Index

A

acceptor_atom (synde.graph.DirectionalFMO attribute) acceptor_component (synde.graph.DirectionalFMO attribute) accessibility_weight (synde.graph.PairScoringConfig attribute) alpha (synde.graph.HuckelParameters attribute) (synde.graph.HuckelSystemResult attribute) applicability (synde.energy.CalibratedPrediction attribute)

aromaticity_reorganization_weight (synde.energy.ITSScoringConfig attribute) assign() (synde.graph.PiSystemAssigner method) assign_pi_systems() (in module synde.graph) atom_a (synde.graph.PairScoreResult attribute) atom_b (synde.graph.PairScoreResult attribute) atom_for() (synde.graph.PiAssignmentResult method) atoms (synde.graph.PiAssignmentResult attribute)

B

beta_aromatic (synde.graph.HuckelParameters attribute) beta_conjugated (synde.graph.HuckelParameters attribute) beta_double (synde.graph.HuckelParameters attribute) bond_changes (synde.energy.ITSScoreResult attribute) (synde.energy.ReactionScoreResult attribute) (synde.graph.ITSGraph attribute)

broken_bond_weight (synde.energy.ITSScoringConfig attribute) build() (synde.graph.ITSGraphBuilder method)

C

CalibratedPrediction (class in synde.energy) CalibrationRecord (class in synde.energy) canonical_smiles (synde.graph.NormalizedMolecularGraph attribute) card (synde.energy.RidgeCalibrator attribute) CascadeReport (class in synde.integration) CascadeRow (class in synde.integration) charge_weight (synde.energy.ITSScoringConfig attribute) (synde.graph.PairScoringConfig attribute) code (synde.graph.GraphWarning attribute) coefficients (synde.graph.HuckelSystemResult attribute)

component_a (synde.graph.PairScoreResult attribute) component_b (synde.graph.PairScoreResult attribute) component_id (synde.graph.ComponentFrontier attribute) (synde.graph.HSABDescriptor attribute) ComponentFrontier (class in synde.graph) components (synde.energy.ITSScoreResult attribute) (synde.energy.MoleculeScoreResult attribute) (synde.energy.ReactionScoreResult attribute) (synde.geometry.GeometryScoreResult attribute) (synde.graph.PairScoreResult attribute) confidence (synde.graph.PiAtom attribute)

D

degeneracy_tolerance (synde.graph.HuckelParameters attribute) descriptors (synde.energy.MoleculeScoreResult attribute) deterministic_split() (in module synde.energy) direction (synde.graph.PairScoreResult attribute)

directional_fmo() (in module synde.graph) DirectionalFMO (class in synde.graph) donor_atom (synde.graph.DirectionalFMO attribute) donor_component (synde.graph.DirectionalFMO attribute)

E

edges (synde.graph.PiSystem attribute) electron_count (synde.graph.HuckelSystemResult attribute) (synde.graph.PiAssignmentResult property) (synde.graph.PiSystem attribute)

electronegativity (synde.graph.HSABDescriptor attribute) electrons (synde.graph.PiAtom attribute) equivalence_key (synde.graph.PairScoreGroup attribute) (synde.graph.PairScoreResult attribute) equivalent_pairs (synde.graph.PairScoreGroup property)

F

feature_names (synde.energy.ModelCard attribute) (synde.energy.RidgeCalibrator attribute) features (synde.energy.CalibrationRecord attribute) fit() (synde.energy.RidgeCalibrator method) fmo_weight (synde.energy.ITSScoringConfig attribute) (synde.graph.PairScoringConfig attribute)

force_field (synde.geometry.GeometryScoringConfig attribute) force_field_energy_kcal_mol (synde.geometry.GeometryScoreResult attribute) formed_bond_weight (synde.energy.ITSScoringConfig attribute) from_graph() (synde.graph.GraphBuilder static method) from_smiles() (synde.graph.GraphBuilder static method) from_synkit_graph() (synde.graph.GraphBuilder static method) frontier_subspaces() (synde.graph.GeneralizedHuckel method)

G

gap (synde.graph.DirectionalFMO attribute) gap_floor (synde.graph.PairScoringConfig attribute) gate (synde.geometry.GeometryScoringConfig attribute) GeneralizedHuckel (class in synde.graph) GeneralizedHuckelResult (class in synde.graph) geometry_corrected_score (synde.geometry.GeometryScoreResult attribute) GeometryScorer (class in synde.geometry) GeometryScoreResult (class in synde.geometry) GeometryScoringConfig (class in synde.geometry) graph (synde.graph.ITSGraph attribute) (synde.graph.NormalizedMolecularGraph attribute)

graph_score (synde.integration.CascadeRow attribute) graph_seconds (synde.integration.CascadeReport attribute) GraphBuilder (class in synde.graph) GraphEnergy (class in synde.energy) GraphNormalizer (class in synde.graph) GraphPairScorer (class in synde.graph) GraphValidationError GraphWarning (class in synde.graph) GraphXTBCascade (class in synde.integration)

H

hamiltonian (synde.graph.HuckelSystemResult attribute) hardness (synde.graph.HSABDescriptor attribute) hetero_beta_scale (synde.graph.HuckelParameters attribute) homo_density (synde.graph.ComponentFrontier attribute) (synde.graph.HuckelSystemResult attribute) homo_energy (synde.graph.ComponentFrontier attribute) (synde.graph.HuckelSystemResult property)

homo_indices (synde.graph.HuckelSystemResult attribute) hsab_descriptor() (in module synde.graph) hsab_weight (synde.energy.ITSScoringConfig attribute) (synde.graph.PairScoringConfig attribute) HSABDescriptor (class in synde.graph) HuckelParameters (class in synde.graph) HuckelSystemResult (class in synde.graph)

I

identifier (synde.energy.CalibrationRecord attribute) identity (synde.graph.NormalizedMolecularGraph attribute) included (synde.graph.PiAtom attribute) its_graph (synde.energy.ITSScoreResult attribute) its_score (synde.energy.ITSScoreResult attribute)

ITSGraph (class in synde.graph) ITSGraphBuilder (class in synde.graph) ITSScorer (class in synde.energy) ITSScoreResult (class in synde.energy) ITSScoringConfig (class in synde.energy)

L

local_electrophilic_softness (synde.graph.HSABDescriptor attribute) local_hsab_compatibility() (in module synde.graph) local_nucleophilic_softness (synde.graph.HSABDescriptor attribute) lumo_density (synde.graph.ComponentFrontier attribute) (synde.graph.HuckelSystemResult attribute)

lumo_energy (synde.graph.ComponentFrontier attribute) (synde.graph.HuckelSystemResult property) lumo_indices (synde.graph.HuckelSystemResult attribute)

M

mean (synde.energy.RidgeCalibrator attribute) message (synde.graph.GraphWarning attribute) metrics (synde.energy.ModelCard attribute) model_card (synde.energy.CalibratedPrediction attribute) model_name (synde.energy.ModelCard attribute) ModelCard (class in synde.energy) module synde.energy synde.geometry synde.graph synde.integration

MoleculeScorer (class in synde.energy) MoleculeScoreResult (class in synde.energy) MoleculeScoringConfig (class in synde.energy)

N

node (synde.graph.PiAtom attribute) nodes (synde.graph.ComponentFrontier attribute) (synde.graph.GraphWarning attribute) (synde.graph.HuckelSystemResult attribute) (synde.graph.PiSystem attribute)

nonbonded_terms_for_positions() (synde.geometry.GeometryScorer static method) normalize() (synde.graph.GraphNormalizer method) normalize_graph() (in module synde.graph) NormalizedMolecularGraph (class in synde.graph) num_conformers (synde.geometry.GeometryScoringConfig attribute)

O

occupations (synde.graph.HuckelSystemResult attribute) occupations() (synde.graph.GeneralizedHuckel static method)

orbital_energies (synde.graph.HuckelSystemResult attribute) order_change_weight (synde.energy.ITSScoringConfig attribute)

P

pair_compatibility_score (synde.graph.PairScoreResult attribute) pairs (synde.graph.PairScoreGroup attribute) PairScoreGroup (class in synde.graph) PairScoreResult (class in synde.graph) PairScoringConfig (class in synde.graph) parameter_set (synde.graph.GeneralizedHuckelResult attribute) (synde.graph.HuckelParameters attribute) pi_graph (synde.graph.PiAssignmentResult attribute) pi_populations (synde.graph.HuckelSystemResult attribute) pi_stabilization (synde.graph.GeneralizedHuckelResult property) (synde.graph.HuckelSystemResult attribute) pi_weight (synde.energy.MoleculeScoringConfig attribute)

PiAssignmentResult (class in synde.graph) PiAtom (class in synde.graph) PiSystem (class in synde.graph) PiSystemAssigner (class in synde.graph) predict() (synde.energy.RidgeCalibrator method) product_graph (synde.graph.ITSGraph attribute) product_score (synde.energy.ReactionScoreResult attribute) proposed_bond_order (synde.graph.PairScoringConfig attribute) provenance (synde.energy.CalibrationRecord attribute) (synde.energy.ITSScoreResult attribute) (synde.energy.MoleculeScoreResult attribute) (synde.energy.ReactionScoreResult attribute) (synde.geometry.GeometryScoreResult attribute)

R

random_seed (synde.geometry.GeometryScoringConfig attribute) rank() (synde.graph.GraphPairScorer method) rank_pairs_from_smiles() (synde.energy.GraphEnergy method) raw_pi_energy (synde.graph.GeneralizedHuckelResult property) (synde.graph.HuckelSystemResult attribute) reactant_graph (synde.graph.ITSGraph attribute) reactant_score (synde.energy.ReactionScoreResult attribute) reacting_atom_maps (synde.energy.ITSScoreResult attribute) (synde.graph.ITSGraph attribute) reaction_delta_score (synde.energy.ReactionScoreResult attribute) reaction_smiles (synde.integration.CascadeRow attribute) ReactionScorer (class in synde.energy)

ReactionScoreResult (class in synde.energy) ReactionScoringConfig (class in synde.energy) reason (synde.graph.PiAtom attribute) reference_pi_energy (synde.graph.GeneralizedHuckelResult property) (synde.graph.HuckelSystemResult attribute) regularized_gap (synde.graph.DirectionalFMO attribute) representative (synde.graph.PairScoreGroup attribute) require_atom_mapping (synde.energy.ReactionScoringConfig attribute) residual_std (synde.energy.RidgeCalibrator attribute) ridge_alpha (synde.energy.ModelCard attribute) RidgeCalibrator (class in synde.energy) rows (synde.integration.CascadeReport attribute)

S

save() (synde.energy.RidgeCalibrator method) scale (synde.energy.RidgeCalibrator attribute) score (synde.energy.MoleculeScoreResult attribute) (synde.graph.DirectionalFMO attribute) score() (synde.energy.ITSScorer method) (synde.energy.MoleculeScorer method) (synde.energy.ReactionScorer method) score_its() (synde.energy.GraphEnergy method) score_molecule_from_graph() (synde.energy.GraphEnergy method) score_molecule_from_smiles() (synde.energy.GraphEnergy method) score_molecule_with_geometry() (synde.energy.GraphEnergy method) score_reaction() (synde.energy.GraphEnergy method) score_smiles() (synde.geometry.GeometryScorer method) screen() (synde.integration.GraphXTBCascade method) selected (synde.integration.CascadeRow attribute) SFEnergy (class in synde.integration) shortlist_size (synde.integration.CascadeReport attribute) should_run() (synde.geometry.GeometryScorer method) softness (synde.graph.HSABDescriptor attribute) solve() (synde.graph.GeneralizedHuckel method) solve_generalized_huckel() (in module synde.graph) sort_reactions() (synde.integration.SFEnergy method)

source (synde.graph.NormalizedMolecularGraph attribute) state_delta_score (synde.energy.ITSScoreResult attribute) state_delta_weight (synde.energy.ITSScoringConfig attribute) status (synde.energy.ITSScoreResult attribute) (synde.energy.MoleculeScoreResult attribute) (synde.energy.ReactionScoreResult attribute) (synde.geometry.GeometryScoreResult attribute) (synde.graph.GeneralizedHuckelResult attribute) (synde.graph.NormalizedMolecularGraph attribute) (synde.graph.PiAssignmentResult attribute) (synde.integration.CascadeRow attribute) subspace_density() (synde.graph.GeneralizedHuckel static method) synde.energy module synde.geometry module synde.graph module synde.integration module systems (synde.graph.GeneralizedHuckelResult attribute) (synde.graph.PiAssignmentResult attribute)

T

target (synde.energy.CalibratedPrediction attribute) (synde.energy.CalibrationRecord attribute) (synde.energy.ModelCard attribute) to_dict() (synde.energy.ITSScoreResult method) (synde.energy.MoleculeScoreResult method) (synde.energy.ReactionScoreResult method) (synde.geometry.GeometryScoreResult method) (synde.graph.NormalizedMolecularGraph method)

training_count (synde.energy.ModelCard attribute)

U

uncertainty (synde.energy.CalibratedPrediction attribute) units (synde.energy.CalibratedPrediction attribute) (synde.energy.ITSScoreResult attribute) (synde.energy.ModelCard attribute) (synde.energy.MoleculeScoreResult attribute) (synde.energy.ReactionScoreResult attribute)

V

valence_reorganization_weight (synde.energy.ITSScoringConfig attribute) valid (synde.graph.DirectionalFMO attribute)

value (synde.energy.CalibratedPrediction attribute) version (synde.energy.ModelCard attribute)

W

warning (synde.graph.DirectionalFMO attribute) warning_codes() (synde.graph.NormalizedMolecularGraph method) (synde.graph.PiAssignmentResult method) warnings (synde.energy.ITSScoreResult attribute) (synde.energy.MoleculeScoreResult attribute) (synde.energy.ReactionScoreResult attribute) (synde.geometry.GeometryScoreResult attribute) (synde.graph.GeneralizedHuckelResult attribute) (synde.graph.NormalizedMolecularGraph attribute) (synde.graph.PairScoreResult attribute) (synde.graph.PiAssignmentResult attribute)

weights (synde.energy.RidgeCalibrator attribute)

X

xtb_delta_e (synde.integration.CascadeRow attribute)

xtb_seconds (synde.integration.CascadeReport attribute)