gatewizard 1.0.44__tar.gz → 1.0.45__tar.gz

{gatewizard-1.0.44/gatewizard.egg-info → gatewizard-1.0.45}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gatewizard
-Version: 1.0.44
+Version: 1.0.45
 Summary: A tool for membrane protein preparation and molecular dynamics analysis
 Author-email: Constanza González <constanza.gonzalez.villagra@gmail.com>, Mauricio Bedoya <mbedoya@ucm.cl>
 License: MIT License

{gatewizard-1.0.44 → gatewizard-1.0.45}/gatewizard/__init__.py

@@ -5,7 +5,7 @@
 Gatewizard - A tool for membrane protein preparation and analysis.
 """
 
-__version__ = "1.0.44"
+__version__ = "1.0.45"
 __author__ = "Constanza González, Mauricio Bedoya"
 __email__ = ""
 __license__ = "MIT"

{gatewizard-1.0.44 → gatewizard-1.0.45}/gatewizard/core/builder.py

@@ -63,7 +63,7 @@ class Builder:
             "dist": 12,  # Minimum solute-to-box-boundary distance in Angstroms
             "dist_wat": 26,  # Default water layer thickness in Angstroms
             "dims": None,  # Explicit box dimensions [X, Y, Z] in Angstroms
-            "notprotonate": False,  # False = allow protonation (default)
+            "notprotonate": True,  # Preserve PropKa residue names (GLH/ASH/…); skip reduce re-protonation
             "two_stage_process": False,  # Enable two-stage packing + parametrization
             "pack_only": False,  # Only perform packing stage
             "parametrize_only": False,  # Only perform parametrization stage
@@ -416,8 +416,10 @@ class Builder:
         else:
             # Use default naming scheme
             pdb_name = os.path.splitext(os.path.basename(pdb_file))[0]
-            timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
-            job_dir = work_dir / f"membrane_{pdb_name}_{timestamp}"
+            job_dir = work_dir / f"02_build_{pdb_name}"
+            if job_dir.exists():
+                timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
+                job_dir = work_dir / f"02_build_{pdb_name}_{timestamp}"
 
         job_dir.mkdir(parents=True, exist_ok=True)
 
@@ -472,8 +474,9 @@ class Builder:
         if config.get("parametrize", True):
             cmd.append("--parametrize")
 
-        # Only add notprotonate if specifically requested for legacy support
-        if config.get("notprotonate", False):
+        # Preserve PropKa / preparation protonation (GLH, ASH, HIP, …).
+        # Without this, packmol-memgen's reduce can rename atoms (e.g. HA→HCA) and break tleap.
+        if config.get("notprotonate", True):
             cmd.append("--notprotonate")
 
         # Add salt options (only for packing stage or single-stage)

{gatewizard-1.0.44 → gatewizard-1.0.45}/gatewizard/tools/__init__.py

@@ -28,6 +28,18 @@ from gatewizard.tools.ligand_parametrization import (
     LIGHT_PALETTE,
 )
 from gatewizard.tools.equilibration import EquilibrationStage
+from gatewizard.tools.packmol_hydration import (
+    build_hydrate_inp_text,
+    check_packmol_available,
+    detect_hydrogen_status,
+    estimate_cavity_volume,
+    hydrate_cavity,
+    prepare_hydration_job,
+    preview_hydrate_inp,
+    run_custom_packmol,
+    run_packmol,
+    PackmolHydrationError,
+)
 
 __all__ = [
     "ForceFieldManager",
@@ -51,4 +63,14 @@ __all__ = [
     "RECOMMENDED_COMBOS",
     "NON_RECOMMENDED_COMBOS",
     "LIGHT_PALETTE",
+    "build_hydrate_inp_text",
+    "check_packmol_available",
+    "detect_hydrogen_status",
+    "estimate_cavity_volume",
+    "hydrate_cavity",
+    "prepare_hydration_job",
+    "preview_hydrate_inp",
+    "run_custom_packmol",
+    "run_packmol",
+    "PackmolHydrationError",
 ]