fix NodeLib

rdkit/VLib/NodeLib/SDSupply.py

@@ -4,6 +4,7 @@
 #     All Rights Reserved
 #
 import sys,os.path
+from rdkit import six
 from rdkit import RDConfig
 from rdkit.VLib.Supply import SupplyNode
 from rdkit import Chem
@@ -42,7 +43,10 @@ class SDSupplyNode(SupplyNode):
     """
 
     """
-    return self._supplier.next()
+    return next(self._supplier)
+
+if six.PY3:
+    SDSupplyNode.__next__ = SDSupplyNode.next
 
   
 #------------------------------------

rdkit/VLib/NodeLib/SmartsMolFilter.py

@@ -4,6 +4,7 @@
 #     All Rights Reserved
 #
 from rdkit import RDConfig
+from rdkit import six
 import sys,os,types
 from rdkit import Chem
 from rdkit.VLib.Filter import FilterNode
@@ -69,7 +70,7 @@ class SmartsFilter(FilterNode):
     for i in range(nPatts):
       p = patterns[i]
       c = counts[i]
-      if type(p) in types.StringTypes:
+      if type(p) in (str,bytes):
         m = Chem.MolFromSmarts(p)
         if not m:
           raise ValueError('bad smarts: %s'%(p))
@@ -89,6 +90,8 @@ class SmartsFilter(FilterNode):
         res = 1
         break
     return res
+if six.PY3:
+    SmartsFilter.__next__ = SmartsFilter.next
       
 #------------------------------------
 #

rdkit/VLib/NodeLib/SmartsRemover.py

@@ -4,6 +4,7 @@
 #     All Rights Reserved
 #
 from rdkit import RDConfig
+from rdkit import six
 import sys,os,types
 from rdkit import Chem
 from rdkit.VLib.Transform import TransformNode
@@ -84,7 +85,7 @@ class SmartsRemover(TransformNode):
     targets = [None]*nPatts
     for i in range(nPatts):
       p = patterns[i]
-      if type(p) in types.StringTypes:
+      if type(p) in (str,bytes):
         m = Chem.MolFromSmarts(p)
         if not m:
           raise ValueError('bad smarts: %s'%(p))
@@ -99,6 +100,10 @@ class SmartsRemover(TransformNode):
       #sys.stderr.write('\t\tAfter %s: %s\n'%(Chem.MolToSmiles(patt),Chem.MolToSmiles(cmpd)))
       
     return cmpd
+
+if six.PY3:
+    SmartsRemover.__next__ = SmartsRemover.next
+
       
 biggerTest="""
 >>> smis = ['CCOC','CCO.Cl','CC(=O)[O-].[Na+]','OCC','C[N+](C)(C)C.[Cl-]']

rdkit/VLib/NodeLib/SmilesDupeFilter.py

@@ -4,6 +4,7 @@
 #     All Rights Reserved
 #
 from rdkit import RDConfig
+from rdkit import six
 import sys,os
 from rdkit import Chem
 from rdkit.VLib.Filter import FilterNode
@@ -52,6 +53,8 @@ class DupeFilter(FilterNode):
     else:
       return 0
   
+if six.PY3:
+    DupeFilter.__next__ = DupeFilter.next
 #------------------------------------
 #
 #  doctest boilerplate

rdkit/VLib/NodeLib/SmilesOutput.py

@@ -5,6 +5,8 @@
 #
 import sys,types
 from rdkit import Chem
+from rdkit import six
+
 
 from rdkit.VLib.Output import OutputNode as BaseOutputNode
 
@@ -23,14 +25,14 @@ class OutputNode(BaseOutputNode):
     >>> mols = [Chem.MolFromSmiles(x) for x in smis]
     >>> from rdkit.VLib.Supply import SupplyNode
     >>> suppl = SupplyNode(contents=mols)
-    >>> import StringIO
-    >>> io = StringIO.StringIO()
-    >>> node = OutputNode(dest=io,delim=', ')
+    >>> from io import StringIO
+    >>> sio = StringIO()
+    >>> node = OutputNode(dest=sio,delim=', ')
     >>> node.AddParent(suppl)
     >>> ms = [x for x in node]
     >>> len(ms)
     4
-    >>> txt = io.getvalue() 
+    >>> txt = sio.getvalue() 
     >>> repr(txt)
     "'1, C1CCC1\\\\n2, C1CC1\\\\n3, C=O\\\\n4, CCN\\\\n'"
 
@@ -48,7 +50,7 @@ class OutputNode(BaseOutputNode):
 
   def smilesOut(self,mol):
     self._nDumped += 1
-    if type(mol) in [types.TupleType,types.ListType]:
+    if type(mol) in (tuple,list):
       args = mol
       mol = args[0]
       if len(args)>1:
@@ -66,6 +68,8 @@ class OutputNode(BaseOutputNode):
     outp = [label,smi]+args
     return '%s\n'%(self._delim.join(outp))
     
+if six.PY3:
+    OutputNode.__next__ = OutputNode.next
 
 #------------------------------------
 #

rdkit/VLib/NodeLib/SmilesSupply.py

@@ -7,6 +7,8 @@ import sys,os.path
 from rdkit import RDConfig
 from rdkit.VLib.Supply import SupplyNode
 from rdkit import Chem
+from rdkit import six
+
 
 class SmilesSupplyNode(SupplyNode):
   """ Smiles supplier
@@ -52,9 +54,11 @@ class SmilesSupplyNode(SupplyNode):
     """
     r = None
     while not r:
-      r = self._supplier.next()
+      r = next(self._supplier)
     return r
 
+if six.PY3:
+    SmilesSupplyNode.__next__ = SmilesSupplyNode.next
   
 #------------------------------------
 #

rdkit/VLib/NodeLib/test_list.py

@@ -13,3 +13,9 @@ tests=[
 longTests=[
 
   ]
+
+if __name__=='__main__':
+  import sys
+  from rdkit import TestRunner
+  failed,tests = TestRunner.RunScript('test_list.py',0,1)
+  sys.exit(len(failed))