chython 2.19__cp313-cp313-win_amd64.whl

chython/containers/chimera.py

@@ -0,0 +1,63 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2025, 2026 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  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/>.
+#
+from .._java import get_cdk
+
+
+class Chimera:
+    __slots__ = ()
+
+    def to_cdk(self):
+        """
+        Convert molecule to CDK Molecule object.
+
+        Due to translation through SMILES string, atom order is not preserved.
+        Use `self.smiles_atoms_order` to map atoms back.
+        """
+        cdk = get_cdk()
+        parser = cdk.smiles.SmilesParser(cdk.DefaultChemObjectBuilder.getInstance())
+        return parser.parseSmiles(str(self))
+
+    def to_openbabel(self):
+        """
+        Convert molecule to OpenBabel OBMol object.
+
+        Due to translation through SMILES string, atom order is not preserved.
+        Use `self.smiles_atoms_order` to map atoms back.
+        """
+        from openbabel import openbabel
+
+        conv = openbabel.OBConversion()
+        conv.SetInFormat('smi')
+        mol = openbabel.OBMol()
+        assert conv.ReadString(mol, str(self)), 'OpenBabel failed to parse smiles'
+        return mol
+
+    def to_indigo(self):
+        """
+        Convert molecule to Indigo molecule object.
+
+        Due to translation through SMILES string, atom order is not preserved.
+        Use `self.smiles_atoms_order` to map atoms back.
+        """
+        from indigo import Indigo
+
+        return Indigo().loadMolecule(str(self))
+
+
+__all__ = ['Chimera']

chython/containers/graph.py

@@ -0,0 +1,199 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2018-2026 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  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/>.
+#
+from abc import ABC, abstractmethod
+from functools import cached_property
+from typing import Dict, Generic, Iterator, Optional, Tuple, TypeVar
+from ..exceptions import AtomNotFound, MappingError, BondNotFound
+
+
+Atom = TypeVar('Atom')
+Bond = TypeVar('Bond')
+
+
+class Graph(Generic[Atom, Bond], ABC):
+    __slots__ = ('_atoms', '_bonds', '__dict__')
+
+    _atoms: Dict[int, Atom]
+    _bonds: Dict[int, Dict[int, Bond]]
+
+    def __init__(self):
+        self._atoms = {}
+        self._bonds = {}
+
+    def atom(self, n: int) -> Atom:
+        return self._atoms[n]
+
+    def has_atom(self, n: int) -> bool:
+        return n in self._atoms
+
+    def atoms(self) -> Iterator[Tuple[int, Atom]]:
+        """
+        iterate over all atoms
+        """
+        return iter(self._atoms.items())
+
+    @property
+    def atoms_count(self) -> int:
+        return len(self._atoms)
+
+    @property
+    def atoms_numbers(self) -> Iterator[int]:
+        return iter(self._atoms)
+
+    def bond(self, n: int, m: int) -> Bond:
+        try:
+            return self._bonds[n][m]
+        except KeyError as e:
+            raise BondNotFound from e
+
+    def has_bond(self, n: int, m: int) -> bool:
+        try:
+            self._bonds[n]  # check if atom exists
+            return n in self._bonds[m]
+        except KeyError:
+            raise AtomNotFound
+
+    def bonds(self) -> Iterator[Tuple[int, int, Bond]]:
+        """
+        iterate other all bonds
+        """
+        seen = set()
+        for n, m_bond in self._bonds.items():
+            seen.add(n)
+            for m, bond in m_bond.items():
+                if m not in seen:
+                    yield n, m, bond
+
+    @cached_property
+    def bonds_count(self) -> int:
+        return sum(len(x) for x in self._bonds.values()) // 2
+
+    @abstractmethod
+    def add_atom(self, atom: Atom, n: Optional[int] = None) -> int:
+        """
+        new atom addition
+        """
+        if n is None:
+            n = max(self._atoms, default=0) + 1
+        elif not isinstance(n, int):
+            raise TypeError('mapping should be integer')
+        elif n in self._atoms:
+            raise MappingError('atom with same number exists')
+
+        self._atoms[n] = atom
+        self._bonds[n] = {}
+        self.flush_cache()
+        return n
+
+    @abstractmethod
+    def add_bond(self, n: int, m: int, bond: Bond):
+        """
+        Add bond.
+        """
+        if n == m:
+            raise MappingError('atom loops impossible')
+        if n not in self._bonds or m not in self._bonds:
+            raise AtomNotFound('atoms not found')
+        if n in self._bonds[m]:
+            raise MappingError('atoms already bonded')
+
+        self._bonds[n][m] = self._bonds[m][n] = bond
+        self.flush_cache()
+
+    def copy(self):
+        """
+        copy of graph
+        """
+        copy = object.__new__(self.__class__)
+        copy._atoms = {n: atom.copy(full=True) for n, atom in self.atoms()}
+        copy._bonds = cb = {}
+        for n, m_bond in self._bonds.items():
+            cb[n] = cbn = {}
+            for m, bond in m_bond.items():
+                if m in cb:  # bond partially exists. need back-connection.
+                    cbn[m] = cb[m][n]
+                else:
+                    cbn[m] = bond.copy(full=True)
+        return copy
+
+    def remap(self, mapping: Dict[int, int]):
+        """
+        Change atom numbers
+
+        :param mapping: mapping of old numbers to the new
+        """
+        if len(mapping) != len(set(mapping.values())) or \
+                not (self._atoms.keys() - mapping.keys()).isdisjoint(mapping.values()):
+            raise ValueError('mapping overlap')
+
+        mg = mapping.get
+        self._atoms = {mg(n, n): atom for n, atom in self.atoms()}
+        self._bonds = {mg(n, n): {mg(m, m): bond for m, bond in m_bond.items()} for n, m_bond in self._bonds.items()}
+        self.flush_cache()
+
+    def union(self, other: 'Graph', *, remap: bool = False, copy: bool = True):
+        """
+        Merge Graphs into one.
+
+        :param remap: if atoms has collisions then remap other graph atoms else raise exception.
+        :param copy: keep original structure and return a new object
+        """
+        if self._atoms.keys() & other._atoms.keys():
+            if not remap:
+                raise MappingError('mapping of graphs is not disjoint')
+            other = other.copy()
+            other.remap({n: i for i, n in enumerate(other, start=max(self._atoms) + 1)})
+        else:
+            other = other.copy()  # make a copy
+        u = self.copy() if copy else self
+        u._atoms.update(other._atoms)
+        u._bonds.update(other._bonds)
+        if not copy:
+            self.flush_cache()
+        return u
+
+    def flush_cache(self):
+        self.__dict__.clear()
+
+    def __copy__(self):
+        return self.copy()
+
+    def __or__(self, other):
+        """
+        G | H is union of graphs
+        """
+        return self.union(other, remap=True)
+
+    def __ior__(self, other):
+        """
+        G =| H is union of graphs
+        """
+        return self.union(other, remap=True, copy=False)
+
+    def __len__(self):
+        return len(self._atoms)
+
+    def __iter__(self) -> Iterator[int]:
+        return iter(self._atoms)
+
+    def __bool__(self):
+        return bool(self._atoms)
+
+
+__all__ = ['Graph']