chython 2.19__cp313-cp313-win_amd64.whl

chython/containers/test/test_molecule.py

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+# -*- coding: utf-8 -*-
+from chython import smiles, MoleculeContainer
+
+
+def test_smiles_parse_ethanol():
+    mol = smiles('CCO')
+    assert len(mol) == 3
+    assert str(mol) == 'CCO'
+
+
+def test_smiles_parse_benzene():
+    mol = smiles('c1ccccc1')
+    assert len(mol) == 6
+    assert str(mol) == 'c1ccccc1'
+
+
+def test_molecule_equality():
+    mol1 = smiles('CCO')
+    mol2 = smiles('OCC')
+    assert mol1 == mol2
+    assert hash(mol1) == hash(mol2)
+
+
+def test_molecule_inequality():
+    mol1 = smiles('CCO')
+    mol2 = smiles('CC=O')
+    assert mol1 != mol2
+
+
+def test_brutto():
+    mol = smiles('CC(=O)Oc1ccccc1C(=O)O')  # aspirin
+    assert mol.brutto == {'C': 9, 'H': 8, 'O': 4}
+
+
+def test_molecular_mass():
+    mol = smiles('O')  # water
+    mass = mol.molecular_mass
+    assert 16 < mass < 20
+
+
+def test_rings():
+    mol = smiles('c1ccc2ccccc2c1')  # naphthalene
+    assert mol.rings_count == 2
+    assert len(mol.sssr) == 2
+
+
+def test_aromatic_rings():
+    mol = smiles('c1ccccc1')
+    assert len(mol.aromatic_rings) == 1
+
+
+def test_connected_components():
+    mol = smiles('[Cl-].[Na+]')
+    assert mol.connected_components_count == 2
+    parts = mol.split()
+    assert len(parts) == 2
+
+
+def test_add_atom_bond():
+    mol = MoleculeContainer()
+    n1 = mol.add_atom('C')
+    n2 = mol.add_atom('C')
+    n3 = mol.add_atom('O')
+    mol.add_bond(n1, n2, 1)
+    mol.add_bond(n2, n3, 1)
+    assert str(mol) == 'CCO'
+
+
+def test_implicit_hydrogens():
+    mol = smiles('C')  # methane
+    atom = mol.atom(next(iter(mol)))
+    assert atom.implicit_hydrogens == 4
+
+
+def test_copy():
+    mol = smiles('CCO')
+    mol2 = mol.copy()
+    assert str(mol) == str(mol2)
+    assert mol is not mol2
+
+
+def test_substructure():
+    mol = smiles('Cc1ccccc1')  # toluene
+    atoms = list(mol)
+    ring_atoms = atoms[1:]
+    sub = mol.substructure(ring_atoms)
+    assert len(sub) == 6
+
+
+def test_union():
+    mol1 = smiles('C')
+    mol2 = smiles('O')
+    merged = mol1.union(mol2, remap=True)
+    assert len(merged) == 2
+
+
+def test_explicify_implicify():
+    mol = smiles('C')
+    n_before = len(mol)
+    mol.explicify_hydrogens()
+    assert len(mol) == 5  # C + 4H
+    mol.implicify_hydrogens()
+    assert len(mol) == n_before
+
+
+def test_pickle():
+    from pickle import loads, dumps
+    mol = smiles('c1ccccc1')
+    data = dumps(mol)
+    mol2 = loads(data)
+    assert str(mol) == str(mol2)
+
+
+def test_format_specifiers():
+    mol = smiles('[CH3:1][OH:2]')
+    s_map = format(mol, 'm')
+    assert ':1]' in s_map or ':2]' in s_map

chython/containers/test/test_pack.py

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+# -*- coding: utf-8 -*-
+from chython import smiles, MoleculeContainer, ReactionContainer, unpack
+
+
+def test_molecule_pack_unpack():
+    mol = smiles('c1ccccc1')
+    data = mol.pack()
+    mol2 = MoleculeContainer.unpack(data)
+    assert str(mol) == str(mol2)
+
+
+def test_molecule_pack_uncompressed():
+    mol = smiles('CCO')
+    data = mol.pack(compressed=False)
+    mol2 = unpack(data, compressed=False)
+    assert str(mol) == str(mol2)
+
+
+def test_molecule_bytes():
+    mol = smiles('[Cu+2]')
+    data = bytes(mol)
+    mol2 = unpack(data)
+    assert str(mol) == str(mol2)
+
+
+def test_pack_preserves_coordinates():
+    mol = smiles('CCO')
+    mol.clean2d()
+    data = mol.pack()
+    mol2 = MoleculeContainer.unpack(data)
+    for n in mol:
+        assert abs(mol.atom(n).x - mol2.atom(n).x) < 0.01
+        assert abs(mol.atom(n).y - mol2.atom(n).y) < 0.01
+
+
+def test_pack_preserves_charge():
+    mol = smiles('[NH4+]')
+    data = mol.pack()
+    mol2 = unpack(data)
+    assert str(mol) == str(mol2)
+
+
+def test_pack_preserves_isotope():
+    mol = smiles('[2H]C([2H])([2H])[2H]')
+    data = mol.pack()
+    mol2 = unpack(data)
+    assert str(mol) == str(mol2)
+
+
+def test_reaction_pack_unpack():
+    rxn = smiles('[CH3:1][OH:2]>>[CH3:1][NH2:3]')
+    data = rxn.pack()
+    rxn2 = ReactionContainer.unpack(data)
+    assert str(rxn) == str(rxn2)
+
+
+def test_pack_len():
+    mol = smiles('CCCCC')
+    data = mol.pack(compressed=False)
+    assert MoleculeContainer.pack_len(data, compressed=False) == 5

chython/containers/test/test_rdkit.py

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+# -*- 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 chython import smiles, from_rdkit_molecule
+from pytest import mark
+from rdkit import Chem
+from rdkit.Chem import AllChem
+
+
+data = [
+    'CCO',
+    'C/C=C/C',
+    'C[C@H](O)CC',
+    'C\C=C/O[C@@H]1OC[C@@H](Oc2ccccc2)[C@@H](O)[C@H]1O\C=C\C',
+    '[nH]1cccc1',
+    'C\C=C\C=C',
+    'C[C@@H](O)[C@H](O)[C@H](C)O'
+]
+
+@mark.parametrize('source', data)
+def test_to_rdkit(source):
+    mol = smiles(source)
+    rd_mol = mol.to_rdkit(keep_mapping=False)
+    rd_mol_mapping = mol.to_rdkit(keep_mapping=True)
+
+    assert format(smiles(Chem.MolToSmiles(rd_mol)), 'h') == format(mol, 'h')
+    assert format(smiles(Chem.MolToSmiles(rd_mol_mapping)), 'm') == format(mol, 'm')
+
+
+@mark.parametrize('source', data)
+def test_from_rdkit(source):
+    assert format(from_rdkit_molecule(Chem.MolFromSmiles(source)), 'h') == format(smiles(source), 'h')
+
+
+def test_coordinates():
+    rd_mol = smiles('CCO').to_rdkit(keep_mapping=False)
+
+    AllChem.Compute2DCoords(rd_mol)
+    mol = from_rdkit_molecule(rd_mol)
+    assert any(a.x for _, a in mol.atoms())
+
+    rd_mol_h = Chem.AddHs(rd_mol)
+    AllChem.EmbedMolecule(rd_mol_h)
+    rd_mol_nh = Chem.RemoveHs(rd_mol_h)
+
+    mol = from_rdkit_molecule(rd_mol_nh)
+    assert hasattr(mol, '_conformers')
+    assert isinstance(mol._conformers, list)
+    assert len(mol._conformers) == 1
+    assert isinstance(mol._conformers[0], dict)
+    assert len(mol._conformers[0]) == 3
+    assert all(tuple(x) for x in mol._conformers[0].values())
+    assert all(len(x) == 3 for x in mol._conformers[0].values())
+    assert all(isinstance(x, float) for x in mol._conformers[0].values() for x in x)
+    assert any(x for x in mol._conformers[0].values() for x in x)

chython/containers/test/test_reaction.py

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+# -*- coding: utf-8 -*-
+from chython import smiles
+
+
+def test_reaction_parse():
+    rxn = smiles('[CH3:1][OH:2]>>[CH3:1][NH2:3]')
+    assert len(rxn.reactants) == 1
+    assert len(rxn.products) == 1
+
+
+def test_reaction_components():
+    rxn = smiles('CCO.CC(=O)O>>CCOC(=O)C.O')
+    assert len(rxn.reactants) == 2
+    assert len(rxn.products) == 2
+
+
+def test_reaction_equality():
+    rxn1 = smiles('[CH3:1][OH:2]>>[CH3:1][NH2:3]')
+    rxn2 = smiles('[CH3:1][OH:2]>>[CH3:1][NH2:3]')
+    assert rxn1 == rxn2
+
+
+def test_reaction_canonicalize():
+    rxn = smiles('CCO.CC(=O)O>>CCOC(=O)C.O')
+    rxn.canonicalize()
+    assert str(rxn)
+
+
+def test_reaction_molecules():
+    rxn = smiles('[CH3:1][OH:2]>>[CH3:1][NH2:3]')
+    mols = list(rxn.molecules())
+    assert len(mols) == 2
+
+
+def test_reaction_pickle():
+    from pickle import loads, dumps
+    rxn = smiles('[CH3:1][OH:2]>>[CH3:1][NH2:3]')
+    data = dumps(rxn)
+    rxn2 = loads(data)
+    assert str(rxn) == str(rxn2)

chython/exceptions.py

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+# -*- coding: utf-8 -*-
+#
+#  Copyright 2017-2026 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/>.
+#
+
+
+class EmptyMolecule(ValueError):
+    """
+    Molecule without atoms
+    """
+
+
+class EmptyReaction(ValueError):
+    """
+    Reaction without molecules
+    """
+
+
+class MappingError(ValueError):
+    """
+    Atom-to-Atom mapping invalid
+    """
+
+
+class AtomNotFound(KeyError):
+    """
+    Bad atom number
+    """
+
+
+class BondNotFound(KeyError):
+    """
+    Bad atoms numbers
+    """
+
+
+class NotChiral(KeyError):
+    """
+    Atom not chiral
+    """
+
+
+class IsChiral(KeyError):
+    """
+    Atom already chiral
+    """
+
+
+class InvalidAromaticRing(ValueError):
+    """
+    Aromatic ring has impossible Kekule structure
+    """
+
+
+class ValenceError(Exception):
+    """
+    Atom has valence error
+    """
+
+
+class IncorrectSmiles(ValueError):
+    """
+    SMILES string invalid
+    """
+
+
+class IncorrectSmarts(IncorrectSmiles):
+    """
+    SMARTS string invalid or unsupported
+    """
+
+
+class ImplementationError(Exception):
+    """
+    Algorithm has errors. Please send example of structure to author for analyze.
+    """
+
+
+class BufferOverflow(BufferError):
+    """
+    Parser buffer overflow
+    """
+
+
+class InvalidV2000(ValueError):
+    """
+    Invalid V2000
+    """
+
+
+class InvalidCharge(ValueError):
+    """
+    Invalid MDL charge
+    """
+
+
+class InvalidMolBlock(ValueError):
+    """
+    Invalid MDL MOL
+    """