AnyMetal query atom added. (#185)

cimm-kzn · Jul 1, 2021 · d4fc2c6 · d4fc2c6
1 parent 4bbb64d
commit d4fc2c6
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Showing 3 changed files with 46 additions and 9 deletions.
diff --git a/CGRtools/periodictable/__init__.py b/CGRtools/periodictable/__init__.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
@@ -43,7 +43,7 @@
 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',
-           'ListElement', 'AnyAtom']
+           'ListElement', 'AnyAtom', 'AnyMetal']
 __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)

diff --git a/CGRtools/periodictable/element/__init__.py b/CGRtools/periodictable/element/__init__.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2019, 2020 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2019-2021 Ramil Nugmanov <nougmanoff@protonmail.com>
 #  Copyright 2019 Tagir Akhmetshin <tagirshin@gmail.com>
 #  Copyright 2019 Dayana Bashirova <dayana.bashirova@yandex.ru>
 #  This file is part of CGRtools.
@@ -26,8 +26,9 @@
 from .dynamic_query import *
 
 
-AnyAtom = Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, DynamicAnyElement, ListElement]
+AnyAtom = Union[Element, DynamicElement, QueryElement, DynamicQueryElement, AnyElement, AnyMetal, DynamicAnyElement,
+                ListElement]
 
 
 __all__ = ['Core', 'Element', 'DynamicElement', 'QueryElement', 'DynamicQueryElement',
-           'AnyElement', 'DynamicAnyElement', 'AnyAtom', 'ListElement']
+           'AnyElement', 'AnyMetal', 'DynamicAnyElement', 'AnyAtom', 'ListElement']
diff --git a/CGRtools/periodictable/element/query.py b/CGRtools/periodictable/element/query.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 #  Copyright 2020, 2021 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2021 Dmitrij Zanadvornykh <>
 #  This file is part of CGRtools.
 #
 #  CGRtools is free software; you can redistribute it and/or modify
@@ -314,6 +315,44 @@ def __hash__(self):
                            self.implicit_hydrogens, self.heteroatoms))
 
 
+class AnyMetal(AnyElement):
+    """
+    Charge and radical ignored any metal.
+    """
+    @property
+    def atomic_symbol(self) -> str:
+        return 'M'
+
+    def __eq__(self, other):
+        if isinstance(other, Element):
+            if other.atomic_symbol not in {'He', 'Ne', 'Ar', 'Kr', 'Xe', 'F', 'Cl', 'Br', 'I', 'C', 'N', 'O', 'H', 'Si',
+                                           'P', 'S', 'Se', 'Ge', 'As', 'Sb', 'Te'}:
+                if self.neighbors and other.neighbors not in self.neighbors:
+                    return False
+                if self.hybridization and other.hybridization not in self.hybridization:
+                    return False
+                if self.ring_sizes:
+                    if self.ring_sizes[0]:
+                        if set(self.ring_sizes).isdisjoint(other.ring_sizes):
+                            return False
+                    elif other.ring_sizes:  # not in ring expected
+                        return False
+                if self.implicit_hydrogens and other.implicit_hydrogens not in self.implicit_hydrogens:
+                    return False
+                if self.heteroatoms and other.heteroatoms not in self.heteroatoms:
+                    return False
+                return True
+        elif isinstance(other, AnyMetal) and self.neighbors == other.neighbors \
+                and self.hybridization == other.hybridization and self.ring_sizes == other.ring_sizes \
+                and self.implicit_hydrogens == other.implicit_hydrogens and self.heteroatoms == other.heteroatoms:
+            return True
+        return False
+
+    def __hash__(self):
+        return tuple_hash((self.neighbors, self.hybridization, self.ring_sizes, self.implicit_hydrogens,
+                           self.heteroatoms))
+
+
 class ListElement(AnyElement):
     __slots__ = ('_elements', '_numbers')
 
@@ -374,9 +413,6 @@ def copy(self) -> 'ListElement':
         return copy
 
     def __hash__(self):
-        """
-        13bit = 4bit | 1bit | 4bit | 4bit
-        """
         return tuple_hash((self._numbers, self.charge, self.is_radical, self.neighbors, self.hybridization,
                            self.ring_sizes, self.implicit_hydrogens, self.heteroatoms))
 
@@ -395,4 +431,4 @@ def __repr__(self):
         return f'{self.__class__.__name__}([{",".join(self._elements)}])'
 
 
-__all__ = ['QueryElement', 'AnyElement', 'ListElement']
+__all__ = ['QueryElement', 'AnyElement', 'AnyMetal', 'ListElement']