pyphyschemtools 0.2.1__py3-none-any.whl → 0.3.3__py3-none-any.whl

pyphyschemtools/.ipynb_checkpoints/Chem3D-checkpoint.py

@@ -283,10 +283,15 @@ class molView:
             and bond orders (detects double/triple bonds). 
             Requires the `rdkit` library. If False, fallback to standard 3Dmol 
             distance-based single bonds.
+        display_now : bool, optional
+                If True (default), renders the molecule immediately. 
+                Set to False to prevent immediate display when you plan to call 
+                further visualization methods provided by the molView class
         viewer : bool, optional
-                If True (default), initializes the py3Dmol viewer and renders the 
-                molecule. If False, operates in 'headless' mode: only coordinates 
-                are processed for calculations (default: True).
+            If True (default), initializes the py3Dmol engine and prepares the 3D model.
+            If False, operates in 'headless' mode: only geometric data is processed 
+            for analysis (volume, CM, etc.), saving significant memory for 
+            high-throughput processing.
         zoom : None, optional
             scaling factor
 
@@ -311,10 +316,12 @@ class molView:
         >>> vol = mv.data.get_cage_volume()
     """
 
-    def __init__(self, mol, source='file', style='bs', displayHbonds=True, cpk_scale=0.6, w=600, h=400,\
+    def __init__(self, mol, source=None, style='bs', displayHbonds=True, cpk_scale=0.6, w=600, h=400,\
                  supercell=(1, 1, 1), display_now=True, detect_BondOrders=True, viewer=True, zoom=None):
+        # For the automatic detection or source validation
+        valid_sources = ['file', 'mol', 'cif', 'cid', 'rscb', 'cod', 'ase']
+
         self.mol = mol
-        self.source = source
         self.style = style
         self.cpk_scale = cpk_scale
         self.displayHbonds = displayHbonds
@@ -324,6 +331,19 @@ class molView:
         self.supercell = supercell
         self.viewer = viewer
         self.zoom = zoom
+        if source is None and os.path.exists(str(mol)):
+            self.source = 'file'
+        elif source in valid_sources:
+            self.source = source
+        else:
+            # Clear error message and early exit if the source is unrecognized
+            error_msg = f"❌ Invalid source: '{source}'. \nAllowed sources are: {', '.join(valid_sources)}"
+            print(error_msg)
+            self.data = None
+            self.v = None
+            return
+        # Viewer initialization and data loading
+        # We only proceed if the source is valid
         self.v = py3Dmol.view(width=self.w, height=self.h) # Création du viewer une seule fois
         self._load_and_display(show=display_now)
 
@@ -670,13 +690,17 @@ class molView:
             try:
                 # On utilise l'alias long d'ASE pour PDB, sinon le format détecté
                 atoms = read(io.StringIO(content), format=fmt)
-            except Exception as e:
+            except (Exception, StopIteration):
                 # Si l'extraction échoue, on tente une dernière fois sans format forcé
                 try:
                     atoms = read(io.StringIO(content))
                 except:
-                    print(f"Extraction of coordinates is impossible ({e})")
-                    atoms = Atoms()
+                    print(f"❌ Extraction of coordinates is impossible for source {self.source}")
+                    self.data = None
+                    # --- CRUCIAL : On arrête tout ici si on n'a pas d'atomes ---
+                    if self.viewer:
+                        self.v.show() # On montre au moins le viewer vide ou l'erreur
+                    return
             
             self.data = XYZData(
                 symbols=atoms.get_chemical_symbols(),

pyphyschemtools/Chem3D.py

@@ -283,10 +283,15 @@ class molView:
             and bond orders (detects double/triple bonds). 
             Requires the `rdkit` library. If False, fallback to standard 3Dmol 
             distance-based single bonds.
+        display_now : bool, optional
+                If True (default), renders the molecule immediately. 
+                Set to False to prevent immediate display when you plan to call 
+                further visualization methods provided by the molView class
         viewer : bool, optional
-                If True (default), initializes the py3Dmol viewer and renders the 
-                molecule. If False, operates in 'headless' mode: only coordinates 
-                are processed for calculations (default: True).
+            If True (default), initializes the py3Dmol engine and prepares the 3D model.
+            If False, operates in 'headless' mode: only geometric data is processed 
+            for analysis (volume, CM, etc.), saving significant memory for 
+            high-throughput processing.
         zoom : None, optional
             scaling factor
 
@@ -311,10 +316,12 @@ class molView:
         >>> vol = mv.data.get_cage_volume()
     """
 
-    def __init__(self, mol, source='file', style='bs', displayHbonds=True, cpk_scale=0.6, w=600, h=400,\
+    def __init__(self, mol, source=None, style='bs', displayHbonds=True, cpk_scale=0.6, w=600, h=400,\
                  supercell=(1, 1, 1), display_now=True, detect_BondOrders=True, viewer=True, zoom=None):
+        # For the automatic detection or source validation
+        valid_sources = ['file', 'mol', 'cif', 'cid', 'rscb', 'cod', 'ase']
+
         self.mol = mol
-        self.source = source
         self.style = style
         self.cpk_scale = cpk_scale
         self.displayHbonds = displayHbonds
@@ -324,6 +331,19 @@ class molView:
         self.supercell = supercell
         self.viewer = viewer
         self.zoom = zoom
+        if source is None and os.path.exists(str(mol)):
+            self.source = 'file'
+        elif source in valid_sources:
+            self.source = source
+        else:
+            # Clear error message and early exit if the source is unrecognized
+            error_msg = f"❌ Invalid source: '{source}'. \nAllowed sources are: {', '.join(valid_sources)}"
+            print(error_msg)
+            self.data = None
+            self.v = None
+            return
+        # Viewer initialization and data loading
+        # We only proceed if the source is valid
         self.v = py3Dmol.view(width=self.w, height=self.h) # Création du viewer une seule fois
         self._load_and_display(show=display_now)
 
@@ -670,13 +690,17 @@ class molView:
             try:
                 # On utilise l'alias long d'ASE pour PDB, sinon le format détecté
                 atoms = read(io.StringIO(content), format=fmt)
-            except Exception as e:
+            except (Exception, StopIteration):
                 # Si l'extraction échoue, on tente une dernière fois sans format forcé
                 try:
                     atoms = read(io.StringIO(content))
                 except:
-                    print(f"Extraction of coordinates is impossible ({e})")
-                    atoms = Atoms()
+                    print(f"❌ Extraction of coordinates is impossible for source {self.source}")
+                    self.data = None
+                    # --- CRUCIAL : On arrête tout ici si on n'a pas d'atomes ---
+                    if self.viewer:
+                        self.v.show() # On montre au moins le viewer vide ou l'erreur
+                    return
             
             self.data = XYZData(
                 symbols=atoms.get_chemical_symbols(),

pyphyschemtools/__init__.py

@@ -1,6 +1,6 @@
 # tools4pyPhysChem/__init__.py
-__version__ = "0.2.1"
-__last_update__ = "2026-02-02"
+__version__ = "0.3.3"
+__last_update__ = "2026-02-03"
 
 import importlib
 import importlib.util

pyphyschemtools/resources/svg/{pyPCBanner.svg → pyPC_LPCNO_Banner.svg}

@@ -7,9 +7,9 @@
    viewBox="0 0 178.01071 29.131533"
    version="1.1"
    id="svg5"
-   inkscape:version="1.4.2 (unknown)"
-   sodipodi:docname="pyPCBanner.svg"
-   inkscape:export-filename="/home/romuald/ENSEIGNEMENT/0-JupyterNotebooks/L2-CHIM2-ON1/Tutos-Vidéo/Pandas-Stats-Iris/svg/logoPytChem.png"
+   inkscape:version="1.4.3 (unknown)"
+   sodipodi:docname="pyPC_LPCNO_Banner.svg"
+   inkscape:export-filename="pyPC_LPCNO_Banner.png"
    inkscape:export-xdpi="300.008"
    inkscape:export-ydpi="300.008"
    xml:space="preserve"
@@ -30,7 +30,7 @@
      inkscape:document-units="mm"
      showgrid="false"
      inkscape:zoom="2.1549693"
-     inkscape:cx="154.75858"
+     inkscape:cx="154.75859"
      inkscape:cy="88.168309"
      inkscape:window-width="2544"
      inkscape:window-height="1344"