chython 2.4__cp312-cp312-win_amd64.whl

chython/files/libinchi/wrapper.py

@@ -0,0 +1,555 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2018-2024 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 ctypes import c_char, c_double, c_short, c_long, c_char_p, c_byte, POINTER, Structure, cdll, byref
+from itertools import count
+from sysconfig import get_platform
+from warnings import warn
+from .._convert import create_molecule
+from ...containers import MoleculeContainer
+from ...containers.bonds import Bond
+from ...exceptions import ValenceError, IsChiral, NotChiral
+from ...periodictable import H as _H
+
+
+try:
+    from importlib.resources import files, as_file
+except ImportError:  # python3.8
+    from importlib_resources import files, as_file
+
+
+H = 1
+
+
+def inchi(data, /, *, ignore_stereo: bool = False, _cls=MoleculeContainer) -> MoleculeContainer:
+    """
+    INCHI string parser
+    """
+    if lib is None:
+        raise ImportError('libINCHI not found')
+
+    structure = INCHIStructure()
+    if lib.GetStructFromINCHI(byref(InputINCHI(data)), byref(structure)):
+        lib.FreeStructFromINCHI(byref(structure))
+        raise ValueError('invalid INCHI')
+
+    atoms, bonds = [], []
+    protium = {}
+    deuterium = {}
+    tritium = {}
+    seen = set()
+    for n in range(structure.num_atoms):
+        seen.add(n)
+        atom = structure.atom[n]
+
+        atoms.append({'element': atom.atomic_symbol, 'charge': atom.charge, 'x': atom.x, 'y': atom.y,
+                      'z': atom.z, 'isotope': atom.isotope, 'is_radical': atom.is_radical,
+                      'implicit_hydrogens': atom.implicit_hydrogens, 'delta_isotope': atom.delta_isotope})
+        if atom.implicit_protium:
+            protium[n] = atom.implicit_protium
+        if atom.implicit_deuterium:
+            deuterium[n] = atom.implicit_deuterium
+        if atom.implicit_tritium:
+            tritium[n] = atom.implicit_tritium
+
+        for k in range(atom.num_bonds):
+            m = atom.neighbor[k]
+            if m in seen:
+                continue
+            order = atom.bond_type[k]
+            if order:
+                bonds.append((n, m, order))
+
+    stereo_atoms = []
+    stereo_allenes = []
+    stereo_cumulenes = []
+    for i in range(structure.num_stereo0D):
+        stereo = structure.stereo0D[i]
+        sign = stereo.sign
+        if sign is not None:
+            if stereo.is_tetrahedral:
+                stereo_atoms.append((stereo.central_atom, stereo.neighbors, sign))
+            elif stereo.is_allene:
+                nn, *_, nm = stereo.neighbors
+                stereo_allenes.append((stereo.central_atom, nn, nm, sign))
+            elif stereo.is_cumulene:
+                nn, n, m, nm = stereo.neighbors
+                stereo_cumulenes.append((n, m, nn, nm, sign))
+
+    lib.FreeStructFromINCHI(byref(structure))
+
+    tmp = {'atoms': atoms, 'bonds': bonds, 'stereo_atoms': stereo_atoms, 'stereo_allenes': stereo_allenes,
+           'stereo_cumulenes': stereo_cumulenes, 'mapping': list(range(1, len(atoms) + 1)),
+           'protium': protium, 'deuterium': deuterium, 'tritium': tritium}
+    mol = create_molecule(tmp, skip_calc_implicit=True, _cls=_cls)
+    postprocess_molecule(mol, tmp, ignore_stereo=ignore_stereo)
+    return mol
+
+
+def postprocess_molecule(molecule, data, *, ignore_stereo=False):
+    atoms = molecule._atoms
+    bonds = molecule._bonds
+
+    # set hydrogen atoms. INCHI designed for hydrogens handling. hope correctly.
+    free = count(len(atoms) + 1)
+    to_add = []
+    for n, atom in atoms.items():
+        # in chython hydrogens never have implicit H. convert to explicit
+        if atom == H and atom.implicit_hydrogens:
+            for _ in range(atom.implicit_hydrogens):
+                to_add.append((n, next(free), _H(implicit_hydrogens=0)))
+            atom._implicit_hydrogens = 0
+
+    for n, p in data['protium'].items():
+        to_add.append((n + 1, next(free), _H(isotope=1, implicit_hydrogens=0)))
+    for n, p in data['deuterium'].items():
+        to_add.append((n + 1, next(free), _H(isotope=2, implicit_hydrogens=0)))
+    for n, p in data['tritium'].items():
+        to_add.append((n + 1, next(free), _H(isotope=3, implicit_hydrogens=0)))
+
+    if to_add:
+        for n, m, a in to_add:
+            atoms[m] = a
+            bonds[n][m] = b = Bond(1)
+            bonds[m] = {n: b}
+        molecule.calc_labels()  # reset labels
+
+    if ignore_stereo or not data['stereo_atoms'] and not data['stereo_cumulenes'] and not data['stereo_allenes']:
+        return
+
+    st = molecule.stereogenic_tetrahedrons
+    sa = molecule.stereogenic_allenes
+    ctc = molecule._stereo_cis_trans_counterpart
+
+    stereo = []
+    for n, ngb, s in data['stereo_atoms']:
+        n += 1
+        if n in st:
+            stereo.append((molecule.add_atom_stereo, n, [x + 1 for x in ngb], s))
+    for n, nn, mn, s in data['stereo_allenes']:
+        n += 1
+        if n in sa:
+            stereo.append((molecule.add_atom_stereo, n, nn + 1, mn + 1, s))
+    for n, m, nn, nm, s in data['stereo_cumulenes']:
+        n += 1
+        if n in ctc:
+            stereo.append((molecule.add_cis_trans_stereo, n, m + 1, nn + 1, nm + 1, s))
+
+    while stereo:
+        fail_stereo = []
+        old_stereo = len(stereo)
+        for f, *args in stereo:
+            try:
+                f(*args, clean_cache=False)
+            except NotChiral:
+                fail_stereo.append((f, *args))
+            except IsChiral:
+                pass
+            except ValenceError:
+                if 'chython_parsing_log' not in molecule.meta:
+                    molecule.meta['chython_parsing_log'] = []
+                molecule.meta['chython_parsing_log'].append('structure has errors, stereo data skipped')
+                molecule.flush_cache()
+                break
+        else:
+            stereo = fail_stereo
+            if len(stereo) == old_stereo:
+                break
+            molecule.flush_stereo_cache()
+            continue
+        break
+
+
+class InputINCHI(Structure):
+    def __init__(self, string, options=None):
+        if options is None:
+            options = b''
+        else:
+            options = ' '.join(f'{opt_flag}{x}' for x in options).encode()
+        super().__init__(string.encode(), options)
+
+    _fields_ = [('szInChI', c_char_p),   # InChI ASCII string to be converted to a strucure
+                ('szOptions', c_char_p)  # InChI options: space-delimited; each is preceded
+                                         # by '/' or '-' depending on OS and compiler
+                ]
+
+
+class Atom(Structure):
+    @property
+    def atomic_symbol(self):
+        return self.elname.decode()
+
+    @property
+    def isotope(self):
+        if 0 < self.isotopic_mass < 9000:  # OVER NINE THOUSANDS!
+            return self.isotopic_mass
+
+    @property
+    def delta_isotope(self):
+        if self.isotopic_mass > 9000:
+            return self.isotopic_mass - 10_000
+
+    @property
+    def is_radical(self):
+        return bool(self.radical)
+
+    @property
+    def implicit_hydrogens(self):
+        return self.num_iso_H[0]
+
+    @property
+    def implicit_protium(self):
+        return self.num_iso_H[1]
+
+    @property
+    def implicit_deuterium(self):
+        return self.num_iso_H[2]
+
+    @property
+    def implicit_tritium(self):
+        return self.num_iso_H[3]
+
+    _fields_ = [('x', c_double), ('y', c_double), ('z', c_double),  # atom coordinates
+                ('neighbor', c_short * 20),    # adjacency list: ordering numbers of the adjacent atoms, >= 0
+                ('bond_type', c_byte * 20),    # inchi_BondType
+                ('bond_stereo', c_byte * 20),  # inchi_BondStereo2D; negative if the sharp end points to opposite atom
+                ('elname', c_char * 6),        # zero-terminated chemical element name: "H", "Si", etc.
+                ('num_bonds', c_short),        # number of neighbors, bond types and bond stereo in the adjacency list
+                ('num_iso_H', c_byte * 4),     # implicit hydrogen atoms
+                                               # [0]: number of implicit non-isotopic H
+                                               # (exception: num_iso_H[0]=-1 means INCHI adds implicit H automatically),
+                                               # [1]: number of implicit isotopic 1H (protium),
+                                               # [2]: number of implicit 2H (deuterium),
+                                               # [3]: number of implicit 3H (tritium)
+                ('isotopic_mass', c_short),    # 0 => non-isotopic; isotopic mass or 10000 + mass - average atomic mass
+                ('radical', c_byte),           # inchi_Radical,
+                ('charge', c_byte)]            # positive or negative; 0 => no charge
+
+
+class Stereo0D(Structure):
+    @property
+    def is_tetrahedral(self):
+        return self.type == 2
+
+    @property
+    def is_allene(self):
+        return self.type == 3
+
+    @property
+    def is_cumulene(self):
+        return self.type == 1
+
+    @property
+    def neighbors(self):
+        return tuple(self.neighbor)
+
+    @property
+    def sign(self):
+        if self.parity == 1:
+            return True
+        elif self.parity == 2:
+            return False
+
+    _fields_ = [('neighbor', c_short * 4),  # 4 atoms always
+                ('central_atom', c_short),  # central tetrahedral atom or a central atom of allene; otherwise NO_ATOM
+                ('type', c_byte),           # inchi_StereoType0D
+                ('parity', c_byte)]         # inchi_StereoParity0D
+
+
+class INCHIStructure(Structure):
+    _fields_ = [('atom', POINTER(Atom)),          # array of num_atoms elements
+                ('stereo0D', POINTER(Stereo0D)),  # array of num_stereo0D 0D stereo elements or NULL
+                ('num_atoms', c_short),           # number of atoms in the structure
+                ('num_stereo0D', c_short),        # number of 0D stereo elements
+                ('szMessage', c_char_p),          # Error/warning ASCII message
+                ('szLog', c_char_p),              # log-file ASCII string, contains a human-readable list
+                                                  # of recognized options and possibly an Error/warn message
+                ('WarningFlags', (c_long * 2) * 2)]
+
+# copy-pasted from INCHI-API
+#  * Notes: 1. Atom ordering numbers (i, k, and atom[i].neighbor[j] below)
+#  *           start from zero; max. ordering number is (num_atoms-1).
+#  *        2. inchi_Atom atom[i] is connected to the atom[atom[i].neighbor[j]]
+#  *           by a bond that has type atom[i].bond_type[j] and 2D stereo type
+#  *           atom[i].bond_stereo[j] (in case of no stereo
+#  *           atom[i].bond_stereo[j] = INCHI_BOND_STEREO_NONE)
+#  *           Index j is in the range 0 <= j <= (atom[i].num_bonds-1)
+#  *        3. Any connection (represented by atom[i].neighbor[j],
+#  *           atom[i].bond_type[j], and atom[i].bond_stereo[j])
+#  *           should be present in one or both adjacency list:
+#  *             if k = atom[i].neighbor[j] then i may or may not be present in
+#  *           atom[k].neighbor[] list. For example, the adjacency lists may be
+#  *           populated with only such neighbors that atom[i].neighbor[j] < i
+#  *           All elements of an adjacency list must be different, that is,
+#  *           a bond must be specified in an adjacency list only once.
+#  *        4. in Molfiles usually
+#  *           (number of implicit H) = Valence - SUM(bond_type[])
+#  *        5. Seemingly illogical order of the inchi_Atom members was
+#  *           chosen in an attempt to avoid alignment problems when
+#  *           accessing inchi_Atom from unrelated to C programming
+#  *           languages such as Visual Basic.
+#  *******************************************************************/
+#
+# /*******************************************************************
+#     0D Stereo Parity and Type definitions
+#  *******************************************************************
+#             Note:
+#             =====
+#             o Below #A is the ordering number of atom A, starting from 0
+#             o See parity values corresponding to 'o', 'e', and 'u' in
+#               inchi_StereoParity0D definition below)
+#
+#            =============================================
+#             stereogenic bond >A=B< or cumulene >A=C=C=B<
+#            =============================================
+#
+#                                  neighbor[4]  : {#X,#A,#B,#Y} in this order
+#      X                           central_atom : NO_ATOM
+#       \            X      Y      type         : INCHI_StereoType_DoubleBond
+#        A==B         \    /
+#            \         A==B
+#             Y
+#
+#     parity= 'e'    parity= 'o'   unknown parity = 'u'
+#
+#     Limitations:
+#     ============
+#     o Atoms A and B in cumulenes MUST be connected by a chain of double bonds;
+#       atoms A and B in a stereogenic 'double bond' may be connected by a double,
+#       single, or alternating bond.
+#     o One atom may belong to up to 3 stereogenic bonds (i.g. in a fused
+#       aromatic structure).
+#     o Multiple stereogenic bonds incident to any given atom should
+#       either all except possibly one have (possibly different) defined
+#       parities ('o' or 'e') or should all have an unknown parity 'u'.
+#
+#       Note on parities of alternating stereobonds
+#       ===========================================
+#                                                      D--E
+#       In large rings  (see Fig. 1, all              //   \\
+#       atoms are C) all alternating bonds         B--C      F--G
+#       are treated as stereogenic.              //              \\
+#       To avoid "undefined" bond parities      A                  H
+#       for bonds BC, DE, FG, HI, JK, LM, AN     \               /
+#       it is recommended to mark them with       N==M       J==I
+#       parities.                                     \     /
+#                                                       L==K    Fig. 1
+#       Such a marking will make
+#       the stereochemical layer unambiguous
+#       and it will be different from the          B--C      F--G
+#       stereochemical layer of the second       //   \\   //    \\
+#       structure (Fig. 2).                     A      D--E        H
+#                                                \               /
+#                                                 N==M       J==I
+#       By default, double and alternating            \     /
+#       bonds in 8-member and greater rings             L==K    Fig. 2
+#       are treated by InChI as stereogenic.
+#
+#
+#            =============================================
+#             tetrahedral atom
+#            =============================================
+#
+#    4 neighbors
+#
+#             X                    neighbor[4] : {#W, #X, #Y, #Z}
+#             |                    central_atom: #A
+#          W--A--Y                 type        : INCHI_StereoType_Tetrahedral
+#             |
+#             Z
+#    parity: if (X,Y,Z) are clockwize when seen from W then parity is 'e' otherwise 'o'
+#    Example (see AXYZW above): if W is above the plane XYZ then parity = 'e'
+#
+#    3 neighbors
+#
+#               Y          Y       neighbor[4] : {#A, #X, #Y, #Z}
+#              /          /        central_atom: #A
+#          X--A  (e.g. O=S   )     type        : INCHI_StereoType_Tetrahedral
+#              \          \
+#               Z          Z
+#
+#    parity: if (X,Y,Z) are clockwize when seen from A then parity is 'e',
+#                                                           otherwise 'o'
+#    unknown parity = 'u'
+#    Example (see AXYZ above): if A is above the plane XYZ then parity = 'e'
+#    This approach may be used also in case of an implicit H attached to A.
+#
+#            =============================================
+#             allene
+#            =============================================
+#
+#        X       Y                 neighbor[4]  : {#X,#A,#B,#Y}
+#         \     /                  central_atom : #C
+#          A=C=B                   type         : INCHI_StereoType_Allene
+#
+#                                       Y      X
+#                                       |      |
+#      when seen from A along A=C=B:  X-A    Y-A
+#
+#                           parity:   'e'    'o'
+#
+#    parity: if A, B, Y are clockwise when seen from X then parity is 'e',
+#                                                           otherwise 'o'
+#    unknown parity = 'u'
+#    Example (see XACBY above): if X on the diagram is above the plane ABY
+#                                                       then parity is 'o'
+#
+#    Limitations
+#    ===========
+#    o Atoms A and B in allenes MUST be connected by a chain of double bonds;
+#
+#
+#    How InChI uses 0D parities
+#    ==========================
+#
+#    1. 0D parities are used if all atom coordinates are zeroes.
+#
+#    In addition to that:
+#
+#    2. 0D parities are used for Stereobonds, Allenes, or Cumulenes if:
+#
+#    2a. A bond to the end-atom is shorter than MIN_BOND_LEN=0.000001
+#    2b. A ratio of two bond lengths to the end-atom is smaller than MIN_SINE=0.03
+#    2c. In case of a linear fragment X-A=B end-atom A is treated as satisfying 2a-b
+#
+#        0D parities are used if 2a or 2b or 2c applies to one or both end-atoms.
+#
+#    3. 0D parities are used for Tetrahedral Atoms if at least one of 3a-c is true:
+#
+#    3a. One of bonds to the central atom is shorter than MIN_BOND_LEN=0.000001
+#    3b. A ratio of two bond lengths to the central atom is smaller than MIN_SINE=0.03
+#    3c. The four neighbors are almost in one plane or the central atom and
+#        its only 3 explicit neighbors are almost in one plane
+#
+#    Notes on 0D parities and 'undefined' stereogenic elements
+#    =========================================================
+#
+#    If 0D parity is to be used according to 1-3 but    CH3     CH3
+#    has not been provided then the corresponding         \    /
+#    stereogenic element is considered 'undefined'.        C=CH
+#                                                         /
+#    For example, if in the structure (Fig. 3)           H
+#    the explicit H has been moved so that it                Fig. 3
+#    has same coordinates as atom >C= (that is,
+#    the length of the bond H-C became zero)
+#    then the double bond is assigned 'undefined'       CH3      CH3
+#    parity which by default is omitted from the          \     /
+#    Identifier.                                           CH=CH
+#
+#    However, the structure on Fig. 4 will have double        Fig. 4
+#    bond parity 'o' and its parity in the Identifier is (-).
+#
+#    Notes on 0D parities in structures containing metals
+#    ====================================================
+#    Since InChI disconnects bonds to metals the 0D parities upon the
+#    disconnection may change in several different ways:
+#
+#    1) previously non-stereogenic bond may become stereogenic:
+#
+#          \     /                            \     /
+#           CH==CH          disconnection      CH==CH
+#            \ /               ======>
+#             M                                  M
+#
+#      before the disconnection:    after the disconnection:
+#      atoms C have valence=5 and   the double bond may become
+#      the double bond is not       stereogenic
+#      recognized as stereogenic
+#
+#    2) previously stereogenic bond may become non-stereogenic:
+#
+#        M                           M(+)
+#         \    /                             /
+#          N==C      disconnection    (-)N==C
+#              \        ======>              \
+#
+#    3) Oddball structures, usually resulting from projecting 3D
+#       structures on the plane, may contain fragment like that
+#       depicted on Fig. 5:
+#
+#               M   A                      M   A
+#               |\ /   B                      /   B
+#               | X   /     disconnection    /   /
+#               |/ \ /         ======>      /   /
+#               C===C                      C===C
+#              Fig. 5
+#      (X stands for bond intersection)
+#
+#      A-C=C-B parity is              A-C=C-B parity is
+#      trans (e)                      cis (o) or undefined
+#      because the bond               because C valence = 3,
+#      orientation is same            not 4.
+#      as on Fig, 6 below:
+#
+#           A       M
+#            \     /     Removal of M from the structure
+#             C===C      on Fig. 5 changes the geometry from trans
+#            /     \     to cis.
+#           M'      B    Removal of M and M' from the structure
+#           Fig. 6       on Fig. 6 does not change the A-C=C-B
+#                        geometry: it is trans.
+#
+#    To resolve the problem InChI API accepts the second parity
+#    corresponding to the metal-disconnected structure.
+#    To store both bond parities use left shift by 3 bits:
+#
+#    inchi_Stereo0D::parity = ParityOfConnected | (ParityOfDisconnected<<3)
+#
+#    In case when only disconnected structure parity exists set
+#    ParityOfConnected = INCHI_PARITY_UNDEFINED.
+#    This is the only case when INCHI_PARITY_UNDEFINED parity
+#    may be fed to the InChI.
+#
+#    In cases when the bond parity in a disconnected structure exists and
+#    differs from the parity in the connected structure the atoms A and B
+#    should be non-metals.
+#
+
+
+lib = None
+
+platform = get_platform()
+if platform == 'win-amd64':
+    opt_flag = '/'
+    libname = 'libinchi.dll'
+elif platform == 'linux-x86_64':
+    opt_flag = '-'
+    libname = 'libinchi.so'
+elif platform.startswith('macosx') and platform.endswith('x86_64'):
+    opt_flag = '-'
+    libname = 'libinchi.dynlib'
+elif platform.startswith('macosx') and platform.endswith('arm64'):
+    opt_flag = '-'
+    libname = 'libinchi_arm64.dylib'
+else:
+    warn('unsupported platform for libinchi', ImportWarning)
+    libname = None
+
+if libname:
+    file = files(__package__).joinpath(libname)
+    if file.is_file():
+        with as_file(file) as f:
+            try:
+                lib = cdll.LoadLibrary(str(f))
+            except OSError:
+                warn('libinchi loading problem', ImportWarning)
+    else:
+        warn('broken package installation. libinchi not found', ImportWarning)
+
+
+__all__ = ['inchi']

chython/files/mdl/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+#
+#  Copyright 2017-2024 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 .mol import parse_mol_v2000
+from .emol import parse_mol_v3000
+from .rxn import parse_rxn_v2000
+from .erxn import parse_rxn_v3000
+from .stereo import postprocess_molecule
+from .read import MDLRead
+from .write import MOLWrite, EMOLWrite