make pyshtools as optional

pyxtal/__init__.py

@@ -2793,10 +2793,14 @@ def from_CSD(self, csd_code):
         from pymatgen.io.cif import CifParser
         try:
             from ccdc import io
-            from rdkit import Chem
         except:
             msg = 'No CSD-python api is available'
             raise CSDError(msg)
+        try:
+            from rdkit import Chem
+        except:
+            msg = 'No rdkit is available'
+            raise CSDError(msg)
 
         try:
             entry = io.EntryReader('CSD').entry(csd_code)

pyxtal/db.py

@@ -7,9 +7,9 @@
 
 def make_entry_from_pyxtal(xtal):
     """
-    make entry from the pyxtal object, assuming that 
+    make entry from the pyxtal object, assuming that
     the smiles/ccdc_number info is given
-    
+
     Args:
         xtal: pyxtal object
 
@@ -19,7 +19,7 @@ def make_entry_from_pyxtal(xtal):
     from rdkit.Chem.Descriptors import ExactMolWt
     from rdkit.Chem.rdMolDescriptors import CalcMolFormula
     from rdkit import Chem
- 
+
     if xtal.valid:
         url0 = "https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid="
         m = Chem.MolFromSmiles(xtal.tag['smiles'])
@@ -54,7 +54,7 @@ def make_entry_from_CSD_web(code, number, smiles, name=None):
         smiles: the corresponding molecular smiles
         name: name of the compound
     """
-   
+
     url0 = "https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid="
     #xtal = pyxtal(molecular=True)
     #

pyxtal/molecule.py

@@ -711,7 +711,7 @@ def rdkit_mol(self, N_confs=1):
         """
         from rdkit import Chem
 
-        mol = Chem.MolFromMolBlock(self.rdkit_mb, removeHs=False)
+        mol = Chem.MolFromMolBlock(self.rdkit_mol, removeHs=False)
         if N_confs > 1:
             conf = mol.GetConformer(0)
             for i in range(N_confs-1):

pyxtal/representation.py

@@ -337,7 +337,6 @@ def to_pyxtal(self, smiles=None, composition=None):
                     dicts['orientation'] = np.array(v[4:7])
                     dicts['rotor'] = v[7:-1]
                     dicts['reflect'] = int(v[-1])
-                print(dicts)
                 site = mol_site.from_1D_dicts(dicts)
                 site.type = i
                 struc.mol_sites.append(site)