Index

A

add_energies() (examol.store.models.MoleculeRecord method) add_energy() (examol.store.models.Conformer method) add_initial_conformer() (in module examol.simulate.initialize) add_possibilities() (examol.select.base.Selector method) add_vacuum_buffer() (in module examol.simulate.ase.utils)

already_in_db (examol.steer.multifi.PipelineThinker attribute) ASESimulator (class in examol.simulate.ase) assemble() (examol.specify.ExaMolSpecification method) atoms (examol.simulate.base.SimResult property) (examol.store.models.Conformer property)

B

BaseSimulator (class in examol.simulate.base)

BOTorchSequentialSelector (class in examol.select.botorch) BruteForceThinker (class in examol.steer.baseline)

C

call() (examol.score.nfp.ReduceAtoms method) charge (examol.simulate.base.SimResult attribute) (examol.store.models.Conformer attribute) (examol.store.models.EnergyEvaluation attribute) (examol.store.models.MissingData attribute) (examol.store.recipes.RequiredEnergy attribute) (examol.store.recipes.RequiredGeometry attribute) (examol.store.recipes.SimulationRequest attribute) colmena_queue (examol.specify.ExaMolSpecification attribute) completed (examol.store.models.EnergyEvaluation attribute) compute_config (examol.specify.ExaMolSpecification attribute) compute_energy() (examol.simulate.ase.ASESimulator method) (examol.simulate.base.BaseSimulator method) compute_property() (examol.store.recipes.PropertyRecipe method) (examol.store.recipes.RedoxEnergy method) (examol.store.recipes.SolvationEnergy method)

config_name (examol.simulate.base.SimResult attribute) (examol.store.models.Conformer attribute) (examol.store.models.EnergyEvaluation attribute) (examol.store.models.MissingData attribute) (examol.store.recipes.RequiredEnergy attribute) (examol.store.recipes.RequiredGeometry attribute) (examol.store.recipes.SimulationRequest attribute) Conformer (class in examol.store.models) conformers (examol.store.models.MoleculeRecord attribute) convert_nx_to_rdkit() (in module examol.utils.conversions) convert_nx_to_smiles() (in module examol.utils.conversions) convert_rdkit_to_nx() (in module examol.utils.conversions) convert_string_to_dict() (in module examol.score.nfp) convert_string_to_nx() (in module examol.utils.conversions) count_training_size() (examol.steer.single.SingleStepThinker method) create_configuration() (examol.simulate.ase.ASESimulator method) (examol.simulate.base.BaseSimulator method)

D

database (examol.specify.ExaMolSpecification attribute) (examol.steer.base.MoleculeThinker attribute)

date_created (examol.store.models.Conformer attribute) dispense() (examol.select.base.Selector method)

E

EHVISelector (class in examol.select.botorch) energies (examol.store.models.Conformer attribute) energy (examol.simulate.base.SimResult attribute) (examol.store.models.EnergyEvaluation attribute) EnergyEvaluation (class in examol.store.models) EnsembleCovarianceModel (class in examol.select.botorch) examol.score module examol.score.base module examol.score.nfp module examol.select module examol.select.base module examol.select.baseline module examol.select.bayes module examol.select.botorch module examol.simulate module examol.simulate.ase module examol.simulate.ase.utils module examol.simulate.base module examol.simulate.initialize module examol.solution module examol.specify module examol.start module

examol.start.base module examol.start.fast module examol.start.kmeans module examol.steer module examol.steer.base module examol.steer.baseline module examol.steer.multifi module examol.steer.single module examol.store module examol.store.db module examol.store.db.base module examol.store.db.memory module examol.store.models module examol.store.recipes module examol.utils module examol.utils.chemistry module examol.utils.conversions module ExaMolSpecification (class in examol.specify) ExpectedImprovement (class in examol.select.bayes) export_records() (examol.store.db.base.MoleculeStore method)

F

find_lowest_conformer() (examol.store.models.MoleculeRecord method) fix_cyclopropenyl() (in module examol.simulate.initialize) forces (examol.simulate.base.SimResult attribute) from_identifier() (examol.store.models.MoleculeRecord class method)

from_name() (examol.store.recipes.PropertyRecipe class method) (examol.store.recipes.RedoxEnergy class method) (examol.store.recipes.SolvationEnergy class method) from_simulation_result() (examol.store.models.Conformer class method) from_xyz() (examol.store.models.Conformer class method)

G

gathering (examol.select.base.Selector attribute) generate_functions() (examol.solution.SingleFidelityActiveLearning method) (examol.solution.SolutionSpecification method) generate_inchi_and_xyz() (in module examol.simulate.initialize) get_additional_training_information() (examol.steer.multifi.PipelineThinker method) (examol.steer.single.SingleStepThinker method) get_baseline_charge() (in module examol.utils.chemistry) get_config() (examol.score.nfp.ReduceAtoms method)

get_energy() (examol.store.models.Conformer method) get_energy_index() (examol.store.models.Conformer method) get_inchi_key_from_molecule_string() (in module examol.utils.chemistry) get_level() (examol.steer.multifi.PipelineThinker method) get_levels_for_property() (examol.solution.MultiFidelityActiveLearning method) get_model() (examol.score.nfp.NFPMessage method) get_or_make_record() (examol.store.db.base.MoleculeStore method) get_relevant_database_records() (examol.steer.multifi.PipelineThinker method) GreedySelector (class in examol.select.baseline)

I

identifier (examol.store.models.MoleculeRecord attribute) Identifiers (class in examol.store.models) inchi (examol.store.models.Identifiers attribute) inference_store (examol.steer.single.SingleStepThinker property)

initialize_charges() (in module examol.simulate.ase.utils) InMemoryStore (class in examol.store.db.memory) iterate_over_records() (examol.store.db.base.MoleculeStore method) (examol.store.db.memory.InMemoryStore method) iterate_over_search_space() (examol.steer.base.MoleculeThinker method)

J

json() (examol.simulate.base.SimResult method)

K

key (examol.store.models.MoleculeRecord attribute)

KMeansStarter (class in examol.start.kmeans)

L

load_database() (examol.specify.ExaMolSpecification method)

lookup() (examol.store.recipes.PropertyRecipe method)

M

make_data_loader() (in module examol.score.nfp) make_ephemeral_calculator() (in module examol.simulate.ase.utils) make_simple_network() (in module examol.score.nfp) minimum_training_size (examol.solution.SingleFidelityActiveLearning attribute) MissingData models (examol.solution.SingleFidelityActiveLearning attribute) module examol.score examol.score.base examol.score.nfp examol.select examol.select.base examol.select.baseline examol.select.bayes examol.select.botorch examol.simulate examol.simulate.ase examol.simulate.ase.utils examol.simulate.base examol.simulate.initialize examol.solution examol.specify examol.start examol.start.base examol.start.fast examol.start.kmeans examol.steer examol.steer.base examol.steer.baseline examol.steer.multifi examol.steer.single examol.store examol.store.db examol.store.db.base examol.store.db.memory examol.store.models examol.store.recipes examol.utils examol.utils.chemistry examol.utils.conversions

MoleculeRecord (class in examol.store.models) MoleculeStore (class in examol.store.db.base) MoleculeThinker (class in examol.steer.base) MultiFidelityActiveLearning (class in examol.solution) MultiFidelityScorer (class in examol.score.base) multiobjective (examol.select.base.Selector attribute) (examol.select.baseline.RandomSelector attribute) (examol.select.botorch.BOTorchSequentialSelector attribute)

N

names (examol.store.models.MoleculeRecord attribute) NFPMessage (class in examol.score.nfp) NFPScorer (class in examol.score.nfp)

num_levels (examol.steer.multifi.PipelineThinker property) num_models (examol.steer.single.SingleStepThinker property) num_outputs (examol.select.botorch.EnsembleCovarianceModel property) num_to_run (examol.solution.SolutionSpecification attribute)

O

optimize (examol.store.recipes.SimulationRequest attribute)

optimize_structure() (examol.simulate.ase.ASESimulator method) (examol.simulate.base.BaseSimulator method)

P

parse_from_molecule_string() (in module examol.utils.chemistry) pipeline_target (examol.solution.MultiFidelityActiveLearning attribute) PipelineThinker (class in examol.steer.multifi) posterior() (examol.select.botorch.EnsembleCovarianceModel method) prepare_message() (examol.score.base.Scorer method) (examol.score.nfp.NFPScorer method)

properties (examol.store.models.MoleculeRecord attribute) PropertyRecipe (class in examol.store.recipes) proxystore (examol.specify.ExaMolSpecification attribute) proxystore_threshold (examol.specify.ExaMolSpecification attribute) pubchem_id (examol.store.models.Identifiers attribute)

R

RandomSelector (class in examol.select.baseline) RandomStarter (class in examol.start.fast) RankingSelector (class in examol.select.base) read_from_string() (in module examol.utils.conversions) recipe (examol.store.recipes.PropertyRecipe property) (examol.store.recipes.RedoxEnergy property) (examol.store.recipes.SolvationEnergy property) recipes (examol.specify.ExaMolSpecification attribute) RedoxEnergy (class in examol.store.recipes)

ReduceAtoms (class in examol.score.nfp) reporters (examol.specify.ExaMolSpecification attribute) RequiredEnergy (class in examol.store.recipes) RequiredGeometry (class in examol.store.recipes) retrain() (examol.score.base.MultiFidelityScorer method) (examol.score.base.Scorer method) (examol.score.nfp.NFPScorer method) (examol.steer.single.SingleStepThinker method) run_dir (examol.specify.ExaMolSpecification attribute) run_inference() (examol.steer.single.SingleStepThinker method)

S

score() (examol.score.base.MultiFidelityScorer method) (examol.score.base.Scorer method) (examol.score.nfp.NFPScorer method) score_options (examol.solution.SingleFidelityActiveLearning attribute) Scorer (class in examol.score.base) scorer (examol.solution.SingleFidelityActiveLearning attribute) (examol.steer.single.SingleStepThinker attribute) search_space (examol.specify.ExaMolSpecification attribute) search_space_dir (examol.steer.single.SingleStepThinker attribute) search_space_inputs (examol.steer.single.SingleStepThinker attribute) search_space_smiles (examol.steer.single.SingleStepThinker attribute) select() (examol.start.base.Starter method) Selector (class in examol.select.base) selector (examol.solution.SingleFidelityActiveLearning attribute) SimResult (class in examol.simulate.base) SimulationRequest (class in examol.store.recipes) simulator (examol.specify.ExaMolSpecification attribute) SingleFidelityActiveLearning (class in examol.solution) SingleStepThinker (class in examol.steer.single) smiles (examol.store.models.Identifiers attribute) solution (examol.specify.ExaMolSpecification attribute) (examol.steer.multifi.PipelineThinker attribute) (examol.steer.single.SingleStepThinker attribute)

SolutionSpecification (class in examol.solution) SolvationEnergy (class in examol.store.recipes) solvent (examol.simulate.base.SimResult attribute) (examol.store.models.EnergyEvaluation attribute) (examol.store.models.MissingData attribute) (examol.store.recipes.RequiredEnergy attribute) (examol.store.recipes.SimulationRequest attribute) source (examol.store.models.Conformer attribute) start_gathering() (examol.select.base.RankingSelector method) (examol.select.base.Selector method) (examol.select.baseline.RandomSelector method) Starter (class in examol.start.base) starter (examol.solution.SolutionSpecification attribute) startup() (examol.steer.baseline.BruteForceThinker method) (examol.steer.single.SingleStepThinker method) steps (examol.solution.MultiFidelityActiveLearning attribute) (examol.steer.multifi.PipelineThinker property) store_simulation() (examol.steer.base.MoleculeThinker method) submit_inference() (examol.steer.multifi.PipelineThinker method) (examol.steer.single.SingleStepThinker method) submit_simulation() (examol.steer.base.MoleculeThinker method) subsets (examol.store.models.MoleculeRecord attribute) suggest_computations() (examol.store.recipes.PropertyRecipe method)

T

task_iterator() (examol.steer.base.MoleculeThinker method) task_queue (examol.steer.base.MoleculeThinker attribute) task_queue_lock (examol.steer.base.MoleculeThinker attribute) thinker (examol.specify.ExaMolSpecification attribute) thinker_options (examol.specify.ExaMolSpecification attribute)

thinker_workers (examol.specify.ExaMolSpecification attribute) to_select (examol.select.base.Selector attribute) train_options (examol.solution.SingleFidelityActiveLearning attribute) transform_inputs() (examol.score.base.Scorer method) (examol.score.nfp.NFPScorer method) transform_outputs() (examol.score.base.Scorer method)

U

update() (examol.score.base.Scorer method) (examol.score.nfp.NFPScorer method) (examol.select.base.Selector method) (examol.select.bayes.ExpectedImprovement method) (examol.select.botorch.BOTorchSequentialSelector method)

update_database() (examol.simulate.ase.ASESimulator method) update_record() (examol.store.db.base.MoleculeStore method) (examol.store.db.memory.InMemoryStore method) (examol.store.recipes.PropertyRecipe method) update_records() (examol.store.db.base.MoleculeStore method)

W

write_to_string() (in module examol.utils.conversions)

write_xyz_from_mol() (in module examol.simulate.initialize)

X

xyz (examol.simulate.base.SimResult attribute) (examol.store.models.Conformer attribute) (examol.store.recipes.SimulationRequest attribute)

xyz_hash (examol.store.models.Conformer attribute)