documentation fixed.

typing added

CGRtools/algorithms/aromatics.py

@@ -18,13 +18,25 @@
 #
 from CachedMethods import cached_property
 from collections import defaultdict, deque
-from typing import List, Optional, Tuple
+from typing import List, Optional, Tuple, TYPE_CHECKING, TypeVar, Type
 from .._functions import lazy_product
 from ..containers import query  # cyclic imports resolve
 from ..exceptions import InvalidAromaticRing
 
 
-class Aromatize:
+if TYPE_CHECKING:
+    from CGRtools import MoleculeContainer
+else:
+    MoleculeContainer = object
+
+T = TypeVar('T')
+
+
+def typehint(baseclass: Type[T]) -> Type[T]:
+    return object
+
+
+class Aromatize(typehint(MoleculeContainer)):
     __slots__ = ()
 
     def thiele(self, *, fix_tautomers=True) -> bool:

CGRtools/algorithms/tautomers.py

@@ -20,17 +20,25 @@
 from CachedMethods import class_cached_property, cached_property
 from collections import deque
 from itertools import product, chain, repeat
-from typing import TYPE_CHECKING, Iterator
+from typing import TYPE_CHECKING, Iterator, Type, TypeVar
 from ..containers import query  # cyclic imports resolve
 from ..containers.bonds import Bond
 from ..periodictable import ListElement
 
 
 if TYPE_CHECKING:
     from CGRtools import MoleculeContainer
+else:
+    MoleculeContainer = object
 
+T = TypeVar('T')
 
-class Tautomers:
+
+def typehint(baseclass: Type[T]) -> Type[T]:
+    return object
+
+
+class Tautomers(typehint(MoleculeContainer)):
     __slots__ = ()
 
     def tautomerize(self, *, prepare_molecules=True) -> bool:

CGRtools/containers/common.py

@@ -34,9 +34,6 @@ class Graph(GraphComponents, Morgan, SSSR, Isomorphism, MCS, ABC):
                  '__dict__', '__weakref__')
 
     def __init__(self):
-        """
-        Empty data object initialization or conversion from another object type
-        """
         self._atoms: Dict[int, AnyAtom] = {}
         self._charges: Dict[int, int] = {}
         self._radicals: Dict[int, bool] = {}

CGRtools/periodictable/__init__.py

@@ -42,7 +42,8 @@
 modules = {v.__name__: v for k, v in globals().items() if k.startswith('group') and k != 'groups'}
 elements = {k: v for k, v in globals().items() if isinstance(v, ABCMeta) and k != 'Element' and issubclass(v, Element)}
 
-__all__ = ['Element', 'DynamicElement', 'QueryElement', 'DynamicQueryElement', 'AnyElement', 'DynamicAnyElement']
+__all__ = ['Element', 'DynamicElement', 'QueryElement', 'DynamicQueryElement', 'AnyElement', 'DynamicAnyElement',
+           'ListElement', 'AnyAtom']
 __all__.extend(k for k in globals() if k.startswith('Group'))
 __all__.extend(k for k in globals() if k.startswith('Period'))
 __all__.extend(elements)

doc/conf.py

@@ -4,8 +4,7 @@
 parent = abspath('..')
 if parent not in path:
     path.insert(0, parent)
-from CGRtools.files._CGRrw import elements_set
-from CGRtools.periodictable import C, DynamicC, QueryC, DynamicQueryC
+from CGRtools.periodictable import C, DynamicC, QueryC, DynamicQueryC, ListElement, AnyElement, DynamicAnyElement
 
 author = 'Dr. Ramil Nugmanov'
 copyright = '2014-2020, Dr. Ramil Nugmanov <nougmanoff@protonmail.com>'

doc/containers.rst

@@ -6,5 +6,4 @@ Data classes.
 .. automodule:: CGRtools.containers
     :members:
     :undoc-members:
-    :show-inheritance:
     :inherited-members:

doc/files.rst

@@ -6,5 +6,3 @@ Available file parsers and writers:
 .. automodule:: CGRtools.files
     :members:
     :undoc-members:
-    :show-inheritance:
-    :inherited-members:

doc/periodictable.rst

@@ -3,7 +3,7 @@ CGRtools\.periodictable package
 
 Contains classes of all elements used in containers: common for `MoleculeContainer`, `Dynamic` for `CGRContainer`,
 `Query` and `DynamicQuery` for `QueryContainer` and `QueryCGRContainer` respectively.
-Also available two special query atom types: `AnyElement` and `DynamicAnyElement`
+Also available 3 special query atom types: `AnyElement`, `DynamicAnyElement` and `ListElement`
 
 Below only carbon atom classes shown.
 
@@ -34,3 +34,24 @@ Below only carbon atom classes shown.
     :show-inheritance:
     :inherited-members:
     :special-members: __hash__, __eq__, __int__
+
+.. autoclass:: CGRtools.periodictable.AnyElement
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+    :special-members: __hash__, __eq__, __int__
+
+.. autoclass:: CGRtools.periodictable.DynamicAnyElement
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+    :special-members: __hash__, __eq__, __int__
+
+.. autoclass:: CGRtools.periodictable.ListElement
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+    :special-members: __hash__, __eq__, __int__

doc/reactor.rst

@@ -4,5 +4,4 @@ CGRtools\.reactor package
 .. automodule:: CGRtools.reactor
     :members:
     :undoc-members:
-    :show-inheritance:
     :inherited-members:

doc/utils.rst

@@ -6,5 +6,4 @@ Utils for data transformation.
 .. automodule:: CGRtools.utils
     :members:
     :undoc-members:
-    :show-inheritance:
     :inherited-members: