emmet-builders 0.84.10rc1__py3-none-any.whl → 0.85.0rc0__py3-none-any.whl

emmet/builders/molecules/bonds.py

@@ -1,329 +0,0 @@
-from __future__ import annotations
-
-from collections import defaultdict
-from datetime import datetime
-from itertools import chain
-from math import ceil
-
-from maggma.builders import Builder
-from maggma.core import Store
-from maggma.utils import grouper
-
-from emmet.builders.settings import EmmetBuildSettings
-from emmet.core.molecules.bonds import BOND_METHODS, MoleculeBondingDoc
-from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
-from emmet.core.qchem.task import TaskDocument
-from emmet.core.utils import jsanitize
-
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    from collections.abc import Iterable, Iterator
-
-__author__ = "Evan Spotte-Smith"
-
-SETTINGS = EmmetBuildSettings()
-
-
-class BondingBuilder(Builder):
-    """
-    The BondingBuilder defines the bonds in a MoleculeDoc.
-
-    Various methods can be used to define bonding, including:
-        - OpenBabelNN + metal_edge_extender: Combining the bond detection algorithms in OpenBabel (OpenBabelNN in
-            pymatgen) with a heuristic to add metal coordinate bonds (metal_edge_extender
-            in pymatgen)
-        - critic2: Using critical points of the electron density to define bonds
-        - nbo: Using Natural Bonding Orbital analysis to define bonds and other
-            interatomic interactions
-
-    NOTE: Only NBO7 can be used to generate bonding. Bonding (especially when metals
-        are involved) is unreliable with earlier version of NBO!
-
-    This builder will attempt to build documents for each molecule, in each solvent,
-    with each method. For each molecule-solvent-method combination, the highest-quality
-    data available (based on level of theory and electronic energy) will be used.
-
-    The process is as follows:
-        1. Gather MoleculeDocs by species hash
-        2. For each molecule, group all tasks by solvent.
-        3. For each solvent, sort tasks by level of theory and electronic energy
-        4. For each method:
-            4.1. Find task docs with necessary data to define bonding by that method
-            4.2. Take best (defined by level of theory and electronic energy) task
-            4.3. Convert TaskDoc to MoleculeBondingDoc
-    """
-
-    def __init__(
-        self,
-        tasks: Store,
-        molecules: Store,
-        bonds: Store,
-        query: dict | None = None,
-        methods: list | None = None,
-        settings: EmmetBuildSettings | None = None,
-        **kwargs,
-    ):
-        self.tasks = tasks
-        self.molecules = molecules
-        self.bonds = bonds
-        self.query = query if query else dict()
-        self.methods = methods if methods else BOND_METHODS
-        self.settings = EmmetBuildSettings.autoload(settings)
-        self.kwargs = kwargs
-
-        super().__init__(sources=[tasks, molecules], targets=[bonds], **kwargs)
-        # Uncomment in case of issue with mrun not connecting automatically to collections
-        # for i in [self.tasks, self.molecules, self.bonds]:
-        #     try:
-        #         i.connect()
-        #     except Exception as e:
-        #         print("Could not connect,", e)
-
-    def ensure_indexes(self):
-        """
-        Ensures indices on the collections needed for building
-        """
-
-        # Basic search index for tasks
-        self.tasks.ensure_index("task_id")
-        self.tasks.ensure_index("last_updated")
-        self.tasks.ensure_index("state")
-        self.tasks.ensure_index("formula_alphabetical")
-        self.tasks.ensure_index("species_hash")
-
-        # 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")
-        self.molecules.ensure_index("species_hash")
-
-        # 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")
-
-    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, "species_hash"])
-        )
-
-        processed_docs = set([e for e in self.bonds.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_hashes = {
-            d["species_hash"]
-            for d in all_mols
-            if d[self.molecules.key] in to_process_docs
-        }
-
-        N = ceil(len(to_process_hashes) / number_splits)
-
-        for hash_chunk in grouper(to_process_hashes, N):
-            query = dict(temp_query)
-            query["species_hash"] = {"$in": list(hash_chunk)}
-            yield {"query": query}
-
-    def get_items(self) -> Iterator[list[dict]]:
-        """
-        Gets all items to process into bonding documents.
-        This does no datetime checking; relying on on whether
-        task_ids are included in the bonds Store
-
-        Returns:
-            generator or list relevant tasks and molecules to process into documents
-        """
-
-        self.logger.info("Bonding 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, "species_hash"])
-        )
-
-        processed_docs = set([e for e in self.bonds.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_hashes = {
-            d["species_hash"]
-            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_hashes)} unprocessed hashes")
-
-        # Set total for builder bars to have a total
-        self.total = len(to_process_hashes)
-
-        for shash in to_process_hashes:
-            mol_query = dict(temp_query)
-            mol_query["species_hash"] = shash
-            molecules = list(self.molecules.query(criteria=mol_query))
-
-            yield molecules
-
-    def process_item(self, items: list[dict]) -> list[dict]:
-        """
-        Process the tasks into MoleculeBondingDocs
-
-        Args:
-            tasks list[dict] : a list of MoleculeDocs in dict form
-
-        Returns:
-            [dict] : a list of new bonding docs
-        """
-
-        mols = [MoleculeDoc(**item) for item in items]
-        shash = mols[0].species_hash
-        mol_ids = [m.molecule_id for m in mols]
-        self.logger.debug(f"Processing {shash} : {mol_ids}")
-
-        bonding_docs = list()
-
-        for mol in mols:
-            correct_charge_spin = [
-                e
-                for e in mol.entries
-                if e["charge"] == mol.charge
-                and e["spin_multiplicity"] == mol.spin_multiplicity
-            ]
-
-            # Organize by solvent environment
-            by_solvent = defaultdict(list)
-            for entry in correct_charge_spin:
-                by_solvent[entry["solvent"]].append(entry)
-
-            for solvent, entries in by_solvent.items():
-                sorted_entries = sorted(
-                    entries,
-                    key=lambda x: (
-                        sum(evaluate_lot(x["level_of_theory"])),
-                        x["energy"],
-                    ),
-                )
-
-                for method in self.methods:
-                    # For each method, grab entries that have the relevant data
-                    if method == "OpenBabelNN + metal_edge_extender":
-                        # This is sort of silly. Since, at the MoleculeDoc level,
-                        # the structures have to be identical, bonding defined
-                        # using heuristic methods like OpenBabel should always
-                        # be identical.
-                        # TODO: Decide if only one OpenBabelNN + m_e_e doc
-                        # TODO: should be allowed.
-                        relevant_entries = sorted_entries
-                    else:
-                        relevant_entries = [
-                            e
-                            for e in sorted_entries
-                            if e.get(method) is not None
-                            or e["output"].get(method) is not None
-                        ]
-
-                    if method == "nbo":
-                        # Only allow NBO7 to be used. No earlier versions can be
-                        # relied upon for bonding
-                        relevant_entries = [
-                            e
-                            for e in relevant_entries
-                            if e["orig"]["rem"].get("run_nbo6", False)
-                            or e["orig"]["rem"].get("nbo_external", False)
-                        ]
-
-                    if len(relevant_entries) == 0:
-                        continue
-
-                    # Grab task document of best entry
-                    best_entry = relevant_entries[0]
-                    task = best_entry["task_id"]
-
-                    tdoc = self.tasks.query_one(
-                        {
-                            "task_id": task,
-                            "species_hash": shash,
-                            "orig": {"$exists": True},
-                        }
-                    )
-
-                    if tdoc is None:
-                        try:
-                            tdoc = self.tasks.query_one(
-                                {
-                                    "task_id": int(task),
-                                    "species_hash": shash,
-                                    "orig": {"$exists": True},
-                                }
-                            )
-                        except ValueError:
-                            tdoc = None
-
-                    if tdoc is None:
-                        continue
-
-                    task_doc = TaskDocument(**tdoc)
-
-                    if task_doc is None:
-                        continue
-
-                    doc = MoleculeBondingDoc.from_task(
-                        task_doc,
-                        molecule_id=mol.molecule_id,
-                        preferred_methods=[method],
-                        deprecated=False,
-                    )
-                    bonding_docs.append(doc)
-
-        self.logger.debug(f"Produced {len(bonding_docs)} bonding docs for {shash}")
-
-        return jsanitize([doc.model_dump() for doc in bonding_docs], allow_bson=True)
-
-    def update_targets(self, items: list[list[dict]]):
-        """
-        Inserts the new documents into the bonds collection
-
-        Args:
-            items [[dict]]: A list of documents to update
-        """
-
-        docs = list(chain.from_iterable(items))  # type: ignore
-
-        # Add timestamp
-        for item in docs:
-            item.update(
-                {
-                    "_bt": self.timestamp,
-                }
-            )
-
-        molecule_ids = list({item["molecule_id"] for item in docs})
-
-        if len(items) > 0:
-            self.logger.info(f"Updating {len(docs)} bonding documents")
-            self.bonds.remove_docs({self.bonds.key: {"$in": molecule_ids}})
-            # Neither molecule_id nor method need to be unique, but the combination must be
-            self.bonds.update(
-                docs=docs,
-                key=["molecule_id", "method", "solvent"],
-            )
-        else:
-            self.logger.info("No items to update")

emmet/builders/molecules/electric.py

@@ -1,287 +0,0 @@
-from __future__ import annotations
-
-from collections import defaultdict
-from datetime import datetime
-from itertools import chain
-from math import ceil
-
-from maggma.builders import Builder
-from maggma.core import Store
-from maggma.utils import grouper
-
-from emmet.builders.settings import EmmetBuildSettings
-from emmet.core.molecules.electric import ElectricMultipoleDoc
-from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
-from emmet.core.qchem.task import TaskDocument
-from emmet.core.utils import jsanitize
-
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    from collections.abc import Iterable, Iterator
-
-__author__ = "Evan Spotte-Smith"
-
-SETTINGS = EmmetBuildSettings()
-
-
-class ElectricMultipoleBuilder(Builder):
-    """
-    The ElectricMultipoleBuilder defines the electric multipole properties of a MoleculeDoc.
-
-    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 and electronic energy) will be used.
-
-    The process is as follows:
-        1. Gather MoleculeDocs by species hash
-        2. For each molecule, group all tasks by solvent.
-        3. For each solvent, grab the best TaskDoc (doc with elecrtric dipole/multipole information
-        that has the highest level of theory with the lowest electronic energy) for the molecule
-        4. Convert TaskDoc to ElectricMultipoleDoc
-    """
-
-    def __init__(
-        self,
-        tasks: Store,
-        molecules: Store,
-        multipoles: Store,
-        query: dict | None = None,
-        settings: EmmetBuildSettings | None = None,
-        **kwargs,
-    ):
-        self.tasks = tasks
-        self.molecules = molecules
-        self.multipoles = multipoles
-        self.query = query if query else dict()
-        self.settings = EmmetBuildSettings.autoload(settings)
-        self.kwargs = kwargs
-
-        super().__init__(sources=[tasks, molecules], targets=[multipoles], **kwargs)
-        # Uncomment in case of issue with mrun not connecting automatically to collections
-        # for i in [self.tasks, self.molecules, self.multipoles]:
-        #     try:
-        #         i.connect()
-        #     except Exception as e:
-        #         print("Could not connect,", e)
-
-    def ensure_indexes(self):
-        """
-        Ensures indices on the collections needed for building
-        """
-
-        # Basic search index for tasks
-        self.tasks.ensure_index("task_id")
-        self.tasks.ensure_index("last_updated")
-        self.tasks.ensure_index("state")
-        self.tasks.ensure_index("formula_alphabetical")
-        self.tasks.ensure_index("species_hash")
-
-        # 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")
-        self.molecules.ensure_index("species_hash")
-
-        # Search index for electric
-        self.multipoles.ensure_index("method")
-        self.multipoles.ensure_index("molecule_id")
-        self.multipoles.ensure_index("task_id")
-        self.multipoles.ensure_index("solvent")
-        self.multipoles.ensure_index("lot_solvent")
-        self.multipoles.ensure_index("property_id")
-        self.multipoles.ensure_index("last_updated")
-        self.multipoles.ensure_index("formula_alphabetical")
-
-    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, "species_hash"])
-        )
-
-        processed_docs = set([e for e in self.multipoles.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_hashes = {
-            d["species_hash"]
-            for d in all_mols
-            if d[self.molecules.key] in to_process_docs
-        }
-
-        N = ceil(len(to_process_hashes) / number_splits)
-
-        for hash_chunk in grouper(to_process_hashes, N):
-            query = dict(temp_query)
-            query["species_hash"] = {"$in": list(hash_chunk)}
-            yield {"query": query}
-
-    def get_items(self) -> Iterator[list[dict]]:
-        """
-        Gets all items to process into multipole documents.
-        This does no datetime checking; relying on on whether
-        task_ids are included in the multipoles Store
-
-        Returns:
-            generator or list relevant tasks and molecules to process into documents
-        """
-
-        self.logger.info("Electric multipoles 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, "species_hash"])
-        )
-
-        processed_docs = set([e for e in self.multipoles.distinct("molecule_id")])
-        to_process_docs = {d[self.molecules.key] for d in all_mols} - processed_docs
-        to_process_hashes = {
-            d["species_hash"]
-            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_hashes)} unprocessed hashes")
-
-        # Set total for builder bars to have a total
-        self.total = len(to_process_hashes)
-
-        for shash in to_process_hashes:
-            mol_query = dict(temp_query)
-            mol_query["species_hash"] = shash
-            molecules = list(self.molecules.query(criteria=mol_query))
-
-            yield molecules
-
-    def process_item(self, items: list[dict]) -> list[dict]:
-        """
-        Process the tasks into ElectricMultipoleDocs
-
-        Args:
-            tasks list[dict] : a list of MoleculeDocs in dict form
-
-        Returns:
-            [dict] : a list of new electric multipole docs
-        """
-
-        mols = [MoleculeDoc(**item) for item in items]
-        shash = mols[0].species_hash
-        mol_ids = [m.molecule_id for m in mols]
-        self.logger.debug(f"Processing {shash} : {mol_ids}")
-
-        multipole_docs = list()
-
-        for mol in mols:
-            # Relevant tasks are those with the correct charge and spin
-            # for which there are AT LEAST electric dipoles present
-            # (ideally, multipole information would also be present)
-            multip_entries = [
-                e
-                for e in mol.entries
-                if e["charge"] == mol.charge
-                and e["spin_multiplicity"] == mol.spin_multiplicity
-                and (e["output"].get("dipoles") is not None)
-            ]
-
-            # Organize by solvent environment
-            by_solvent = defaultdict(list)
-            for entry in multip_entries:
-                by_solvent[entry["solvent"]].append(entry)
-
-            for solvent, entries in by_solvent.items():
-                # No documents with enthalpy and entropy
-                if len(entries) == 0:
-                    continue
-                else:
-                    best = sorted(
-                        entries,
-                        key=lambda x: (
-                            sum(evaluate_lot(x["level_of_theory"])),
-                            x["energy"],
-                        ),
-                    )[0]
-                    task = best["task_id"]
-
-                tdoc = self.tasks.query_one(
-                    {
-                        "task_id": task,
-                        "species_hash": shash,
-                        "orig": {"$exists": True},
-                    }
-                )
-
-                if tdoc is None:
-                    try:
-                        tdoc = self.tasks.query_one(
-                            {
-                                "task_id": int(task),
-                                "species_hash": shash,
-                                "orig": {"$exists": True},
-                            }
-                        )
-                    except ValueError:
-                        tdoc = None
-
-                if tdoc is None:
-                    continue
-
-                task_doc = TaskDocument(**tdoc)
-
-                if task_doc is None:
-                    continue
-
-                multipole_doc = ElectricMultipoleDoc.from_task(
-                    task_doc, molecule_id=mol.molecule_id, deprecated=False
-                )
-                multipole_docs.append(multipole_doc)
-
-        self.logger.debug(
-            f"Produced {len(multipole_docs)} electric multipole docs for {shash}"
-        )
-
-        return jsanitize([doc.model_dump() for doc in multipole_docs], allow_bson=True)
-
-    def update_targets(self, items: list[list[dict]]):
-        """
-        Inserts the new documents into the multipoles collection
-
-        Args:
-            items [[dict]]: A list of documents to update
-        """
-
-        docs = list(chain.from_iterable(items))  # type: ignore
-
-        # Add timestamp
-        for item in docs:
-            item.update(
-                {
-                    "_bt": self.timestamp,
-                }
-            )
-
-        molecule_ids = list({item["molecule_id"] for item in docs})
-
-        if len(items) > 0:
-            self.logger.info(f"Updating {len(docs)} electric multipole documents")
-            self.multipoles.remove_docs({self.multipoles.key: {"$in": molecule_ids}})
-            # Neither molecule_id nor method need to be unique, but the combination must be
-            self.multipoles.update(
-                docs=docs,
-                key=["molecule_id", "solvent"],
-            )
-        else:
-            self.logger.info("No items to update")