clean2d fixed for Queries.

CGRtools/algorithms/calculate2d.py

@@ -119,17 +119,31 @@ def _clean2d_prepare(self):
         return ''.join(smiles), order
 
 
-class Calculate2DCGR(Calculate2D):
+class Calculate2DQuery(Calculate2D):
     __slots__ = ()
 
     def _clean2d_prepare(self):
-        charges = self._charges
         radicals = self._radicals
+        self._radicals = {n: False for n in radicals}
+        try:
+            smiles, order = self._smiles(self._smiles_order, _return_order=True, stereo=False, hybridization=False,
+                                         neighbors=False, rings=False, hydrogens=False, heteroatoms=False)
+        except Exception:
+            raise
+        else:
+            return ''.join(smiles), order
+        finally:
+            self._radicals = radicals
 
+
+class Calculate2DCGR(Calculate2D):
+    __slots__ = ()
+
+    def _clean2d_prepare(self):
         mol = molecule.MoleculeContainer()
         for n, atom in self._atoms.items():
-            atom = Element.from_atomic_number(atom.atomic_number)(atom.isotope)
-            mol.add_atom(atom, n, charge=charges[n], is_radical=radicals[n], xy=(0., 0.))
+            atom = Element.from_atomic_number(atom.atomic_number or 6)()
+            mol.add_atom(atom, n)
         for n, m, bond in self.bonds():
             if bond.order == bond.p_order:
                 mol.add_bond(n, m, bond.order)
@@ -179,4 +193,4 @@ def clean2d(self):
             raise NotImplemented('py-mini-racer required for clean2d')
 
 
-__all__ = ['Calculate2DMolecule', 'Calculate2DCGR']
+__all__ = ['Calculate2DMolecule', 'Calculate2DCGR', 'Calculate2DQuery']

CGRtools/containers/query.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2018-2020 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2018-2021 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -20,15 +20,15 @@
 from . import molecule  # cyclic imports resolve
 from .bonds import Bond, QueryBond
 from .common import Graph
-from ..algorithms.calculate2d import Calculate2DMolecule
+from ..algorithms.calculate2d import Calculate2DQuery
 from ..algorithms.components import StructureComponents
 from ..algorithms.depict import DepictQuery
 from ..algorithms.smiles import QuerySmiles
 from ..algorithms.stereo import QueryStereo
 from ..periodictable import Element, QueryElement, AnyElement
 
 
-class QueryContainer(QueryStereo, Graph, QuerySmiles, StructureComponents, DepictQuery, Calculate2DMolecule):
+class QueryContainer(QueryStereo, Graph, QuerySmiles, StructureComponents, DepictQuery, Calculate2DQuery):
     __slots__ = ('_neighbors', '_hybridizations', '_atoms_stereo', '_cis_trans_stereo', '_allenes_stereo',
                  '_hydrogens', '_rings_sizes', '_heteroatoms')
 
@@ -236,7 +236,7 @@ def substructure(self, atoms, **kwargs) -> 'QueryContainer':
         sub._rings_sizes = {n: srs[n] for n in atoms}
         sub._heteroatoms = {n: sha[n] for n in atoms}
 
-        lost = {n for n, a in sa.items() if a.atomic_number != 1} - set(atoms)  # atoms not in substructure
+        lost = sa.keys() - set(atoms)  # atoms not in substructure
         not_skin = {n for n in atoms if lost.isdisjoint(sb[n])}
         sub._atoms_stereo = {n: s for n, s in self._atoms_stereo.items() if n in not_skin}
         sub._allenes_stereo = {n: s for n, s in self._allenes_stereo.items() if