prep for v0.3.5

doc/Others.rst

@@ -18,9 +18,9 @@ There are 4 options for defining molecules within the molecular_crystal class. Y
 
 ::
 
-    $ conda install -c conda-forge rdkit==2020.09.5
+    $ conda install -c conda-forge rdkit==2020.03.5
 
-Note that the current code is designed for version no later than ``2020.09.5``.
+Note that the current code is designed for version no later than ``2021.03.5``.
 
 Below is an example to generate a random molecular crystal from smile string.
 

pyxtal/molecule.py

@@ -441,6 +441,9 @@ def rdkit_mol_init(self, smile, fix, torsions):
                 ps = AllChem.ETKDGv3()
                 ps.randomSeed=self.seed
                 AllChem.EmbedMultipleConfs(mol, 1, ps)
+                if mol.GetNumConformers() == 0:
+                    AllChem.EmbedMultipleConfs(mol, 3, ps)
+
             res = AllChem.MMFFOptimizeMoleculeConfs(mol)
             engs = [c[1] for c in res]
             cid = engs.index(min(engs))
@@ -761,7 +764,7 @@ def apply_inversion(self):
         xyz *= -1
         self.reset_positions(xyz)
 
-    def get_symmetry(self, symmetrize=False):
+    def get_symmetry(self, symmetrize=False, rtol=0.30):
         """
         Set the molecule's point symmetry.
             - pga: pymatgen.symmetry.analyzer.PointGroupAnalyzer object
@@ -777,12 +780,12 @@ def get_symmetry(self, symmetrize=False):
             mol._spin_multiplicity = None #don't check spin
 
         if symmetrize:
-            pga = PointGroupAnalyzer(mol)
+            pga = PointGroupAnalyzer(mol, rtol, eigen_tolerance=1e-3)
             mol = pga.symmetrize_molecule()["sym_mol"]
-
-        pga = PointGroupAnalyzer(mol)#0.3)
+        pga = PointGroupAnalyzer(mol, rtol, eigen_tolerance=1e-3)
         self.mol_no_h = mol
 
+        #print(mol.to(fmt='xyz'), pga.sch_symbol)
         # For single atoms, we cannot represent the point group using a list of operations
         if len(mol) == 1:
             symm_m = []
@@ -822,6 +825,7 @@ def get_symmetry(self, symmetrize=False):
                         break
         self.symops = symm_m
         self.pga = pga
+        if symbol == 'S2': symbol = 'Ci'
         self.pg = Group(symbol, dim=0)
 
     def get_orientations_in_wps(self, wps=None, rtol=1e-2):

pyxtal/util.py

@@ -197,6 +197,26 @@ def parse_cif(filename, header=False, spg=False, eng=False, csd=False, sim=False
     else:
         return strings
 
+def process_csd_cif(cif, remove_H=False):
+    """
+    process cif from CSD, sometimes it contains multiple 
+    """
+    lines = cif.split('\n')
+    tmp = []
+    for l in lines:
+        if len(re.findall(r"[0-9][A-Z]", l))>0 or len(re.findall(r"[A-Z]\?", l))>0 or \
+            len(re.findall(r"[0-9]\?", l))>0 or \
+            len(re.findall(r"[A-Z][0-9]\' [0-9]", l))>0:
+            #len(re.findall(r"[0-9]_[0-9]", l))>0 or \
+            #print(l) #; import sys; sys.exit()
+            continue
+        else:
+            if remove_H and len(re.findall(r" H ", l))>0:
+                continue
+            else:
+                tmp.append(l+'\n')
+    return listToString(tmp)
+
 def get_similar_cids_from_pubchem(base, MaxRecords):
 
     """