Source code for MDAnalysis.converters.RDKit

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# MDAnalysis ---
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# (see the file AUTHORS for the full list of names)
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# Please cite your use of MDAnalysis in published work:
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787

"""RDKit molecule I/O --- :mod:`MDAnalysis.converters.RDKit`

Read coordinates data from an `RDKit <>`__ :class:`rdkit.Chem.rdchem.Mol` with
:class:`RDKitReader` into an MDAnalysis Universe. Convert it back to a
:class:`rdkit.Chem.rdchem.Mol` with :class:`RDKitConverter`.


To read an RDKit molecule and then convert the AtomGroup back to an RDKit

    >>> from rdkit import Chem
    >>> import MDAnalysis as mda
    >>> mol = Chem.MolFromMol2File("docking_poses.mol2", removeHs=False)
    >>> u = mda.Universe(mol)
    >>> u
    <Universe with 42 atoms>
    >>> u.trajectory
    <RDKitReader with 10 frames of 42 atoms>
    >>> u.atoms.convert_to("RDKIT")
    <rdkit.Chem.rdchem.Mol object at 0x7fcebb958148>

.. warning::
    The RDKit converter is currently *experimental* and may not work as
    expected for all molecules. Currently the converter accurately
    infers the structures of approximately 99% of the `ChEMBL27`_ dataset.
    Work is currently ongoing on further improving this and updates to the
    converter are expected in future releases of MDAnalysis.
    Please see `Issue #3339`_ and the `RDKitConverter benchmark`_ for more


.. autoclass:: RDKitReader

.. autoclass:: RDKitConverter

.. autofunction:: _infer_bo_and_charges

.. autofunction:: _standardize_patterns

.. autofunction:: _rebuild_conjugated_bonds

.. Links

.. _`ChEMBL27`:
.. _`Issue #3339`:
.. _`RDKitConverter benchmark`:

import warnings
import copy
from functools import lru_cache
from io import StringIO

import numpy as np

from ..exceptions import NoDataError
from ..core.topologyattrs import _TOPOLOGY_ATTRS
from ..coordinates import memory
from ..coordinates import base
from ..coordinates.PDB import PDBWriter

    from rdkit import Chem
    from rdkit.Chem import AllChem
except ImportError:
        1: Chem.BondType.SINGLE,
        1.5: Chem.BondType.AROMATIC,
        "ar": Chem.BondType.AROMATIC,
        2: Chem.BondType.DOUBLE,
        3: Chem.BondType.TRIPLE,
    # add string version of the key for each bond
    RDBONDORDER.update({str(key): value for key, value in RDBONDORDER.items()})
        "altLocs": "AltLoc",
        "chainIDs": "ChainId",
        "icodes": "InsertionCode",
        "names": "Name",
        "occupancies": "Occupancy",
        "resnames": "ResidueName",
        "resids": "ResidueNumber",
        "segindices": "SegmentNumber",
        "tempfactors": "TempFactor",
    PERIODIC_TABLE = Chem.GetPeriodicTable()

_deduce_PDB_atom_name = PDBWriter(StringIO())._deduce_PDB_atom_name

[docs]class RDKitReader(memory.MemoryReader): """Coordinate reader for RDKit. .. versionadded:: 2.0.0 """ format = 'RDKIT' # Structure.coordinates always in Angstrom units = {'time': None, 'length': 'Angstrom'} @staticmethod def _format_hint(thing): """Can this reader read *thing*?""" try: from rdkit import Chem except ImportError: # if we can't import rdkit, it's probably not rdkit return False else: return isinstance(thing, Chem.Mol) def __init__(self, filename, **kwargs): """Read coordinates from an RDKit molecule. Each conformer in the original RDKit molecule will be read as a frame in the resulting universe. Parameters ---------- filename : rdkit.Chem.rdchem.Mol RDKit molecule """ n_atoms = filename.GetNumAtoms() coordinates = np.array([ conf.GetPositions() for conf in filename.GetConformers()], dtype=np.float32) if coordinates.size == 0: warnings.warn("No coordinates found in the RDKit molecule") coordinates = np.empty((1, n_atoms, 3), dtype=np.float32) coordinates[:] = np.nan super(RDKitReader, self).__init__(coordinates, order='fac', **kwargs)
[docs]class RDKitConverter(base.ConverterBase): """Convert MDAnalysis :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` to RDKit :class:`~rdkit.Chem.rdchem.Mol` MDanalysis attributes are stored in each RDKit :class:`~rdkit.Chem.rdchem.Atom` of the resulting molecule in two different ways: * in an :class:`~rdkit.Chem.rdchem.AtomPDBResidueInfo` object available through the :meth:`~rdkit.Chem.rdchem.Atom.GetMonomerInfo` method if it's an attribute that is typically found in a PDB file, * directly as an atom property available through the :meth:`~rdkit.Chem.rdchem.Atom.GetProp` methods for the others. Supported attributes: +-----------------------+-------------------------------------------+ | MDAnalysis attribute | RDKit | +=======================+===========================================+ | altLocs | atom.GetMonomerInfo().GetAltLoc() | +-----------------------+-------------------------------------------+ | chainIDs | atom.GetMonomerInfo().GetChainId() | +-----------------------+-------------------------------------------+ | icodes | atom.GetMonomerInfo().GetInsertionCode() | +-----------------------+-------------------------------------------+ | names | atom.GetMonomerInfo().GetName() | | | atom.GetProp("_MDAnalysis_name") | +-----------------------+-------------------------------------------+ | occupancies | atom.GetMonomerInfo().GetOccupancy() | +-----------------------+-------------------------------------------+ | resnames | atom.GetMonomerInfo().GetResidueName() | +-----------------------+-------------------------------------------+ | resids | atom.GetMonomerInfo().GetResidueNumber() | +-----------------------+-------------------------------------------+ | segindices | atom.GetMonomerInfo().GetSegmentNumber() | +-----------------------+-------------------------------------------+ | tempfactors | atom.GetMonomerInfo().GetTempFactor() | +-----------------------+-------------------------------------------+ | charges | atom.GetDoubleProp("_MDAnalysis_charge") | +-----------------------+-------------------------------------------+ | indices | atom.GetIntProp("_MDAnalysis_index") | +-----------------------+-------------------------------------------+ | segids | atom.GetProp("_MDAnalysis_segid") | +-----------------------+-------------------------------------------+ | types | atom.GetProp("_MDAnalysis_type") | +-----------------------+-------------------------------------------+ Example ------- To access MDAnalysis properties:: >>> import MDAnalysis as mda >>> from MDAnalysis.tests.datafiles import PDB_full >>> u = mda.Universe(PDB_full) >>> mol = u.select_atoms('resname DMS').convert_to('RDKIT') >>> mol.GetAtomWithIdx(0).GetMonomerInfo().GetResidueName() 'DMS' To create a molecule for each frame of a trajectory:: from MDAnalysisTests.datafiles import PSF, DCD from rdkit.Chem.Descriptors3D import Asphericity u = mda.Universe(PSF, DCD) elements = mda.topology.guessers.guess_types(u.atoms.names) u.add_TopologyAttr('elements', elements) ag = u.select_atoms("resid 1-10") for ts in u.trajectory: mol = ag.convert_to("RDKIT") x = Asphericity(mol) Notes ----- The converter requires the :class:`~MDAnalysis.core.topologyattrs.Elements` attribute to be present in the topology, else it will fail. It also requires the `bonds` attribute, although they will be automatically guessed if not present. Hydrogens should be explicit in the topology file. If this is not the case, use the parameter ``NoImplicit=False`` when using the converter to allow implicit hydrogens and disable inferring bond orders and charges. Since one of the main use case of the converter is converting trajectories and not just a topology, creating a new molecule from scratch for every frame would be too slow so the converter uses a caching system. The cache only stores the 2 most recent AtomGroups that were converted, and is sensitive to the arguments that were passed to the converter. The number of objects cached can be changed with the function :func:`set_converter_cache_size`. However, ``ag.convert_to("RDKIT")`` followed by ``ag.convert_to("RDKIT", NoImplicit=False)`` will not use the cache since the arguments given are different. You can pass a ``cache=False`` argument to the converter to bypass the caching system. The ``_MDAnalysis_index`` property of the resulting molecule corresponds to the index of the specific :class:`~MDAnalysis.core.groups.AtomGroup` that was converted, which may not always match the ``index`` property. To get a better understanding of how the converter works under the hood, please refer to the following RDKit UGM presentation: * `Video (4:55 to 8:05) <>`__ * `Slides <>`__ There are some molecules containing specific patterns that the converter cannot currently tackle correctly. See `Issue #3339 <>`__ for more info. .. versionadded:: 2.0.0 .. versionchanged:: 2.2.0 Improved the accuracy of the converter. Atoms in the resulting molecule now follow the same order as in the AtomGroup. The output of ``atom.GetMonomerInfo().GetName()`` now follows the guidelines for PDB files while the original name is still available through ``atom.GetProp("_MDAnalysis_name")`` """ lib = 'RDKIT' units = {'time': None, 'length': 'Angstrom'}
[docs] def convert(self, obj, cache=True, NoImplicit=True, max_iter=200, force=False): """Write selection at current trajectory frame to :class:`~rdkit.Chem.rdchem.Mol`. Parameters ----------- obj : :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` cache : bool Use a cached copy of the molecule's topology when available. To be used, the cached molecule and the new one have to be made from the same AtomGroup selection and with the same arguments passed to the converter NoImplicit : bool Prevent adding hydrogens to the molecule max_iter : int Maximum number of iterations to standardize conjugated systems. See :func:`_rebuild_conjugated_bonds` force : bool Force the conversion when no hydrogens were detected but ``NoImplicit=True``. Useful for inorganic molecules mostly. """ try: from rdkit import Chem except ImportError: raise ImportError("RDKit is required for the RDKitConverter but " "it's not installed. Try installing it with \n" "conda install -c conda-forge rdkit") try: # make sure to use atoms (Issue 46) ag = obj.atoms except AttributeError: raise TypeError("No `atoms` attribute in object of type {}, " "please use a valid AtomGroup or Universe".format( type(obj))) from None # parameters passed to atomgroup_to_mol kwargs = dict(NoImplicit=NoImplicit, max_iter=max_iter, force=force) if cache: mol = atomgroup_to_mol(ag, **kwargs) mol = copy.deepcopy(mol) else: mol = atomgroup_to_mol.__wrapped__(ag, **kwargs) # add a conformer for the current Timestep if hasattr(ag, "positions"): if np.isnan(ag.positions).any(): warnings.warn("NaN detected in coordinates, the output " "molecule will not have 3D coordinates assigned") else: # assign coordinates conf = Chem.Conformer(mol.GetNumAtoms()) for atom in mol.GetAtoms(): idx = atom.GetIdx() xyz = ag.positions[idx].astype(float) conf.SetAtomPosition(idx, xyz) mol.AddConformer(conf) # assign R/S to atoms and Z/E to bonds Chem.AssignStereochemistryFrom3D(mol) Chem.SetDoubleBondNeighborDirections(mol) return mol
@lru_cache(maxsize=2) def atomgroup_to_mol(ag, NoImplicit=True, max_iter=200, force=False): """Converts an AtomGroup to an RDKit molecule without coordinates. Parameters ----------- ag : MDAnalysis.core.groups.AtomGroup The AtomGroup to convert NoImplicit : bool Prevent adding hydrogens to the molecule and allow bond orders and formal charges to be guessed from the valence of each atom. max_iter : int Maximum number of iterations to standardize conjugated systems. See :func:`_rebuild_conjugated_bonds` force : bool Force the conversion when no hydrogens were detected but ``NoImplicit=True``. Mostly useful for inorganic molecules. """ try: elements = ag.elements except NoDataError: raise AttributeError( "The `elements` attribute is required for the RDKitConverter " "but is not present in this AtomGroup. Please refer to the " "documentation to guess elements from other attributes or " "type `help(MDAnalysis.topology.guessers)`") from None if "H" not in ag.elements: if force: warnings.warn( "No hydrogen atom found in the topology. " "Forcing to continue the conversion." ) elif NoImplicit: raise AttributeError( "No hydrogen atom could be found in the topology, but the " "converter requires all hydrogens to be explicit. You can use " "the parameter ``NoImplicit=False`` when using the converter " "to allow implicit hydrogens and disable inferring bond " "orders and charges. You can also use ``force=True`` to " "ignore this error.") # attributes accepted in PDBResidueInfo object pdb_attrs = {} for attr in RDATTRIBUTES.keys(): if hasattr(ag, attr): pdb_attrs[attr] = getattr(ag, attr) resnames = pdb_attrs.get("resnames", None) if resnames is None: def get_resname(idx): return "" else: def get_resname(idx): return resnames[idx] other_attrs = {} for attr in ["charges", "segids", "types", "names"]: if hasattr(ag, attr): other_attrs[attr] = getattr(ag, attr) mol = Chem.RWMol() # map index in universe to index in mol atom_mapper = {} for i, (atom, element) in enumerate(zip(ag, elements)): # create atom rdatom = Chem.Atom(element.capitalize()) # enable/disable adding implicit H to the molecule rdatom.SetNoImplicit(NoImplicit) # add PDB-like properties mi = Chem.AtomPDBResidueInfo() for attr, values in pdb_attrs.items(): _add_mda_attr_to_rdkit(attr, values[i], mi, get_resname(i)) rdatom.SetMonomerInfo(mi) # other properties for attr in other_attrs.keys(): value = other_attrs[attr][i] attr = "_MDAnalysis_%s" % _TOPOLOGY_ATTRS[attr].singular _set_atom_property(rdatom, attr, value) _set_atom_property(rdatom, "_MDAnalysis_index", i) # add atom index = mol.AddAtom(rdatom) atom_mapper[atom.ix] = index try: ag.bonds except NoDataError: warnings.warn( "No `bonds` attribute in this AtomGroup. Guessing bonds based " "on atoms coordinates") ag.guess_bonds() for bond in ag.bonds: try: bond_indices = [atom_mapper[i] for i in bond.indices] except KeyError: continue bond_type = RDBONDORDER.get(bond.order, Chem.BondType.SINGLE) mol.AddBond(*bond_indices, bond_type) mol.UpdatePropertyCache(strict=False) if NoImplicit: # infer bond orders and formal charges from the connectivity _infer_bo_and_charges(mol) mol = _standardize_patterns(mol, max_iter) # reorder atoms to match MDAnalysis, since the reactions from # _standardize_patterns will mess up the original order order = np.argsort([atom.GetIntProp("_MDAnalysis_index") for atom in mol.GetAtoms()]) mol = Chem.RenumberAtoms(mol, order.astype(int).tolist()) # sanitize if possible err = Chem.SanitizeMol(mol, catchErrors=True) if err: warnings.warn("Could not sanitize molecule: " f"failed during step {err!r}") return mol def set_converter_cache_size(maxsize): """Set the maximum cache size of the RDKit converter Parameters ---------- maxsize : int or None If int, the cache will only keep the ``maxsize`` most recent conversions in memory. Using ``maxsize=None`` will remove all limits to the cache size, i.e. everything is cached. """ global atomgroup_to_mol # pylint: disable=global-statement atomgroup_to_mol = lru_cache(maxsize=maxsize)(atomgroup_to_mol.__wrapped__) def _add_mda_attr_to_rdkit(attr, value, mi, resname=""): """Converts an MDAnalysis atom attribute into the RDKit equivalent and stores it into an RDKit :class:`~rdkit.Chem.rdchem.AtomPDBResidueInfo`. Parameters ---------- attr : str Name of the atom attribute in MDAnalysis in the singular form value : object, or np.float Attribute value as found in the AtomGroup mi : rdkit.Chem.rdchem.AtomPDBResidueInfo MonomerInfo object that will store the relevant atom attributes resname : str Residue name of the atom, if available """ if isinstance(value, np.generic): # convert numpy types to python standard types value = value.item() if attr == "names": # RDKit needs the name to be properly formatted for a PDB file value = _deduce_PDB_atom_name(value, resname) # set attribute value in RDKit MonomerInfo rdattr = RDATTRIBUTES[attr] getattr(mi, "Set%s" % rdattr)(value) def _set_str_prop(atom, attr, value): atom.SetProp(attr, value) def _set_float_prop(atom, attr, value): atom.SetDoubleProp(attr, value) def _set_np_float_prop(atom, attr, value): atom.SetDoubleProp(attr, float(value)) def _set_int_prop(atom, attr, value): atom.SetIntProp(attr, value) def _set_np_int_prop(atom, attr, value): atom.SetIntProp(attr, int(value)) def _ignore_prop(atom, attr, value): pass _atom_property_dispatcher = { str: _set_str_prop, float: _set_float_prop, np.float32: _set_np_float_prop, np.float64: _set_np_float_prop, int: _set_int_prop, np.int8: _set_np_int_prop, np.int16: _set_np_int_prop, np.int32: _set_np_int_prop, np.int64: _set_np_int_prop, np.uint8: _set_np_int_prop, np.uint16: _set_np_int_prop, np.uint32: _set_np_int_prop, np.uint64: _set_np_int_prop, } def _set_atom_property(atom, attr, value): """Saves any attribute and value into an RDKit atom property""" _atom_property_dispatcher.get(type(value), _ignore_prop)(atom, attr, value)
[docs]def _infer_bo_and_charges(mol): """Infer bond orders and formal charges from a molecule. Since most MD topology files don't explicitly retain information on bond orders or charges, it has to be guessed from the topology. This is done by looping over each atom and comparing its expected valence to the current valence to get the Number of Unpaired Electrons (NUE). If an atom has a negative NUE, it needs a positive formal charge (-NUE). If two neighbouring atoms have UEs, the bond between them most likely has to be increased by the value of the smallest NUE. If after this process, an atom still has UEs, it needs a negative formal charge of -NUE. Parameters ---------- mol : rdkit.Chem.rdchem.RWMol The molecule is modified inplace and must have all hydrogens added Notes ----- This algorithm is order dependant. For example, for a carboxylate group R-C(-O)-O the first oxygen read will receive a double bond and the other one will be charged. It will also affect more complex conjugated systems. """ # sort atoms according to their NUE atoms = sorted([a for a in mol.GetAtoms() if a.GetAtomicNum() > 1], reverse=True, key=lambda a: _get_nb_unpaired_electrons(a)[0]) # charges that should be assigned to monatomic cations # structure --> atomic number : formal charge # anion charges are directly handled by the code using the typical valence # of the atom MONATOMIC_CATION_CHARGES = { 3: 1, 11: 1, 19: 1, 37: 1, 47: 1, 55: 1, 12: 2, 20: 2, 29: 2, 30: 2, 38: 2, 56: 2, 26: 2, # Fe could also be +3 13: 3, } for atom in atoms: # monatomic ions if atom.GetDegree() == 0: atom.SetFormalCharge(MONATOMIC_CATION_CHARGES.get( atom.GetAtomicNum(), -_get_nb_unpaired_electrons(atom)[0])) mol.UpdatePropertyCache(strict=False) continue # get NUE for each possible valence nue = _get_nb_unpaired_electrons(atom) # if there's only one possible valence state and the corresponding # NUE is negative, it means we can only add a positive charge to # the atom if (len(nue) == 1) and (nue[0] < 0): atom.SetFormalCharge(-nue[0]) mol.UpdatePropertyCache(strict=False) # go to next atom if above case or atom has no unpaired electron if (len(nue) == 1) and (nue[0] <= 0): continue else: neighbors = sorted(atom.GetNeighbors(), reverse=True, key=lambda a: _get_nb_unpaired_electrons(a)[0]) # check if one of the neighbors has a common NUE for na in neighbors: # get NUE for the neighbor na_nue = _get_nb_unpaired_electrons(na) # smallest common NUE common_nue = min( min([i for i in nue if i >= 0], default=0), min([i for i in na_nue if i >= 0], default=0) ) # a common NUE of 0 means we don't need to do anything if common_nue != 0: # increase bond order bond = mol.GetBondBetweenAtoms( atom.GetIdx(), na.GetIdx()) order = common_nue + 1 bond.SetBondType(RDBONDORDER[order]) mol.UpdatePropertyCache(strict=False) # go to next atom if one of the valences is complete nue = _get_nb_unpaired_electrons(atom) if any([n == 0 for n in nue]): break # if atom valence is still not filled nue = _get_nb_unpaired_electrons(atom) if not any([n == 0 for n in nue]): # transform nue to charge atom.SetFormalCharge(-nue[0]) atom.SetNumRadicalElectrons(0) mol.UpdatePropertyCache(strict=False)
def _get_nb_unpaired_electrons(atom): """Calculate the number of unpaired electrons (NUE) of an atom Parameters ---------- atom: rdkit.Chem.rdchem.Atom The atom for which the NUE will be computed Returns ------- nue : list The NUE for each possible valence of the atom """ expected_vs = PERIODIC_TABLE.GetValenceList(atom.GetAtomicNum()) current_v = atom.GetTotalValence() - atom.GetFormalCharge() return [v - current_v for v in expected_vs]
[docs]def _standardize_patterns(mol, max_iter=200): """Standardizes functional groups Uses :func:`_rebuild_conjugated_bonds` to standardize conjugated systems, and SMARTS reactions for other functional groups. Due to the way reactions work, we first have to split the molecule by fragments. Then, for each fragment, we apply the standardization reactions. Finally, the fragments are recombined. Parameters ---------- mol : rdkit.Chem.rdchem.RWMol The molecule to standardize max_iter : int Maximum number of iterations to standardize conjugated systems Returns ------- mol : rdkit.Chem.rdchem.Mol The standardized molecule Notes ----- The following functional groups are transformed in this order: +---------------+------------------------------------------------------------------------------+ | Name | Reaction | +===============+==============================================================================+ | conjugated | ``[*-:1]-[*:2]=[*:3]-[*-:4]>>[*+0:1]=[*:2]-[*:3]=[*+0:4]`` | +---------------+------------------------------------------------------------------------------+ | conjugated N+ | ``[N;X3;v3:1]-[*:2]=[*:3]-[*-:4]>>[N+:1]=[*:2]-[*:3]=[*+0:4]`` | +---------------+------------------------------------------------------------------------------+ | conjugated O- | ``[O:1]=[#6+0,#7+:2]-[*:3]=[*:4]-[*-:5]>>[O-:1]-[*:2]=[*:3]-[*:4]=[*+0:5]`` | +---------------+------------------------------------------------------------------------------+ | conjug. S=O | ``[O-:1]-[S;D4;v4:2]-[*:3]=[*:4]-[*-:5]>>[O+0:1]=[*:2]=[*:3]-[*:4]=[*+0:5]`` | +---------------+------------------------------------------------------------------------------+ | Cterm | ``[C-;X2;H0:1]=[O:2]>>[C+0:1]=[O:2]`` | +---------------+------------------------------------------------------------------------------+ | Nterm | ``[N-;X2;H1;$(N-[*^3]):1]>>[N+0:1]`` | +---------------+------------------------------------------------------------------------------+ | keto-enolate | ``[#6-:1]-[#6:2]=[O:3]>>[#6+0:1]=[#6:2]-[O-:3]`` | +---------------+------------------------------------------------------------------------------+ | arginine | ``[C-;v3:1]-[#7+0;v3;H2:2]>>[#6+0:1]=[#7+:2]`` | +---------------+------------------------------------------------------------------------------+ | histidine | ``[#6+0;H0:1]=[#6+0:2]-[#7;X3:3]-[#6-;X3:4]>>[#6:1]=[#6:2]-[#7+:3]=[#6+0:4]``| +---------------+------------------------------------------------------------------------------+ | sulfone | ``[S;D4;!v6:1]-[*-:2]>>[S;v6:1]=[*+0:2]`` | +---------------+------------------------------------------------------------------------------+ | charged N | ``[#7+0;X3:1]-[*-:2]>>[#7+:1]=[*+0:2]`` | +---------------+------------------------------------------------------------------------------+ """ # standardize conjugated systems _rebuild_conjugated_bonds(mol, max_iter) # list of sanitized reactions reactions = [] for rxn in [ "[C-;X2;H0:1]=[O:2]>>[C+0:1]=[O:2]", # Cterm "[N-;X2;H1;$(N-[*^3]):1]>>[N+0:1]", # Nterm "[#6-:1]-[#6:2]=[O:3]>>[#6+0:1]=[#6:2]-[O-:3]", # keto-enolate "[C-;v3:1]-[#7+0;v3;H2:2]>>[#6+0:1]=[#7+:2]", # ARG "[#6+0;H0:1]=[#6+0:2]-[#7;X3:3]-[#6-;X3:4]" ">>[#6:1]=[#6:2]-[#7+:3]=[#6+0:4]", # HIP "[S;D4;!v6:1]-[*-:2]>>[S;v6:1]=[*+0:2]", # sulfone "[#7+0;X3:1]-[*-:2]>>[#7+:1]=[*+0:2]", # charged-N ]: reaction = AllChem.ReactionFromSmarts(rxn) reactions.append(reaction) fragments = [] for reactant in Chem.GetMolFrags(mol, asMols=True): for reaction in reactions: reactant = _run_reaction(reaction, reactant) fragments.append(reactant) # recombine fragments newmol = fragments.pop(0) for fragment in fragments: newmol = Chem.CombineMols(newmol, fragment) # reassign all properties _transfer_properties(mol, newmol) return newmol
def _run_reaction(reaction, reactant): """Runs a reaction until all reactants are transformed If a pattern is matched N times in the molecule, the reaction will return N products as an array of shape (N, 1). Only the first product will be kept and the same reaction will be reapplied to the product N times in total. Parameters ---------- reaction : rdkit.Chem.rdChemReactions.ChemicalReaction Reaction from SMARTS reactant : rdkit.Chem.rdchem.Mol The molecule to transform Returns ------- product : rdkit.Chem.rdchem.Mol The final product of the reaction """ # repeat the reaction until all matching moeities have been transformed # note: this loop is meant to be ended by a `break` statement # but let's avoid using `while` loops just in case for n in range(reactant.GetNumAtoms()): reactant.UpdatePropertyCache(strict=False) Chem.Kekulize(reactant) products = reaction.RunReactants((reactant,)) if products: # structure: tuple[tuple[mol]] # length of 1st tuple: number of matches in reactant # length of 2nd tuple: number of products yielded by the reaction # if there's no match in reactant, returns an empty tuple # here we have at least one match, and the reaction used yield # a single product hence `products[0][0]` product = products[0][0] # map back atom properties from the reactant to the product _reassign_index_after_reaction(reactant, product) # apply the next reaction to the product reactant = product # exit the loop if there was nothing to transform else: break reactant.UpdatePropertyCache(strict=False) Chem.Kekulize(reactant) return reactant
[docs]def _rebuild_conjugated_bonds(mol, max_iter=200): """Rebuild conjugated bonds without negatively charged atoms at the beginning and end of the conjugated system Depending on the order in which atoms are read during the conversion, the :func:`_infer_bo_and_charges` function might write conjugated systems with a double bond less and both edges of the system as anions instead of the usual alternating single and double bonds. This function corrects this behaviour by using an iterative procedure. The problematic molecules always follow the same pattern: ``anion[-*=*]n-anion`` instead of ``*=[*-*=]n*``, where ``n`` is the number of successive single and double bonds. The goal of the iterative procedure is to make ``n`` as small as possible by consecutively transforming ``anion-*=*`` into ``*=*-anion`` until it reaches the smallest pattern with ``n=1``. This last pattern is then transformed from ``anion-*=*-anion`` to ``*=*-*=*``. Since ``anion-*=*`` is the same as ``*=*-anion`` in terms of SMARTS, we can control that we don't transform the same triplet of atoms back and forth by adding their indices to a list. This function also handles conjugated systems with triple bonds. The molecule needs to be kekulized first to also cover systems with aromatic rings. Parameters ---------- mol : rdkit.Chem.rdchem.RWMol The molecule to transform, modified inplace max_iter : int Maximum number of iterations performed by the function Notes ----- The molecule is modified inplace """ mol.UpdatePropertyCache(strict=False) Chem.Kekulize(mol) # pattern used to find problematic conjugated bonds # there's usually an even number of matches for this pattern = Chem.MolFromSmarts("[*-{1-2}]-,=[*+0]=,#[*+0]") # pattern used to finish fixing a series of conjugated bonds base_end_pattern = Chem.MolFromSmarts( "[*-{1-2}]-,=[*+0]=,#[*+0]-,=[*-{1-2}]") # used when there's an odd number of matches for `pattern` odd_end_pattern = Chem.MolFromSmarts( "[*-]-[*+0]=[*+0]-[*-,$([#7;X3;v3]),$([#6+0,#7+1]=O)," "$([S;D4;v4]-[O-])]") # number of unique matches with the pattern n_matches = len(set([match[0] for match in mol.GetSubstructMatches(pattern)])) # nothing to standardize if n_matches == 0: return # single match (unusual) elif n_matches == 1: # as a last resort, the only way to standardize is to find a nitrogen # that can accept a double bond and a positive charge # or a carbonyl that will become an enolate end_pattern = odd_end_pattern # at least 2 matches else: # give priority to base end pattern and then deal with the odd one if # necessary end_pattern = base_end_pattern backtrack = [] backtrack_cycles = 0 for _ in range(max_iter): # check for ending pattern end_match = mol.GetSubstructMatch(end_pattern) if end_match: # index of each atom anion1, a1, a2, anion2 = end_match term_atom = mol.GetAtomWithIdx(anion2) # edge-case 1: C-[O-] or [N+]-[O-] # [*-]-*=*-[C,N+]=O --> *=*-*=[C,N+]-[O-] # transform the =O to -[O-] if ( term_atom.GetAtomicNum() == 6 and term_atom.GetFormalCharge() == 0 ) or ( term_atom.GetAtomicNum() == 7 and term_atom.GetFormalCharge() == 1 ): for neighbor in term_atom.GetNeighbors(): bond = mol.GetBondBetweenAtoms(anion2, neighbor.GetIdx()) if (neighbor.GetAtomicNum() == 8 and bond.GetBondTypeAsDouble() == 2): bond.SetBondType(Chem.BondType.SINGLE) neighbor.SetFormalCharge(-1) break # edge-case 2: S=O # [*-]-*=*-[Sv4]-[O-] --> *=*-*=[Sv6]=O # transform -[O-] to =O elif (term_atom.GetAtomicNum() == 16 and term_atom.GetFormalCharge() == 0): for neighbor in term_atom.GetNeighbors(): bond = mol.GetBondBetweenAtoms(anion2, neighbor.GetIdx()) if (neighbor.GetAtomicNum() == 8 and neighbor.GetFormalCharge() == -1 and bond.GetBondTypeAsDouble() == 1): bond.SetBondType(Chem.BondType.DOUBLE) neighbor.SetFormalCharge(0) break # not an edge case: # increment the charge else: term_atom.SetFormalCharge(term_atom.GetFormalCharge() + 1) # common to all cases: # [*-]-*=*-[R] --> *=*-*=[R] # increment the charge and switch single and double bonds a = mol.GetAtomWithIdx(anion1) a.SetFormalCharge(a.GetFormalCharge() + 1) b = mol.GetBondBetweenAtoms(anion1, a1) b.SetBondType(RDBONDORDER[b.GetBondTypeAsDouble() + 1]) b = mol.GetBondBetweenAtoms(a1, a2) b.SetBondType(RDBONDORDER[b.GetBondTypeAsDouble() - 1]) b = mol.GetBondBetweenAtoms(a2, anion2) b.SetBondType(RDBONDORDER[b.GetBondTypeAsDouble() + 1]) mol.UpdatePropertyCache(strict=False) continue # switch the position of the charge and the double bond matches = mol.GetSubstructMatches(pattern) if matches: # check if we haven't already transformed this triplet for match in matches: # store order-independent atom indices g = set(match) # already transformed --> try the next one if g in backtrack: continue # add to backtracking and start the switch else: anion, a1, a2 = match backtrack.append(g) break # already performed all changes else: if backtrack_cycles == 1: # might be stuck because there were 2 "odd" end patterns # misqualified as a single base one end_pattern = odd_end_pattern elif backtrack_cycles > 1: # likely stuck changing the same bonds over and over so # let's stop here mol.UpdatePropertyCache(strict=False) return match = matches[0] anion, a1, a2 = match backtrack = [set(match)] backtrack_cycles += 1 # switch charges a = mol.GetAtomWithIdx(anion) a.SetFormalCharge(a.GetFormalCharge() + 1) a = mol.GetAtomWithIdx(a2) a.SetFormalCharge(a.GetFormalCharge() - 1) # switch bond orders b = mol.GetBondBetweenAtoms(anion, a1) b.SetBondType(RDBONDORDER[b.GetBondTypeAsDouble() + 1]) b = mol.GetBondBetweenAtoms(a1, a2) b.SetBondType(RDBONDORDER[b.GetBondTypeAsDouble() - 1]) mol.UpdatePropertyCache(strict=False) # update number of matches for the end pattern n_matches = len(set([match[0] for match in matches])) if n_matches == 1: end_pattern = odd_end_pattern # start new iteration continue # no more changes to apply mol.UpdatePropertyCache(strict=False) return # reached max_iter warnings.warn("The standardization could not be completed within a " "reasonable number of iterations")
def _reassign_index_after_reaction(reactant, product): """Maps back MDAnalysis index from the reactant to the product. The product molecule is modified inplace. """ prop = "_MDAnalysis_index" if reactant.GetAtoms()[0].HasProp(prop): for atom in product.GetAtoms(): idx = atom.GetUnsignedProp("react_atom_idx") old_atom = reactant.GetAtomWithIdx(idx) value = old_atom.GetIntProp(prop) _set_atom_property(atom, prop, value) def _transfer_properties(mol, newmol): """Transfer properties between two RDKit molecules. Requires the `_MDAnalysis_index` property to be present. Modifies `newmol` inplace. """ atoms = mol.GetAtoms() if atoms[0].HasProp("_MDAnalysis_index"): props = {} for atom in atoms: ix = atom.GetIntProp("_MDAnalysis_index") props[ix] = atom.GetPropsAsDict() for atom in newmol.GetAtoms(): ix = atom.GetIntProp("_MDAnalysis_index") for attr, value in props[ix].items(): _set_atom_property(atom, attr, value) # remove properties assigned during reactions atom.ClearProp("old_mapno") atom.ClearProp("react_atom_idx")