pyphyschemtools 0.1.4__py3-none-any.whl → 0.2.1__py3-none-any.whl

pyphyschemtools/.ipynb_checkpoints/Chem3D-checkpoint.py

@@ -615,7 +615,9 @@ 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 +636,21 @@ 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 +664,24 @@ 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 as e:
+                # 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()
             
             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

@@ -615,7 +615,9 @@ 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 +636,21 @@ 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 +664,24 @@ 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 as e:
+                # 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()
             
             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

@@ -1,5 +1,5 @@
 # tools4pyPhysChem/__init__.py
-__version__ = "0.1.4"
+__version__ = "0.2.1"
 __last_update__ = "2026-02-02"
 
 import importlib

{pyphyschemtools-0.1.4.dist-info → pyphyschemtools-0.2.1.dist-info}/METADATA

@@ -1,9 +1,8 @@
 Metadata-Version: 2.4
 Name: pyphyschemtools
-Version: 0.1.4
+Version: 0.2.1
 Summary: A comprehensive Python toolbox for physical chemistry and cheminformatics
 Author-email: "Romuald POTEAU, LPCNO" <romuald.poteau@utoulouse.fr>
-Project-URL: Homepage, https://github.com/rpoteau/pyphyschemtools
 Project-URL: Repository, https://github.com/rpoteau/pyphyschemtools
 Project-URL: Changelog, https://github.com/rpoteau/pyphyschemtools/blob/main/CHANGELOG.md
 Project-URL: Documentation, https://pyphyschemtools.readthedocs.io/en/latest/

{pyphyschemtools-0.1.4.dist-info → pyphyschemtools-0.2.1.dist-info}/RECORD

@@ -1,8 +1,8 @@
 pyphyschemtools/.readthedocs.yaml,sha256=ZTw2bOyF9p3JpeF8Ux0fwhYWO6KHCsroNEOvnXxbYGM,469
-pyphyschemtools/Chem3D.py,sha256=LGMZYXF3iKaXERZGFCaqql3mQMN3di47TWv39FWSj3U,32719
+pyphyschemtools/Chem3D.py,sha256=zhqUz3g7ubAKLBknsZGWPCuvjhC1V8HyRaDIDqY6vuo,33458
 pyphyschemtools/ML.py,sha256=kR_5vm5TOOjVef8uXCW57y7685ts6K6OkRMBYKP_cYw,1599
 pyphyschemtools/PeriodicTable.py,sha256=LfLSFOzRkirREQlwfeSR3TyvgHyjGiltIZXNmvBkbhQ,13526
-pyphyschemtools/__init__.py,sha256=90ivOc9adepjq3sDAgNk6CprOKVhp-SoDq3r1UWZQvA,1442
+pyphyschemtools/__init__.py,sha256=JIOLN4KtCr8ZUvH8R-l3weEmOY9tJM5L-_bAkEsdMXU,1442
 pyphyschemtools/aithermo.py,sha256=kF8wtuYIJzkUKM2AGubmn9haAJKz-XaBskZ7HjivJeY,14984
 pyphyschemtools/cheminformatics.py,sha256=Qps_JSYWOzZQcXwKElI1iWGjWAPDgwmtDKuJwONsKmI,8977
 pyphyschemtools/core.py,sha256=5fRu83b125w2p_m2H521fLjktyswZHJXNKww1wfBwbU,4847
@@ -13,7 +13,7 @@ pyphyschemtools/sympyUtilities.py,sha256=LgLloh9dD9Mkff2WNoSnrJa3hxK0axOnK-4GS9w
 pyphyschemtools/tools4AS.py,sha256=BVfxf6bHnCciBMdQBSJ76Ja_aA-I_iOqQHZuVb-DsdY,44783
 pyphyschemtools/visualID.py,sha256=JlAd5nnZIliHOiKvkToArYhkbty-OntuFGf2CdPbgo8,3061
 pyphyschemtools/visualID_Eng.py,sha256=o-EdCOduo_qruRrr5kkplixaT1t79f3I3M1Ya5TOc_Q,5244
-pyphyschemtools/.ipynb_checkpoints/Chem3D-checkpoint.py,sha256=LGMZYXF3iKaXERZGFCaqql3mQMN3di47TWv39FWSj3U,32719
+pyphyschemtools/.ipynb_checkpoints/Chem3D-checkpoint.py,sha256=zhqUz3g7ubAKLBknsZGWPCuvjhC1V8HyRaDIDqY6vuo,33458
 pyphyschemtools/.ipynb_checkpoints/PeriodicTable-checkpoint.py,sha256=LfLSFOzRkirREQlwfeSR3TyvgHyjGiltIZXNmvBkbhQ,13526
 pyphyschemtools/.ipynb_checkpoints/aithermo-checkpoint.py,sha256=kF8wtuYIJzkUKM2AGubmn9haAJKz-XaBskZ7HjivJeY,14984
 pyphyschemtools/.ipynb_checkpoints/core-checkpoint.py,sha256=5fRu83b125w2p_m2H521fLjktyswZHJXNKww1wfBwbU,4847
@@ -82,8 +82,8 @@ pyphyschemtools/resources/svg/pyPhysChemBanner.png,sha256=sK5NwjbEYJvMAAzPBCqwvr
 pyphyschemtools/resources/svg/pyPhysChemBanner.svg,sha256=39LrLnFn7R681Hh3YXB3K17Sp0Xp3ynDOGUbXuORQ3s,4388883
 pyphyschemtools/resources/svg/qrcode-pyPhysChem.png,sha256=rP7X-9eHL7HYj4ffmwBMLfQTaRIOyzShVfavRXiomtw,71070
 pyphyschemtools/resources/svg/repository-open-graph-template.png,sha256=UlnW5BMkLGOv6IAnEi7teDYS_5qeSLmpxRMT9r9m-5Q,51470
-pyphyschemtools-0.1.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-pyphyschemtools-0.1.4.dist-info/METADATA,sha256=qu0k1TVSty1j3CxRDtETUfX7pBBxK81BPFZwxzgnBms,1339
-pyphyschemtools-0.1.4.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-pyphyschemtools-0.1.4.dist-info/top_level.txt,sha256=N92w2qk4LQ42OSdzK1R2h_x1CyUFaFBOrOML2RnmFgE,16
-pyphyschemtools-0.1.4.dist-info/RECORD,,
+pyphyschemtools-0.2.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+pyphyschemtools-0.2.1.dist-info/METADATA,sha256=BioidHl3jFOUaFy17bWIswfdStVkoTtR4SIrLi140gA,1273
+pyphyschemtools-0.2.1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+pyphyschemtools-0.2.1.dist-info/top_level.txt,sha256=N92w2qk4LQ42OSdzK1R2h_x1CyUFaFBOrOML2RnmFgE,16
+pyphyschemtools-0.2.1.dist-info/RECORD,,