pyphyschemtools 0.1.5__py3-none-any.whl → 0.3.2__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)
 
@@ -615,7 +635,9 @@ class molView:
             response = requests.get(url)
             if response.status_code == 200:
                 content = response.text
-                fmt = "pdb"
+                fmt = "proteindatabank"
+            else:
+                raise ValueError(f"Could not find PDB ID: {self.mol} on RSCB")
                 
         elif self.source == 'cod':
             url = f"https://www.crystallography.net/cod/{self.mol}.cif"
@@ -634,8 +656,21 @@ class molView:
         if self.source == 'file':
             if not os.path.exists(self.mol):
                 raise FileNotFoundError(f"File not found: {self.mol}")
+            
+            # Extraction de l'extension sans le point
             ext = os.path.splitext(self.mol)[1].lower().replace('.', '')
-            fmt = 'cif' if ext == 'cif' else ext
+            
+            # Mapping explicite pour ASE
+            if ext == 'pdb':
+                fmt = 'proteindatabank'
+            elif ext == 'xyz':
+                fmt = 'xyz'
+            elif ext == 'cif':
+                fmt = 'cif'
+            else:
+                # Fallback sur l'extension si format exotique
+                fmt = ext
+                
             with open(self.mol, 'r') as f:
                 content = f.read()
         
@@ -649,19 +684,28 @@ class molView:
 
         # --- EXTRACTION XYZData (Interne) ---
         # On extrait les données ici avant toute modification (RDKit ou Supercell)
-        try:
-            if self.source == 'ase':
-                temp_atoms = self.mol
-            else:
-                temp_atoms = read(io.StringIO(content), format=fmt)
+        if self.source == 'ase':
+            atoms = self.mol
+        else:
+            try:
+                # On utilise l'alias long d'ASE pour PDB, sinon le format détecté
+                atoms = read(io.StringIO(content), format=fmt)
+            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 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=temp_atoms.get_chemical_symbols(),
-                positions=temp_atoms.get_positions()
+                symbols=atoms.get_chemical_symbols(),
+                positions=atoms.get_positions()
             )
-        except Exception as e:
-            print(f"Note: Extraction des coordonnées impossible ({e})")
-            self.data = None            
             
         # --- Modern Bond Perception with RDKit ---
         if self.detect_bonds and self.source in ['file', 'mol', 'xyz'] and fmt == 'xyz':

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)
 
@@ -615,7 +635,9 @@ class molView:
             response = requests.get(url)
             if response.status_code == 200:
                 content = response.text
-                fmt = "pdb"
+                fmt = "proteindatabank"
+            else:
+                raise ValueError(f"Could not find PDB ID: {self.mol} on RSCB")
                 
         elif self.source == 'cod':
             url = f"https://www.crystallography.net/cod/{self.mol}.cif"
@@ -634,8 +656,21 @@ class molView:
         if self.source == 'file':
             if not os.path.exists(self.mol):
                 raise FileNotFoundError(f"File not found: {self.mol}")
+            
+            # Extraction de l'extension sans le point
             ext = os.path.splitext(self.mol)[1].lower().replace('.', '')
-            fmt = 'cif' if ext == 'cif' else ext
+            
+            # Mapping explicite pour ASE
+            if ext == 'pdb':
+                fmt = 'proteindatabank'
+            elif ext == 'xyz':
+                fmt = 'xyz'
+            elif ext == 'cif':
+                fmt = 'cif'
+            else:
+                # Fallback sur l'extension si format exotique
+                fmt = ext
+                
             with open(self.mol, 'r') as f:
                 content = f.read()
         
@@ -649,19 +684,28 @@ class molView:
 
         # --- EXTRACTION XYZData (Interne) ---
         # On extrait les données ici avant toute modification (RDKit ou Supercell)
-        try:
-            if self.source == 'ase':
-                temp_atoms = self.mol
-            else:
-                temp_atoms = read(io.StringIO(content), format=fmt)
+        if self.source == 'ase':
+            atoms = self.mol
+        else:
+            try:
+                # On utilise l'alias long d'ASE pour PDB, sinon le format détecté
+                atoms = read(io.StringIO(content), format=fmt)
+            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 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=temp_atoms.get_chemical_symbols(),
-                positions=temp_atoms.get_positions()
+                symbols=atoms.get_chemical_symbols(),
+                positions=atoms.get_positions()
             )
-        except Exception as e:
-            print(f"Note: Extraction des coordonnées impossible ({e})")
-            self.data = None            
             
         # --- Modern Bond Perception with RDKit ---
         if self.detect_bonds and self.source in ['file', 'mol', 'xyz'] and fmt == 'xyz':

pyphyschemtools/__init__.py

@@ -1,6 +1,6 @@
 # tools4pyPhysChem/__init__.py
-__version__ = "0.1.5"
-__last_update__ = "2026-02-02"
+__version__ = "0.3.2"
+__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"