Feat/bugfix

src/colbuilder/chimera_scripts/generate_copies.py

@@ -46,10 +46,10 @@ def apply_unit_cell_translation(model, translation, cell_params):
 TRANSLATIONS = [
     # (-4, 0, -4),  # D4 = For strand 1 (blue) - top (1-2 interactions)
     # (-3, 0, -3),  # D3 =For strand 2 (green)
-    # (-2, 0, -2),  # D2 =For strand 3 (pink)
-    # (-1, 0, -1),  # D1 = For strand 4 (purple)
-    (0, 0, 0),  # D0 = For strand 5 (orange) - reference position
-    (-5, 0, -4),  # D5 = For strand 1 (blue) - bottom (5-1 interactions)
+    (-2, 0, -2),  # D2 =For strand 3 (pink)
+    (-1, 0, -1),  # D1 = For strand 4 (purple)
+    # (0, 0, 0),  # D0 = For strand 5 (orange) - reference position
+    # (-5, 0, -4),  # D5 = For strand 1 (blue) - bottom (5-1 interactions)
 ]
 
 input_pdb = os.environ.get("INPUT_PDB")

src/colbuilder/core/geometry/crosslink.py

@@ -137,4 +137,21 @@ def read_crosslink(pdb_file: Union[str, Path]) -> List[Crosslink]:
                     )
                 )
 
+            elif (line[17:20] in ("LZD") and line[13:15] == "CE") or (
+                line[17:20] in ("LZS") and line[13:15] == "NZ1"
+            ):
+                crosslinks.append(
+                    Crosslink(
+                        resid=line[22:26].strip(),
+                        resname=line[17:20],
+                        chain=line[21],
+                        position=[
+                            float(line[29:38]),
+                            float(line[38:46]),
+                            float(line[46:56]),
+                        ],
+                        type="D",
+                    )
+                )
+
     return crosslinks

src/colbuilder/core/sequence/optimize_crosslinks.py

@@ -1012,6 +1012,7 @@ def optimize_crosslink(
     LOG.debug("\nPhase 1: Backbone exploration")
     angle_steps = np.linspace(-np.pi / 2, np.pi / 2, 8)
     for residue_type in residue_types:
+        #restype_best_tracker = TransformationTracker()
         for angle in angle_steps:
             structures_copy = {k: v.copy() for k, v in best_structures.items()}
             temp_tracker = TransformationTracker()
@@ -1032,12 +1033,13 @@ def optimize_crosslink(
             if current_distance < best_distance:
                 best_distance = current_distance
                 best_structures = {k: v.copy() for k, v in structures_copy.items()}
-                best_tracker = temp_tracker.copy()
+                #restype_best_tracker = temp_tracker.copy()
                 current_tracker.update_from(temp_tracker)
                 if is_divalent:
                     LOG.debug(f"Improved distance: {dist1:.2f}")
                 else:
                     LOG.debug(f"Improved: {dist1:.2f}, {dist2:.2f}")
+    best_tracker = current_tracker.copy()
 
     # Phase 2: Main optimization
     LOG.debug("\nPhase 2: Main optimization")
@@ -1151,6 +1153,7 @@ def optimize_crosslink(
 
         if accept:
             current_tracker.update_from(temp_tracker)
+            best_tracker.update_from(temp_tracker)
             if new_max_distance < best_max_distance:
                 best_max_distance = new_max_distance
                 best_structures = {k: v.copy() for k, v in structures.items()}

src/colbuilder/core/utils/crosslinks.py

@@ -249,8 +249,11 @@ async def optimize(self, input_pdb: Path, output_pdb: Path) -> Tuple[float, Path
 
                 # Generate new copies based on the current best input
                 generated_pdbs = await self._generate_copies(best_input)
+
+
                 all_generated_pdbs.extend(generated_pdbs)
 
+
                 if len(generated_pdbs) < 2:
                     raise SequenceGenerationError(
                         "Not enough PDB copies generated for optimization",
@@ -333,6 +336,7 @@ async def optimize(self, input_pdb: Path, output_pdb: Path) -> Tuple[float, Path
     async def _generate_copies(self, input_pdb: Path) -> List[Path]:
         """Generate copies using Chimera."""
         try:
+
             generate_copies_script = self.chimera_scripts_dir / "generate_copies.py"
             generated_pdbs_file = Path("generated_pdbs.txt")