Fixed multiple bugs for ListElement.

CGRtools/containers/common.py

@@ -366,7 +366,7 @@ def substructure(self, atoms: Iterable[int], *, meta: bool = False, graph_type:
         sub._atoms = ca = {}
         for n in atoms:
             atom = sa[n]
-            atom = atom_type.from_atomic_number(atom.atomic_number)(atom.isotope)
+            atom = atom_type.from_atom(atom)
             ca[n] = atom
             atom._attach_to_graph(sub, n)
 
@@ -443,7 +443,7 @@ def union(self, other: 'Graph', *, remap=False,
 
         ua = u._atoms
         for n, atom in other._atoms.items():
-            atom = atom_type.from_atomic_number(atom.atomic_number)(atom.isotope)
+            atom = atom_type.from_atom(atom)
             ua[n] = atom
             atom._attach_to_graph(u, n)
 

CGRtools/periodictable/element/dynamic.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2020, 2021 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -16,8 +16,9 @@
 #  You should have received a copy of the GNU Lesser General Public License
 #  along with this program; if not, see <https://www.gnu.org/licenses/>.
 #
-from typing import Type
+from typing import Type, Union
 from .core import Core
+from .element import Element
 from ..._functions import tuple_hash
 from ...exceptions import IsNotConnectedAtom
 
@@ -115,6 +116,17 @@ def from_atomic_number(cls, number: int) -> Type['DynamicElement']:
             raise ValueError(f'DynamicElement with number "{number}" not found')
         return element
 
+    @classmethod
+    def from_atom(cls, atom: Union['Element', 'DynamicElement']) -> 'DynamicElement':
+        """
+        get DynamicElement object from Element object or copy of DynamicElement object
+        """
+        if isinstance(atom, Element):
+            return cls.from_atomic_number(atom.atomic_number)(atom.isotope)
+        elif not isinstance(atom, DynamicElement):
+            raise TypeError('Element or DynamicElement expected')
+        return atom.copy()
+
     @property
     def neighbors(self):
         try:

CGRtools/periodictable/element/dynamic_query.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2020, 2021 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -19,6 +19,8 @@
 from typing import Tuple, Dict, Type, Union
 from .core import Core
 from .dynamic import Dynamic, DynamicElement
+from .element import Element
+from .query import QueryElement, AnyElement
 from ..._functions import tuple_hash
 from ...exceptions import IsNotConnectedAtom
 
@@ -130,6 +132,20 @@ def from_atomic_number(cls, number: int) -> Type[Union['DynamicQueryElement', 'D
             raise ValueError(f'DynamicQueryElement with number "{number}" not found')
         return element
 
+    @classmethod
+    def from_atom(cls, atom: Union['Element', 'DynamicElement', 'DynamicQueryElement', 'DynamicAnyElement',
+                                   'QueryElement', 'AnyElement']) -> Union['DynamicQueryElement', 'DynamicAnyElement']:
+        """
+        get DynamicQueryElement or DynamicAnyElement object from Element or DynamicElement or QueryElement object or
+        copy of DynamicQueryElement or DynamicAnyElement
+        """
+        if isinstance(atom, (Element, DynamicElement, QueryElement, AnyElement)):
+            return cls.from_atomic_number(atom.atomic_number)(atom.isotope)
+        elif not isinstance(atom, (DynamicQueryElement, DynamicAnyElement)):
+            raise TypeError('Element, DynamicElement, DynamicQueryElement, DynamicAnyElement,'
+                            ' QueryElement or AnyElement expected')
+        return atom.copy()
+
     def __eq__(self, other):
         if isinstance(other, DynamicElement):
             if self.atomic_number == other.atomic_number and \

CGRtools/periodictable/element/element.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2020, 2021 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -112,6 +112,15 @@ def from_atomic_number(cls, number: int) -> Type['Element']:
             raise ValueError(f'Element with number "{number}" not found')
         return element
 
+    @classmethod
+    def from_atom(cls, atom: 'Element') -> 'Element':
+        """
+        get Element copy
+        """
+        if not isinstance(atom, Element):
+            raise TypeError('Element expected')
+        return atom.copy()
+
     def __eq__(self, other):
         """
         compare attached to molecules elements

CGRtools/periodictable/element/query.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2020, 2021 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -148,6 +148,17 @@ def from_atomic_number(cls, number: int) -> Type[Union['QueryElement', 'AnyEleme
             raise ValueError(f'QueryElement with number "{number}" not found')
         return element
 
+    @classmethod
+    def from_atom(cls, atom: Union['Element', 'QueryElement', 'AnyElement']) -> Union['QueryElement', 'AnyElement']:
+        """
+        get QueryElement or AnyElement object from Element object or copy of QueryElement or AnyElement
+        """
+        if isinstance(atom, Element):
+            return cls.from_atomic_number(atom.atomic_number)(atom.isotope)
+        elif not isinstance(atom, (QueryElement, AnyElement)):
+            raise TypeError('Element, QueryElement or AnyElement expected')
+        return atom.copy()
+
     @Core.charge.setter
     def charge(self, charge):
         try:
@@ -344,7 +355,7 @@ def copy(self) -> 'ListElement':
         Detached from graph copy of element
         """
         copy = object.__new__(self.__class__)
-        copy._Core__isotope = self.__isotope
+        copy._Core__isotope = self._Core__isotope
         copy._elements = self._elements
         copy._numbers = self._numbers
         return copy

setup.py

@@ -54,7 +54,7 @@ def finalize_options(self):
 
 setup(
     name='CGRtools',
-    version='4.1.12',
+    version='4.1.13',
     packages=['CGRtools', 'CGRtools.algorithms', 'CGRtools.algorithms.components', 'CGRtools.containers',
               'CGRtools.files', 'CGRtools.files._mdl', 'CGRtools.periodictable', 'CGRtools.periodictable.element',
               'CGRtools.utils', 'CGRtools.attributes'],