emmet-builders 0.78.3__py3-none-any.whl → 0.86.0__py3-none-any.whl

emmet/builders/molecules/metal_binding.py

@@ -1,526 +0,0 @@
-from datetime import datetime
-from itertools import chain
-from math import ceil
-from typing import Optional, Iterable, Iterator, List, Dict
-import copy
-
-from pymatgen.core.structure import Molecule
-from pymatgen.util.graph_hashing import weisfeiler_lehman_graph_hash
-
-from maggma.builders import Builder
-from maggma.core import Store
-from maggma.utils import grouper
-
-from emmet.core.qchem.molecule import MoleculeDoc
-from emmet.core.molecules.atomic import PartialChargesDoc, PartialSpinsDoc
-from emmet.core.molecules.bonds import MoleculeBondingDoc, metals
-from emmet.core.molecules.thermo import MoleculeThermoDoc
-from emmet.core.molecules.metal_binding import MetalBindingDoc, METAL_BINDING_METHODS
-from emmet.core.utils import jsanitize
-from emmet.builders.settings import EmmetBuildSettings
-
-
-__author__ = "Evan Spotte-Smith"
-
-SETTINGS = EmmetBuildSettings()
-
-
-class MetalBindingBuilder(Builder):
-    """
-    The MetalBindingBuilder extracts information about metal binding in molecules
-    from MoleculeDocs, MoleculeThermoDocs, MoleculeBondingDocs, PartialChargesDocs,
-    and PartialSpinsDocs.
-
-    NBO is the strongly preferred method to approximate partial charges and bonding,
-    and so if NBO bonding and partial charges/spins documents are available, they will
-    be used.
-
-    If NBO docs are not available, then bonding can be taken from the "OpenBabelNN + metal_edge_extender"
-    method, and partial charges and spins can be taken from "mulliken".
-
-    This builder will attempt to build documents for each molecule in each solvent.
-    For each molecule-solvent combination, the highest-quality data available
-    (based on level of theory, electronic energy, and the method used to generate bonding/charges/spins)
-    will be used.
-
-    The process is as follows:
-        1. Gather MoleculeDocs by formula
-        2. For each molecule, first identify if there are any metals. If not, then no MetalBindingDoc can be made.
-            If so, then identify the possible solvents that can be used to generate MetalBindingDocs
-        3. For each combination of Molecule ID and solvent, search for additional documents:
-            - MoleculeBondingDocs
-            - PartialChargesDocs
-            - PartialSpinsDocs (for open-shell molecules)
-            - MoleculeThermoDocs
-        4. Group these additional documents by level of theory and (where applicable) method, and choose the best
-            possible methods for which all required data is available
-        5. For each metal in the molecule:
-            5.1 Use partial charge and spin information to determine the oxidation and spin state of the metal
-            5.2 Search for MoleculeThermoDocs for the metal atom/ion with appropriate charge and spin with the
-                chosen level of theory
-            5.3 Use graph comparisons (hashing or isomorphism) to identify a molecule with the same structure as
-                the molecule of interest WITHOUT the metal of interest, as well as the appropriate charge and spin
-            5.4 If an appropriate metal-less molecule can be found, search for a MoleculeThermoDoc for that molecule'
-                with the chosen level of theory
-        6. Use the obtained bonding, charges, spins, and thermo docs to construct a MetalBindingDoc
-    """
-
-    def __init__(
-        self,
-        molecules: Store,
-        charges: Store,
-        spins: Store,
-        bonds: Store,
-        thermo: Store,
-        metal_binding: Store,
-        query: Optional[Dict] = None,
-        methods: Optional[List] = None,
-        settings: Optional[EmmetBuildSettings] = None,
-        **kwargs,
-    ):
-        self.molecules = molecules
-        self.charges = charges
-        self.spins = spins
-        self.bonds = bonds
-        self.thermo = thermo
-        self.metal_binding = metal_binding
-        self.query = query if query else dict()
-        self.methods = methods if methods else METAL_BINDING_METHODS
-        self.settings = EmmetBuildSettings.autoload(settings)
-        self.kwargs = kwargs
-
-        super().__init__(
-            sources=[molecules, charges, spins, bonds, thermo],
-            targets=[metal_binding],
-            **kwargs,
-        )
-        # Uncomment in case of issue with mrun not connecting automatically to collections
-        # for i in [self.molecules, self.charges, self.spins, self.bonds, self.thermo, self.metal_binding]:
-        #     try:
-        #         i.connect()
-        #     except Exception as e:
-        #         print("Could not connect,", e)
-
-    def ensure_indexes(self):
-        """
-        Ensures indices on the collections needed for building
-        """
-
-        # Search index for molecules
-        self.molecules.ensure_index("molecule_id")
-        self.molecules.ensure_index("last_updated")
-        self.molecules.ensure_index("task_ids")
-        self.molecules.ensure_index("formula_alphabetical")
-
-        # Search index for charges
-        self.charges.ensure_index("molecule_id")
-        self.charges.ensure_index("task_id")
-        self.charges.ensure_index("method")
-        self.charges.ensure_index("solvent")
-        self.charges.ensure_index("lot_solvent")
-        self.charges.ensure_index("property_id")
-        self.charges.ensure_index("last_updated")
-        self.charges.ensure_index("formula_alphabetical")
-
-        # Search index for spins
-        self.spins.ensure_index("molecule_id")
-        self.spins.ensure_index("task_id")
-        self.spins.ensure_index("method")
-        self.spins.ensure_index("solvent")
-        self.spins.ensure_index("lot_solvent")
-        self.spins.ensure_index("property_id")
-        self.spins.ensure_index("last_updated")
-        self.spins.ensure_index("formula_alphabetical")
-
-        # Search index for bonds
-        self.bonds.ensure_index("molecule_id")
-        self.bonds.ensure_index("method")
-        self.bonds.ensure_index("task_id")
-        self.bonds.ensure_index("solvent")
-        self.bonds.ensure_index("lot_solvent")
-        self.bonds.ensure_index("property_id")
-        self.bonds.ensure_index("last_updated")
-        self.bonds.ensure_index("formula_alphabetical")
-
-        # Search index for thermo
-        self.thermo.ensure_index("molecule_id")
-        self.thermo.ensure_index("task_id")
-        self.thermo.ensure_index("solvent")
-        self.thermo.ensure_index("lot_solvent")
-        self.thermo.ensure_index("property_id")
-        self.thermo.ensure_index("last_updated")
-        self.thermo.ensure_index("formula_alphabetical")
-
-        # Search index for metal_binding
-        self.metal_binding.ensure_index("molecule_id")
-        self.metal_binding.ensure_index("solvent")
-        self.metal_binding.ensure_index("lot_solvent")
-        self.metal_binding.ensure_index("property_id")
-        self.metal_binding.ensure_index("last_updated")
-        self.metal_binding.ensure_index("formula_alphabetical")
-        self.metal_binding.ensure_index("method")
-
-    def prechunk(self, number_splits: int) -> Iterable[Dict]:  # pragma: no cover
-        """Prechunk the builder for distributed computation"""
-
-        temp_query = dict(self.query)
-        temp_query["deprecated"] = False
-
-        self.logger.info("Finding documents to process")
-        all_mols = list(
-            self.molecules.query(
-                temp_query, [self.molecules.key, "formula_alphabetical"]
-            )
-        )
-
-        processed_docs = set([e for e in self.metal_binding.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_forms = {
-            d["formula_alphabetical"]
-            for d in all_mols
-            if d[self.molecules.key] in to_process_docs
-        }
-
-        N = ceil(len(to_process_forms) / number_splits)
-
-        for formula_chunk in grouper(to_process_forms, N):
-            yield {"query": {"formula_alphabetical": {"$in": list(formula_chunk)}}}
-
-    def get_items(self) -> Iterator[List[Dict]]:
-        """
-        Gets all items to process into metal_binding documents.
-
-        Returns:
-            generator or list relevant molecules to process into documents
-        """
-
-        self.logger.info("Metal binding builder started")
-        self.logger.info("Setting indexes")
-        self.ensure_indexes()
-
-        # Save timestamp to mark buildtime
-        self.timestamp = datetime.utcnow()
-
-        # Get all processed molecules
-        temp_query = dict(self.query)
-        temp_query["deprecated"] = False
-
-        self.logger.info("Finding documents to process")
-        all_mols = list(
-            self.molecules.query(
-                temp_query, [self.molecules.key, "formula_alphabetical"]
-            )
-        )
-
-        processed_docs = set([e for e in self.metal_binding.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_forms = {
-            d["formula_alphabetical"]
-            for d in all_mols
-            if d[self.molecules.key] in to_process_docs
-        }
-
-        self.logger.info(f"Found {len(to_process_docs)} unprocessed documents")
-        self.logger.info(f"Found {len(to_process_forms)} unprocessed formulas")
-
-        # Set total for builder bars to have a total
-        self.total = len(to_process_forms)
-
-        for formula in to_process_forms:
-            mol_query = dict(temp_query)
-            mol_query["formula_alphabetical"] = formula
-            molecules = list(self.molecules.query(criteria=mol_query))
-
-            yield molecules
-
-    def process_item(self, items: List[Dict]) -> List[Dict]:
-        """
-        Process molecule, bonding, partial charges, partial spins, and thermo documents into MetalBindingDocs
-
-        Args:
-            tasks List[Dict] : a list of MoleculeDocs in dict form
-
-        Returns:
-            [dict] : a list of new metal binding docs
-        """
-
-        mols = [MoleculeDoc(**item) for item in items]
-        formula = mols[0].formula_alphabetical
-        mol_ids = [m.molecule_id for m in mols]
-        self.logger.debug(f"Processing {formula} : {mol_ids}")
-
-        binding_docs = list()
-
-        for mol in mols:
-            # First: do we need to do this? Are there actually metals in this molecule? And species other than metals?
-            species = mol.species
-            metal_indices = [i for i, e in enumerate(species) if e in metals]
-            if len(metal_indices) == 0 or len(species) == 1:
-                # print(mol.molecule_id, mol.formula_alphabetical)
-                continue
-
-            # Grab the basic documents needed to create a metal binding document
-            molecule_id = mol.molecule_id
-            solvents = mol.unique_solvents
-            charges = [
-                PartialChargesDoc(**e)
-                for e in self.charges.query({"molecule_id": molecule_id})
-            ]
-            if mol.spin_multiplicity != 1:
-                spins = [
-                    PartialSpinsDoc(**e)
-                    for e in self.spins.query({"molecule_id": molecule_id})
-                ]
-            else:
-                spins = list()
-            bonds = [
-                MoleculeBondingDoc(**e)
-                for e in self.bonds.query({"molecule_id": molecule_id})
-            ]
-            thermo = [
-                MoleculeThermoDoc(**e)
-                for e in self.thermo.query({"molecule_id": molecule_id})
-            ]
-
-            if any([len(x) == 0 for x in [charges, bonds, thermo]]):
-                # Not enough information to construct MetalBindingDoc
-                continue
-            elif mol.spin_multiplicity != 1 and len(spins) == 0:
-                # For open-shell molecule, partial spins information needed
-                continue
-
-            # Group by solvent and (where appropriate) method
-            charge_bysolv_meth = dict()
-            for c in charges:
-                if c.solvent not in charge_bysolv_meth:
-                    charge_bysolv_meth[c.solvent] = {c.method: c}
-                else:
-                    charge_bysolv_meth[c.solvent][c.method] = c
-
-            spins_bysolv_meth = dict()
-            for s in spins:
-                if s.solvent not in spins_bysolv_meth:
-                    spins_bysolv_meth[s.solvent] = {s.method: s}
-                else:
-                    spins_bysolv_meth[s.solvent][s.method] = s
-
-            bonds_bysolv_meth = dict()
-            for b in bonds:
-                if b.solvent not in bonds_bysolv_meth:
-                    bonds_bysolv_meth[b.solvent] = {b.method: b}
-                else:
-                    bonds_bysolv_meth[b.solvent][b.method] = b
-
-            thermo_bysolv = {t.solvent: t for t in thermo}
-
-            for solvent in solvents:
-                this_charge = charge_bysolv_meth.get(solvent)  # type: ignore
-                this_spin = spins_bysolv_meth.get(solvent)  # type: ignore
-                this_bond = bonds_bysolv_meth.get(solvent)  # type: ignore
-                base_thermo_doc = thermo_bysolv.get(solvent)  # type: ignore
-
-                # Do we have the requisite docs for this solvent?
-                if mol.spin_multiplicity == 1:
-                    needed = [this_charge, this_bond, base_thermo_doc]
-                else:
-                    needed = [this_charge, this_spin, this_bond, base_thermo_doc]
-
-                if any([x is None for x in needed]):
-                    continue
-
-                # What method will we use?
-                # Currently allows two options:
-                # 1. Using NBO for everything ("nbo")
-                # 2. Using Mulliken for charges/spins and OpenBabel + metal_edge_extender for bonding
-                #   ("mulliken-OB-mee")
-                for method in self.methods:
-                    plan = False
-                    if mol.spin_multiplicity == 1:
-                        if method == "nbo" and all(
-                            [x.get("nbo") is not None for x in [this_charge, this_bond]]  # type: ignore
-                        ):  # type: ignore
-                            plan = True
-                            charge_doc = this_charge.get("nbo")  # type: ignore
-                            spin_doc = None
-                            bond_doc = this_bond.get("nbo")  # type: ignore
-                        elif method == "mulliken-OB-mee" and (
-                            this_charge.get("mulliken") is not None  # type: ignore
-                            and this_bond.get("OpenBabelNN + metal_edge_extender") is not None  # type: ignore
-                        ):
-                            plan = True
-                            charge_doc = this_charge.get("mulliken")  # type: ignore
-                            spin_doc = None
-                            bond_doc = this_bond.get("OpenBabelNN + metal_edge_extender")  # type: ignore
-                    else:
-                        if method == "nbo" and all(
-                            [x.get("nbo") is not None for x in [this_charge, this_spin, this_bond]]  # type: ignore
-                        ):  # type: ignore
-                            charge_lot = this_charge.get("nbo").level_of_theory  # type: ignore
-                            spin_lot = this_spin.get("nbo").level_of_theory  # type: ignore
-                            if charge_lot == spin_lot:  # type: ignore
-                                plan = True
-                                charge_doc = this_charge.get("nbo")  # type: ignore
-                                spin_doc = this_spin.get("nbo")  # type: ignore
-                                bond_doc = this_bond.get("nbo")  # type: ignore
-                        elif (
-                            method == "mulliken-OB-mee"
-                            and this_charge.get("mulliken") is not None  # type: ignore
-                            and this_spin.get("mulliken") is not None  # type: ignore
-                            and this_bond.get("OpenBabelNN + metal_edge_extender") is not None  # type: ignore
-                        ):
-                            charge_lot = this_charge.get("mulliken").level_of_theory  # type: ignore
-                            spin_lot = this_spin.get("mulliken").level_of_theory  # type: ignore
-                            if charge_lot == spin_lot:  # type: ignore
-                                plan = True
-                                charge_doc = this_charge.get("mulliken")  # type: ignore
-                                spin_doc = this_spin.get("mulliken")  # type: ignore
-                                bond_doc = this_bond.get("OpenBabelNN + metal_edge_extender")  # type: ignore
-
-                    # Don't have the right combinations of level of theory and method
-                    if plan is False:
-                        continue
-
-                    # Obtain relevant thermo documents for each metal atom/ion in the molecule
-                    metal_thermo = dict()
-                    nometal_thermo = dict()
-                    for metal_index in metal_indices:
-                        # First, determine the appropriate charge and spin of the metal
-                        # TODO: figure out better charge assignment
-                        partial_charge = charge_doc.partial_charges[metal_index]  # type: ignore
-
-                        if mol.spin_multiplicity == 1:
-                            # For now, just round to nearest whole number
-                            charge = round(partial_charge)
-                            spin = 1
-                        else:
-                            partial_spin = spin_doc.partial_spins[metal_index]  # type: ignore
-                            charge = round(partial_charge)
-                            spin = round(abs(partial_spin)) + 1
-
-                        # Sanity check that charge and spin are compatible
-                        metal_species = species[metal_index]
-                        try:
-                            _ = Molecule(
-                                [metal_species],
-                                [[0.0, 0.0, 0.0]],
-                                charge=charge,
-                                spin_multiplicity=spin,
-                            )
-                        except ValueError:
-                            # Assume spin assignment is correct, and change charge accordingly
-                            diff_up = abs(partial_charge - (charge + 1))
-                            diff_down = abs(partial_charge - (charge - 1))
-                            if diff_up < diff_down:
-                                charge += 1
-                            else:
-                                charge -= 1
-
-                        # Grab thermo doc for the relevant metal ion/atom (if available)
-                        this_metal_thermo = [
-                            MoleculeThermoDoc(**e)
-                            for e in self.thermo.query(
-                                {
-                                    "formula_alphabetical": f"{metal_species}1",
-                                    "charge": charge,
-                                    "spin_multiplicity": spin,
-                                    "lot_solvent": base_thermo_doc.lot_solvent,  # type: ignore
-                                }
-                            )
-                        ]
-                        if len(this_metal_thermo) == 0:
-                            continue
-
-                        this_metal_thermo = this_metal_thermo[0]
-                        metal_thermo[metal_index] = this_metal_thermo
-
-                        # Now the (somewhat) harder part - finding the document for this molecule without the metal
-                        # Make sure charges and spins add up
-                        nometal_charge = mol.charge - charge
-                        nometal_spin = mol.spin_multiplicity - spin + 1
-                        mg_copy = copy.deepcopy(bond_doc.molecule_graph)  # type: ignore
-                        mg_copy.remove_nodes([metal_index])
-                        new_hash = weisfeiler_lehman_graph_hash(
-                            mg_copy.graph.to_undirected(), node_attr="specie"
-                        )
-                        nometal_mol_doc = [
-                            MoleculeDoc(**e)
-                            for e in self.molecules.query(
-                                {
-                                    "species_hash": new_hash,
-                                    "charge": nometal_charge,
-                                    "spin_multiplicity": nometal_spin,
-                                }
-                            )
-                        ]
-                        if len(nometal_mol_doc) == 0:
-                            continue
-
-                        nometal_mol_id = nometal_mol_doc[0].molecule_id
-                        this_nometal_thermo = [
-                            MoleculeThermoDoc(**e)
-                            for e in self.thermo.query(
-                                {
-                                    "molecule_id": nometal_mol_id,
-                                    "lot_solvent": base_thermo_doc.lot_solvent,  # type: ignore
-                                }
-                            )
-                        ]
-                        if len(this_nometal_thermo) == 0:
-                            continue
-
-                        this_nometal_thermo = this_nometal_thermo[0]
-                        nometal_thermo[metal_index] = this_nometal_thermo
-
-                    doc = MetalBindingDoc.from_docs(
-                        method=method,
-                        metal_indices=metal_indices,
-                        base_molecule_doc=mol,
-                        partial_charges=charge_doc,
-                        partial_spins=spin_doc,
-                        bonding=bond_doc,
-                        base_thermo=base_thermo_doc,
-                        metal_thermo=metal_thermo,
-                        nometal_thermo=nometal_thermo,
-                    )
-
-                    if doc is not None and len(doc.binding_data) != 0:
-                        binding_docs.append(doc)
-
-        self.logger.debug(
-            f"Produced {len(binding_docs)} metal binding docs for {formula}"
-        )
-
-        return jsanitize([doc.model_dump() for doc in binding_docs], allow_bson=True)
-
-    def update_targets(self, items: List[List[Dict]]):
-        """
-        Inserts the new documents into the metal_binding collection
-
-        Args:
-            items [[dict]]: A list of documents to update
-        """
-
-        docs = list(chain.from_iterable(items))  # type: ignore
-
-        # Add timestamp
-        for item in docs:
-            item.update(
-                {
-                    "_bt": self.timestamp,
-                }
-            )
-
-        molecule_ids = list({item["molecule_id"] for item in docs})
-
-        if len(items) > 0:
-            self.logger.info(f"Updating {len(docs)} metal binding documents")
-            self.metal_binding.remove_docs(
-                {self.metal_binding.key: {"$in": molecule_ids}}
-            )
-            # Neither molecule_id nor solvent need to be unique, but the combination must be
-            self.metal_binding.update(
-                docs=docs,
-                key=["molecule_id", "solvent", "method"],
-            )
-        else:
-            self.logger.info("No items to update")