components/upload_panel.py

@@ -114,7 +114,18 @@ async def download_structure():
                     url = f"https://files.rcsb.org/download/{safe_pdb_id}.cif"
                     filename = f"{pdb_id}.cif"
 
+                # Validate URL scheme and domain before opening
+                parsed = urllib.parse.urlparse(url)
+                if parsed.scheme != "https" or not parsed.netloc.endswith("rcsb.org"):
+                    ui.notify(
+                        "Invalid URL scheme or domain",
+                        type="negative",
+                        position="top-left",
+                    )
+                    return
+
                 # Add timeout for security (30 seconds)
+                # URL is validated to be https://files.rcsb.org only
                 with urllib.request.urlopen(url, timeout=30) as response:  # nosec B310
                     content = response.read()
 
@@ -192,7 +203,9 @@ async def download_structure():
                     label="PDB ID",
                     placeholder="e.g., 1BHL or pdb_00001abc",
                     validation={
-                        "Invalid PDB ID format": lambda v: validate_pdb_id(v)[0] if v else True
+                        "Invalid PDB ID format": lambda v: (
+                            validate_pdb_id(v)[0] if v else True
+                        )
                     },
                 )
                 .props("maxlength=12")