valiaafo · Dec 18, 2024 · Dec 18, 2024 · Dec 18, 2024 · Dec 23, 2024 · Dec 23, 2024
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/MathHelper.py b/chython/algorithms/calculate2d/MathHelper.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
@@ -1,7 +1,8 @@
 # -*- coding: utf-8 -*-
 #
-#  Copyright 2019-2024 Ramil Nugmanov <nougmanoff@protonmail.com>
-#  Copyright 2019, 2020 Dinar Batyrshin <batyrshin-dinar@mail.ru>
+#  Copyright 2024 Denis Lipatov <denis.lipatov163@gmail.com>
+#  Copyright 2024 Vyacheslav Grigorev <slavick2000@yandex.ru>
+#  Copyright 2024 Timur Gimadiev <timur.gimadiev@gmail.com>
 #  This file is part of chython.
 #
 #  chython is free software; you can redistribute it and/or modify
@@ -17,189 +18,4 @@
 #  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
-from ...exceptions import ImplementationError
-
-
-try:
-    from importlib.resources import files
-except ImportError:  # python3.8
-    from importlib_resources import files
-
-
-if TYPE_CHECKING:
-    from chython import ReactionContainer, MoleculeContainer
-
-try:
-    from py_mini_racer.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
-
-
-class Calculate2DMolecule:
-    __slots__ = ()
-
-    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
-
-        shift_x, shift_y = xy[0]
-        for n, (x, y) in zip(order, xy):
-            plane[n] = (x - shift_x, shift_y - y)
-
-        bonds = []
-        for n, m, _ in self.bonds():
-            xn, yn = plane[n]
-            xm, ym = plane[m]
-            bonds.append(sqrt((xm - xn) ** 2 + (ym - yn) ** 2))
-        if bonds:
-            bond_reduce = sum(bonds) / len(bonds) / .825
-        else:
-            bond_reduce = 1.
-
-        atoms = self._atoms
-        for n, (x, y) in plane.items():
-            a = atoms[n]
-            a._x = x / bond_reduce
-            a._y = y / bond_reduce
-
-        if self.connected_components_count > 1:
-            shift_x = 0.
-            for c in self.connected_components:
-                shift_x = self._fix_plane_mean(shift_x, component=c) + .9
-        self.__dict__.pop('__cached_method__repr_svg_', None)
-
-    def _fix_plane_mean(self: 'MoleculeContainer', shift_x: float, shift_y=0., component=None) -> float:
-        atoms = self._atoms
-        if component is None:
-            component = atoms
-
-        left_atom = atoms[min(component, key=lambda x: atoms[x].x)]
-        right_atom = atoms[max(component, key=lambda x: atoms[x].x)]
-
-        min_x = left_atom.x - shift_x
-        if len(left_atom.atomic_symbol) == 2:
-            min_x -= .2
-
-        max_x = right_atom.x - min_x
-        min_y = min(atoms[x].y for x in component)
-        max_y = max(atoms[x].y for x in component)
-        mean_y = (max_y + min_y) / 2 - shift_y
-        for n in component:
-            a = atoms[n]
-            a._x -= min_x
-            a._y -= mean_y
-
-        if -.18 <= right_atom.y <= .18:
-            factor = right_atom.implicit_hydrogens
-            if factor == 1:
-                max_x += .15
-            elif factor:
-                max_x += .25
-        return max_x
-
-    def _fix_plane_min(self: 'MoleculeContainer', shift_x: float, shift_y=0., component=None) -> float:
-        atoms = self._atoms
-        if component is None:
-            component = atoms
-
-        right_atom = atoms[max(component, key=lambda x: atoms[x].x)]
-        min_x = min(atoms[x].x for x in component) - shift_x
-        max_x = right_atom.x - min_x
-        min_y = min(atoms[x].y for x in component) - shift_y
-
-        for n in component:
-            a = atoms[n]
-            a._x -= min_x
-            a._y -= min_y
-
-        if shift_y - .18 <= right_atom.y <= shift_y + .18:
-            factor = right_atom.implicit_hydrogens
-            if factor == 1:
-                max_x += .15
-            elif factor:
-                max_x += .25
-        return max_x
-
-    def __clean2d_prepare(self: 'MoleculeContainer', entry):
-        w = {n: random() for n in self._atoms}
-        w[entry] = -1
-        smiles, order = self._smiles(w.__getitem__, random=True, charges=False, stereo=False, _return_order=True)
-        return ''.join(smiles).replace('~', '-'), order
-
-
-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
-        signs = []
-        for m in reactants:
-            max_x = m._fix_plane_mean(shift_x)
-            if amount:
-                max_x += .2
-                signs.append(max_x)
-                amount -= 1
-            shift_x = max_x + 1
-        arrow_min = shift_x
-
-        if self.reagents:
-            shift_x += .4
-            for m in self.reagents:
-                max_x = m._fix_plane_min(shift_x, .5)
-                shift_x = max_x + 1
-            shift_x += .4
-            if shift_x - arrow_min < 3:
-                shift_x = arrow_min + 3
-        else:
-            shift_x += 3
-        arrow_max = shift_x - 1
-
-        products = self.products
-        amount = len(products) - 1
-        for m in products:
-            max_x = m._fix_plane_mean(shift_x)
-            if amount:
-                max_x += .2
-                signs.append(max_x)
-                amount -= 1
-            shift_x = max_x + 1
-        self._arrow = (arrow_min, arrow_max)
-        self._signs = tuple(signs)
-        self.flush_cache()
-
-
-__all__ = ['Calculate2DMolecule', 'Calculate2DReaction']
+from .clean2d import Calculate2DMolecule, Calculate2DReaction
diff --git a/chython/algorithms/calculate2d/clean2d.js b/chython/algorithms/calculate2d/clean2d.js
diff --git a/clean2d/README b/clean2d/README