chython 2.19__cp313-cp313-win_amd64.whl

chython/utils/free_wilson.py

@@ -0,0 +1,114 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2022-2026 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 itertools import product
+from typing import Union, List
+from .retro import Tree
+from ..containers import MoleculeContainer, QueryContainer
+from ..periodictable import H
+
+
+def fw_prepare_groups(core: Union[MoleculeContainer, QueryContainer], molecule: MoleculeContainer) -> \
+       List[MoleculeContainer]:
+    """
+    Prepare list of core with connected groups. Hydrogens added to groups for marking connection point.
+    Hydrogens have isotope marks equal to mapping of core atoms.
+    Groups connected multiple times (rings) - contains multiple hydrogens.
+
+    :param core: core structure for searching
+    :param molecule: target structure
+    """
+    try:
+        core_map = next(core.get_mapping(molecule))
+    except StopIteration:
+        return []
+
+    reverse = {v: k for k, v in core_map.items()}
+    cs = set(core_map.values())
+    groups = molecule.substructure(molecule._atoms.keys() - cs, recalculate_hydrogens=False)
+    gs = set(groups)
+
+    cf = molecule.substructure(cs, recalculate_hydrogens=False)
+
+    for n, m, b in molecule.bonds():
+        if n in cs:
+            if m in gs:
+                a = molecule.atom(n)
+                h = H(x=a.x, y=a.y)
+                h._isotope = reverse[n]  # mark mapping to isotope
+                groups.add_bond(groups.add_atom(h, _skip_calculation=True), m, b.copy(), _skip_calculation=True)
+
+                a = molecule.atom(m)
+                h = H(x=a.x, y=a.y)
+                h._isotope = reverse[n]  # mark mapping to isotope
+                cf.add_bond(cf.add_atom(h, _skip_calculation=True), n, b.copy(), _skip_calculation=True)
+        elif m in cs and n in gs:
+            a = molecule.atom(m)
+            h = H(x=a.x, y=a.y)
+            h._isotope = reverse[m]
+            groups.add_bond(groups.add_atom(h, _skip_calculation=True), n, b.copy(), _skip_calculation=True)
+
+            a = molecule.atom(n)
+            h = H(x=a.x, y=a.y)
+            h._isotope = reverse[m]  # mark mapping to isotope
+            cf.add_bond(cf.add_atom(h.copy(), _skip_calculation=True), n, b.copy(), _skip_calculation=True)
+    groups = groups.split()
+    groups.insert(0, cf)
+    return groups
+
+
+def fw_decomposition_tree(groups: List[MoleculeContainer]) -> Tree:
+    assert len(groups) == len(set(groups))
+
+    pred = {}  # directed graph from substructures to superstructures
+    succ = {}
+    for m in groups:
+        pred[m] = set()
+        succ[m] = set()
+
+    for m in groups:
+        for n in groups:
+            if m < n:
+                pred[n].add(m)
+                succ[m].add(n)
+
+    # break triangles
+    scope = {m for m, ns in succ.items() if len(ns) > 1}
+    while scope:
+        m = sorted(scope, key=lambda x: len(pred[x]))[0]
+        s = succ[m]
+        scope.discard(m)
+        while True:
+            for x, y in product((x for x in s if succ[x]), (x for x in s if len(pred[x]) > 1)):
+                if y in succ[x]:
+                    s.discard(y)
+                    pred[y].discard(m)
+                    break
+            else:
+                break
+
+    def _rec_tree(x):
+        return x, [_rec_tree(y) for y in succ[x]]
+
+    m = MoleculeContainer()
+    m.add_atom('H')
+
+    return m, [_rec_tree(x) for x, p in pred.items() if not p]
+
+
+__all__ = ['fw_prepare_groups', 'fw_decomposition_tree']

chython/utils/grid.py

@@ -0,0 +1,130 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2021-2026 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2024 Philippe Gantzer <p.gantzer@icredd.hokudai.ac.jp>
+#  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 itertools import zip_longest
+from typing import List, Optional
+from ..containers import MoleculeContainer
+from ..algorithms.depict import _render_config, _graph_svg
+
+
+def grid_depict(molecules: List[MoleculeContainer], labels: Optional[List[str]] = None, *, cols: int = 3,
+                width=None, height=None, clean2d: bool = True):
+    """
+    Depict molecules grid.
+
+    :param molecules: list of molecules
+    :param labels: optional list of text labels
+    :param cols: number of molecules per row
+    :param width: set svg width param. by default auto-calculated.
+    :param height: set svg height param. by default auto-calculated.
+    :param clean2d: calculate coordinates if necessary.
+    """
+    font_size = _render_config['font_size']
+    symbols_font_style = _render_config['symbols_font_style']
+    font125 = 1.25 * font_size
+    font75 = .75 * font_size
+
+    planes = []
+    render = []
+    render_labels = []
+    shift_y = 0.
+    shift_x = 0.
+    if labels is not None:
+        assert len(molecules) == len(labels)
+        labels = iter(labels)
+
+    if clean2d:
+        for m in molecules:
+            if len(m) > 1:
+                min_x = min(a.x for _, a in m.atoms())
+                max_x = max(a.x for _, a in m.atoms())
+                min_y = min(a.y for _, a in m.atoms())
+                max_y = max(a.y for _, a in m.atoms())
+                if max_y - min_y < .01 and max_x - min_x < 0.01:
+                    m.clean2d()
+
+    for ms in zip_longest(*[iter(molecules)] * cols):
+        row_height = 0.
+        for m in ms:
+            if m is None:
+                break
+            min_y = min(a.y for _, a in m.atoms())
+            max_y = max(a.y for _, a in m.atoms())
+            h = max_y - min_y
+            if row_height < h:  # get height of row
+                row_height = h
+            planes.append([a.xy for _, a in m.atoms()])
+
+        max_x = 0.
+        for m in ms:
+            if m is None:
+                break
+            if labels is not None:
+                render_labels.append(f'    <text x="{max_x:.2f}" y="{-shift_y:.2f}">{next(labels)}</text>')
+                y = shift_y - row_height / 2. - font125  # blank
+            else:
+                y = shift_y - row_height / 2.
+            max_x = m._fix_plane_mean(max_x, y) + 4. * font_size
+            render.append(m.depict(_embedding=True)[:5])
+            if max_x > shift_x:  # get total width
+                shift_x = max_x
+        shift_y -= row_height + 4. * font_size
+
+    # restore planes
+    for m, p in zip(molecules, planes):
+        for (_, a), xy in zip(m.atoms(), p):
+            a.xy = xy
+
+    _width = shift_x - 1.5 * font_size
+    _height = -shift_y - 1.5 * font_size
+    if width is None:
+        width = f'{_width:.2f}cm'
+    if height is None:
+        height = f'{_height:.2f}cm'
+    svg = [f'<svg width="{width}" height="{height}" '
+           f'viewBox="{-font125:.2f} {-font125:.2f} {_width:.2f} {_height:.2f}" '
+           'xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1">']
+    for atoms, bonds, define, masks, uid in render:
+        svg.extend(_graph_svg(atoms, bonds, define, masks, uid, -font125, -font125, _width, _height))
+    svg.append(f'  <g font-size="{font75:.2f}" font-family="{symbols_font_style}">')
+    svg.extend(render_labels)
+    svg.append('  </g>')
+    svg.append('</svg>')
+    return '\n'.join(svg)
+
+
+class GridDepict:
+    """
+    Grid depict for Jupyter notebooks.
+    """
+    def __init__(self, molecules: List[MoleculeContainer], labels: Optional[List[str]] = None, *, cols: int = 3):
+        """
+        :param molecules: list of molecules
+        :param labels: optional list of text labels
+        :param cols: number of molecules per row
+        """
+        self.molecules = molecules
+        self.labels = labels
+        self.cols = cols
+
+    def _repr_svg_(self):
+        return grid_depict(self.molecules, self.labels, cols=self.cols)
+
+
+__all__ = ['grid_depict', 'GridDepict']

chython/utils/retro.py

@@ -0,0 +1,139 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2021-2026 Ramil Nugmanov <nougmanoff@protonmail.com>
+#  Copyright 2021 Alexander Sizov <murkyrussian@gmail.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 MoleculeContainer
+from typing import Tuple, List
+from ..algorithms.depict import _render_config, _graph_svg
+
+
+Tree = Tuple[MoleculeContainer, List['Tree']]
+
+
+def retro_depict(tree: Tree, *, y_gap=3., x_gap=5., width=None, height=None, clean2d: bool = True) -> str:
+    """
+    Depict retrosynthetic tree.
+
+    :param tree: Graph of molecules with recursive structure. Each node is tuple of molecule and list of child nodes.
+        Child nodes list can be empty.
+    :param y_gap: vertical gap between molecules.
+    :param x_gap: horizontal gap between molecules.
+    :param width: set svg width param. by default auto-calculated.
+    :param height: set svg height param. by default auto-calculated.
+    :param clean2d: calculate coordinates if necessary.
+    """
+    font_size = _render_config['font_size']
+    font125 = 1.25 * font_size
+
+    arrows = []
+    columns = [[tree[0]]]
+    current_layer = [(0, x) for x in tree[1]]
+    while current_layer:
+        next_layer = []
+        column = []
+        columns.append(column)
+        for i, (j, (m, ms)) in enumerate(current_layer):
+            column.append(m)
+            arrows.append(j)  # i-th molecule in current column connected to j-th molecule in previous.
+            next_layer.extend((i, x) for x in ms)
+        current_layer = next_layer
+
+    x_shift = 0.
+    c_max_x = 0.
+    c_max_y = 0.
+    arrows = iter(arrows)
+    render = []
+    last_layer = []
+    arrows_coords = []
+    for column in columns:
+        current_layer = []
+
+        if clean2d:
+            for m in column:
+                if len(m) > 1:
+                    min_x = min(a.x for _, a in m.atoms())
+                    max_x = max(a.x for _, a in m.atoms())
+                    min_y = min(a.y for _, a in m.atoms())
+                    max_y = max(a.y for _, a in m.atoms())
+                    if max_y - min_y < .01 and max_x - min_x < 0.01:
+                        m.clean2d()
+
+        heights = [max(a.y for _, a in m.atoms()) - min(a.y for _, a in m.atoms()) for m in column]
+        y_shift = sum(heights) + y_gap * (len(heights) - 1)  # column height with gaps
+        if y_shift > c_max_y:
+            c_max_y = y_shift
+        y_shift /= 2.  # center align
+
+        for m, h in zip(column, heights):
+            plane = [a.xy for _, a in m.atoms()]  # backup
+            mx = m._fix_plane_min(x_shift, -y_shift)
+            if mx > c_max_x:
+                c_max_x = mx
+
+            current_layer.append((mx + 1., y_shift - h / 2.))
+            if x_shift:  # except first column
+                arrows_coords.append((*last_layer[next(arrows)], x_shift - 1., y_shift - h / 2.))
+                y_shift -= h + y_gap
+
+            render.append(m.depict(_embedding=True)[:5])
+            for (_, a), xy in zip(m.atoms(), plane):  # restore
+                a.xy = xy
+
+        x_shift = c_max_x + x_gap  # between columns gap
+        last_layer = current_layer
+
+    _width = c_max_x + 3.0 * font_size
+    _height = c_max_y + 2.5 * font_size
+    box_y = _height / 2.
+    if width is None:
+        width = f'{_width:.2f}cm'
+    if height is None:
+        height = f'{_height:.2f}cm'
+    svg = [f'<svg width="{width}" height="{height}" '
+           f'viewBox="{-font125:.2f} {-box_y:.2f} {_width:.2f} {_height:.2f}" '
+           'xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1">',
+           '  <defs>\n    <marker id="arrow" markerWidth="10" markerHeight="10" '
+           'refX="0" refY="3" orient="auto">\n      <path d="M0,0 L0,6 L9,3"/>\n    </marker>\n  </defs>']
+    for atoms, bonds, define, masks, uid in render:
+        svg.extend(_graph_svg(atoms, bonds, define, masks, uid, -font125, -box_y, _width, _height))
+
+    svg.append('  <g fill="none" stroke="black" stroke-width=".04" marker-end="url(#arrow)">')
+    for x1, y1, x2, y2 in arrows_coords:
+        svg.append(f'    <line x1="{x1:.2f}" y1="{y1:.2f}" x2="{x2:.2f}" y2="{y2:.2f}"/>')
+    svg.append('  </g>')
+    svg.append('</svg>')
+    return '\n'.join(svg)
+
+
+class RetroDepict:
+    """
+    Grid depict for Jupyter notebooks.
+    """
+    def __init__(self, tree: Tree):
+        """
+        :param tree: Graph of molecules with recursive structure.
+            Each node is tuple of molecule and list of child nodes.
+            Child nodes list can be empty.
+        """
+        self.tree = tree
+
+    def _repr_svg_(self):
+        return retro_depict(self.tree)
+
+
+__all__ = ['retro_depict', 'RetroDepict']

chython-2.19.dist-info/METADATA

@@ -0,0 +1,105 @@
+Metadata-Version: 2.4
+Name: chython
+Version: 2.19
+Summary: Library for processing molecules and reactions in python way
+License: LGPLv3
+License-File: LICENSE
+Author: Ramil Nugmanov
+Author-email: nougmanoff@protonmail.com
+Requires-Python: >=3.10
+Classifier: Environment :: Plugins
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
+Classifier: License :: Other/Proprietary License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Provides-Extra: extra-clean2d
+Provides-Extra: extra-clean3d
+Provides-Extra: mapping
+Provides-Extra: png
+Provides-Extra: racer-default
+Provides-Extra: racer-deprecated
+Provides-Extra: rdkit
+Requires-Dist: cdpkit (>=1.2.3) ; extra == "extra-clean3d"
+Requires-Dist: chython-rxnmap (>=2.0) ; extra == "mapping"
+Requires-Dist: jpype1 (>=1.6.0) ; extra == "extra-clean2d"
+Requires-Dist: lazy-object-proxy (>=1.6)
+Requires-Dist: mini-racer (>=0.12.4) ; extra == "racer-default"
+Requires-Dist: numpy (>=1.21.0)
+Requires-Dist: onnxruntime (>=1.16) ; extra == "mapping"
+Requires-Dist: openbabel-wheel (>=3.1.1.22) ; extra == "extra-clean2d"
+Requires-Dist: py-mini-racer (>=0.6.0) ; extra == "racer-deprecated"
+Requires-Dist: pyppeteer (>=2.0.0) ; extra == "png"
+Requires-Dist: rdkit (>=2023.9) ; extra == "rdkit"
+Requires-Dist: scipy (>=1.10) ; extra == "mapping"
+Project-URL: Documentation, https://chython.readthedocs.io
+Project-URL: Homepage, https://github.com/chython/chython
+Description-Content-Type: text/x-rst
+
+Chython [ˈkʌɪθ(ə)n]
+===================
+
+Library for processing molecules and reactions in python way.
+
+Features:
+   - Read/write/convert formats: MDL .RDF (.RXN) and .SDF (.MOL), .MRV, SMILES, INCHI (inchi-trust library), .XYZ, .PDB
+   - Standardize molecules and reactions and valid structures checker
+   - Supported python-magic
+   - Tetrahedron, Allene and CIS-TRANS stereo supported
+   - Perform subgraph search
+   - Build/edit molecules and reactions with Python API
+   - 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/3d depiction with Jupyter support
+   - SMARTS parser with restrictions
+   - Protective groups remover
+   - Common reaction templates collection
+
+Full documentation can be found `here <https://chython.readthedocs.io>`_.
+
+CGRtools
+========
+
+Chython is fork of `CGRtools <https://github.com/stsouko/CGRtools>`_.
+
+Install
+=======
+
+Only python 3.10+.
+
+    pip install chython[racer-default]
+
+Copyright
+=========
+
+* 2014-2026 Ramil Nugmanov nougmanoff@protonmail.com main developer
+
+Contributors
+============
+
+CGRtools contributors are included too.
+
+* Adelia Fatykhova adelik21979@gmail.com
+* Aleksandr Sizov murkyrussian@gmail.com
+* Dinar Batyrshin batyrshin-dinar@mail.ru
+* Dmitrij Zanadvornykh zandmitrij@gmail.com
+* Ravil Mukhametgaleev sonic-mc@mail.ru
+* Tagir Akhmetshin tagirshin@gmail.com
+* Timur Gimadiev timur.gimadiev@gmail.com
+* Zarina Ibragimova
+

chython-2.19.dist-info/RECORD

@@ -0,0 +1,175 @@
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+chython/_functions.py,sha256=M7hf233sOMfPnZBU2qM_wHEA91U8vZS75ImKGEq7XWE,3165
+chython/_java.py,sha256=7xfzzMuqV0A5-s07sPUSyO-sMZ9IgMjvUAnj-sY4j2o,1964
+chython/algorithms/__init__.py,sha256=eNVN6eBm4mTtGVPMesiyyoTpENP4XwZgu7JjcLDIG7U,806
+chython/algorithms/_isomorphism.cp313-win_amd64.pyd,sha256=cQXs6F3tH8pxuTTcwgJBsAnIsADpfxHTOYmKEfSFUdk,148480
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+chython/algorithms/_rings.pyx,sha256=_L7-1X8dkAF6QKUAwyWDEN8oORyLA_sXyXZ_1xqexlY,16619
+chython/algorithms/aromatics/__init__.py,sha256=uSuYDKaZnZ15-Lttsx8emiwqOWDud37RBqdalNqtpOI,939
+chython/algorithms/aromatics/_rules.py,sha256=gYQkJD45IcLnr46Tkr-uJ-Sps-yOboqYQMs2Rnaxnmw,3406
+chython/algorithms/aromatics/kekule.py,sha256=B8bbIL541LkZgnGMdvXQytJ676hIdzGwe8edrxdYQB8,25043
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+chython/algorithms/aromatics/test/test_kekule.py,sha256=7q-t0ryVwMLkLMNjVyHsPIDyv5IV9sQ4yl60dMgw5Zw,5110
+chython/algorithms/aromatics/test/test_thiele.py,sha256=T6Nmmr1H-Me3rpgYP3R_FirEa2MxoTMVRmCaUxGuTEw,8397
+chython/algorithms/aromatics/thiele.py,sha256=qEANH25o-ZhvBQv-Dx6MOTBmQv7DiK2QjVL4iId_9vI,8803
+chython/algorithms/calculate2d/__init__.py,sha256=pj1_m9UatAK0fAtZf7HYNdUR31jE5qpmwn5S_E5zFMM,918
+chython/algorithms/calculate2d/clean2d.js,sha256=CCpXfNK3L7f4AVTuKJ3jAGq2Zh3gZiVt7s1g5W0jwOc,92275
+chython/algorithms/calculate2d/molecule.py,sha256=sSjKZrN6xsfEE23OrF9Hp-nCa0l9fanm3EhvTPMrosE,7194
+chython/algorithms/calculate2d/reaction.py,sha256=Hu1vq0OhnGSCjsQDLerh0rNLk4kfAM-Qw39vtVN0Li0,2358
+chython/algorithms/conformers.py,sha256=YS6VZjGUWcl-xOE-PsPav2Pm3tun5dARPi2ff6sWKoI,4728
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