chython · valiaafo · Dec 18, 2024 · Dec 18, 2024 · Dec 18, 2024 · Dec 23, 2024
diff --git a/README.rst b/README.rst
@@ -13,7 +13,7 @@ Features:
    - Produce template based reactions and molecules
    - Atom-to-atom mapping, checking and rule-based fixing
    - Perform MCS search
-   - 2d coordinates generation (based on `SmilesDrawer <https://github.com/reymond-group/smilesDrawer>`_)
+   - 2d coordinates generation 
    - 2d/3d depiction with Jupyter support
    - SMARTS parser with restrictions
    - Protective groups remover

diff --git a/chython/algorithms/calculate2d/Calculate2d.py b/chython/algorithms/calculate2d/Calculate2d.py
diff --git a/chython/algorithms/calculate2d/KKLayout.py b/chython/algorithms/calculate2d/KKLayout.py
diff --git a/chython/algorithms/calculate2d/Properties.py b/chython/algorithms/calculate2d/Properties.py
diff --git a/chython/algorithms/calculate2d/__init__.py b/chython/algorithms/calculate2d/__init__.py
@@ -1,6 +1,9 @@
 # -*- coding: utf-8 -*-
 #
 #  Copyright 2019-2025 Ramil Nugmanov <[email protected]>
+#  Copyright 2024, 2025 Denis Lipatov <[email protected]>
+#  Copyright 2024, 2025 Vyacheslav Grigorev <[email protected]>
+#  Copyright 2024, 2025 Timur Gimadiev <[email protected]>
 #  This file is part of chython.
 #
 #  chython is free software; you can redistribute it and/or modify
@@ -19,5 +22,4 @@
 from .molecule import *
 from .reaction import *
 
-
 __all__ = ['Calculate2DMolecule', 'Calculate2DReaction']
diff --git a/chython/algorithms/calculate2d/clean2d.js b/chython/algorithms/calculate2d/clean2d.js
diff --git a/chython/algorithms/calculate2d/molecule.py b/chython/algorithms/calculate2d/molecule.py
@@ -2,6 +2,9 @@
 #
 #  Copyright 2019-2025 Ramil Nugmanov <[email protected]>
 #  Copyright 2019, 2020 Dinar Batyrshin <[email protected]>
+#  Copyright 2024, 2025 Denis Lipatov <[email protected]>
+#  Copyright 2024, 2025 Vyacheslav Grigorev <[email protected]>
+#  Copyright 2024, 2025 Timur Gimadiev <[email protected]>
 #  This file is part of chython.
 #
 #  chython is free software; you can redistribute it and/or modify
@@ -17,12 +20,12 @@
 #  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 math import sqrt
 from random import random
-from typing import TYPE_CHECKING, Union, Dict
-from ...exceptions import ImplementationError
+from typing import TYPE_CHECKING, Union, Dict, TypeVar, List
 from ...periodictable.base.vector import Vector
-
+from .Calculate2d import calculate2d_coord
 
 try:
     from importlib.resources import files
@@ -31,17 +34,11 @@
 
 
 if TYPE_CHECKING:
-    from chython import MoleculeContainer
-
-try:
-    from py_mini_racer import MiniRacer, JSEvalException
-
-    ctx = MiniRacer()
-    ctx.eval('const self = this')
-    ctx.eval(files(__package__).joinpath('clean2d.js').read_text())
-except RuntimeError:
-    ctx = None
-
+    from ...containers import MoleculeContainer
+    Element = TypeVar('Element')
+    Bond = TypeVar('Bond')
+    Coords = Vector[float, float]
+
 
 class Calculate2DMolecule:
     __slots__ = ()
@@ -52,20 +49,10 @@ def clean2d(self: Union['MoleculeContainer', 'Calculate2DMolecule']):
         """
         Calculate 2d layout of graph. https://pubs.acs.org/doi/10.1021/acs.jcim.7b00425 JS implementation used.
         """
-        if ctx is None:
-            raise ImportError('py_mini_racer is not installed or broken')
         plane = {}
         entry = iter(sorted(self, key=lambda n: len(self._bonds[n])))
-        for _ in range(min(5, len(self))):
-            smiles, order = self.__clean2d_prepare(next(entry))
-            try:
-                xy = ctx.call('$.clean2d', smiles)
-            except JSEvalException:
-                continue
-            break
-        else:
-            raise ImplementationError
-
+        smiles, order = self.__clean2d_prepare(next(entry))
+        xy: List[Coords] = calculate2d_coord(order, self)
         shift_x, shift_y = xy[0]
         for n, (x, y) in zip(order, xy):
             plane[n] = (x - shift_x, shift_y - y)
@@ -144,6 +131,6 @@ def __clean2d_prepare(self: 'MoleculeContainer', entry):
         w[entry] = -1
         smiles, order = self._smiles(w.__getitem__, random=True, charges=False, stereo=False, _return_order=True)
         return ''.join(smiles).replace('~', '-'), order
-
-
-__all__ = ['Calculate2DMolecule']
+    
+    
+__all__ = ['Calculate2DMolecule']
diff --git a/chython/algorithms/calculate2d/polygon.py b/chython/algorithms/calculate2d/polygon.py
@@ -0,0 +1,124 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2024, 2025 Denis Lipatov <[email protected]>
+#  Copyright 2024, 2025 Vyacheslav Grigorev <[email protected]>
+#  Copyright 2024, 2025 Timur Gimadiev <[email protected]>
+#  This file is part of chython.
+#
+#  chython is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU Lesser General Public License as published by
+#  the Free Software Foundation; either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#  GNU Lesser General Public License for more details.
+#
+#  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/>.
+#
+
+"""
+This module introduces the `Polygon` class, designed to perform mathematical 
+calculations relevant to two-dimensional Cartesian coordinate systems and regular polygons. 
+
+The `Polygon` class focuses on properties and calculations related to regular polygons, such as 
+finding the circumradius, calculating central angles, determining the apothem, and identifying 
+the type of polygon based on its number of sides. It also includes static methods for 
+calculating normals to lines defined by two points and for adding, averaging, and mirroring points.
+
+This class provides a comprehensive toolkit for performing geometric computations 
+essential in fields such as computer graphics, physics simulations, and computational chemistry, 
+where precise manipulation and analysis of spatial relationships is required.
+"""
+import math
+
+class Polygon:
+    """
+    The `Polygon` class focuses on properties and calculations related to regular polygons, such as 
+    finding the circumradius, calculating central angles, determining the apothem, and identifying 
+    the type of polygon based on its number of sides. It also includes static methods for 
+    calculating normals to lines defined by two vectors and for adding, averaging, and mirroring 
+    vectors.
+    """
+
+    def __init__(self, edge_number: float) -> None:
+        """
+        Initializes a Polygon with a specified number of edges.
+
+        Parameters:
+        :param edge_number float: 
+                The number of edges (sides) of the polygon.
+        """
+        self.edge_number: float = edge_number
+
+
+    @staticmethod
+    def find_polygon_radius(edge_length: float, edge_number: float) -> float:
+        """
+        Calculates the radius of the circumcircle of a regular polygon.
+
+        Parameters:
+        :param edge_length float: 
+            The length of one edge of the polygon.
+        :param edge_number float: 
+            The number of edges (sides) of the polygon.
+
+        Returns float: 
+            The radius of the circumcircle.
+        """
+        return edge_length / (2 * math.sin(math.pi / edge_number))
+
+
+    @staticmethod
+    def get_central_angle(edge_number: float) -> float:
+        """
+        Calculates the central angle of a regular polygon.
+
+        Parameters:
+        :param edge_number float: 
+            The number of edges (sides) of the polygon.
+
+        Returns float:
+            The central angle in radians.
+        """
+        return math.radians(float(360) / edge_number)
+
+
+    @staticmethod
+    def get_apothem(radius: float, edge_number: float) -> float:
+        """
+        Calculates the apothem of a regular polygon.
+
+        Parameters:
+        :param radius float: 
+            The radius of the circumcircle of the polygon.
+        :param edge_number float: 
+            The number of edges (sides) of the polygon.
+
+        Returns float:
+            The length of the apothem.
+        """
+        return radius * math.cos(math.pi / edge_number)
+
+
+    @staticmethod
+    def get_apothem_from_side_length(length: float, edge_number: float) -> float:
+        """
+        Calculates the apothem of a regular polygon given the side length.
+
+        Parameters:
+        :param length float: 
+            The length of one edge of the polygon.
+        :param edge_number float: 
+            The number of edges (sides) of the polygon.
+
+        Returns float: 
+            The length of the apothem.
+        """
+        radius: float = Polygon.find_polygon_radius(length, edge_number)
+        return Polygon.get_apothem(radius, edge_number)
+
+__all__ = ['Polygon']
+
diff --git a/chython/algorithms/calculate2d/reaction.py b/chython/algorithms/calculate2d/reaction.py
@@ -1,6 +1,9 @@
 # -*- coding: utf-8 -*-
 #
 #  Copyright 2019-2025 Ramil Nugmanov <[email protected]>
+#  Copyright 2024, 2025 Denis Lipatov <[email protected]>
+#  Copyright 2024, 2025 Vyacheslav Grigorev <[email protected]>
+#  Copyright 2024, 2025 Timur Gimadiev <[email protected]>
 #  This file is part of chython.
 #
 #  chython is free software; you can redistribute it and/or modify
@@ -16,28 +19,27 @@
 #  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_CHECKING
 
+try:
+    from importlib.resources import files
+except ImportError:  # python3.8
+    from importlib_resources import files
 
 if TYPE_CHECKING:
-    from chython import ReactionContainer
-
-
+    from ...containers import ReactionContainer
+    
+    
 class Calculate2DReaction:
     __slots__ = ()
 
     def clean2d(self: 'ReactionContainer'):
-        """
-        Recalculate 2d coordinates
-        """
         for m in self.molecules():
             m.clean2d()
         self.fix_positions()
 
     def fix_positions(self: 'ReactionContainer'):
-        """
-        Fix coordinates of molecules in reaction
-        """
         shift_x = 0
         reactants = self.reactants
         amount = len(reactants) - 1
@@ -74,7 +76,7 @@ def fix_positions(self: 'ReactionContainer'):
             shift_x = max_x + 1
         self._arrow = (arrow_min, arrow_max)
         self._signs = tuple(signs)
-        self.flush_cache(keep_molecule_cache=True)
+        self.flush_cache()
 
 
-__all__ = ['Calculate2DReaction']
+__all__ = ['Calculate2DReaction']