Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | X A addChannel() (molfoundry.MultiPhaseStochsim method) addCoupledChannel() (molfoundry.MultiPhaseStochsim method) addDerivation() (molfoundry.DG.Builder method) addInitial() (molfoundry.MultiPhaseStochsim.Phase method) addPartition() (molfoundry.MultiPhaseStochsim method) addPhase() (molfoundry.MultiPhaseStochsim method) addSubset() (in module molfoundry) addUniverse() (in module molfoundry) apply() (molfoundry.DG.Builder method) Aromatic (molfoundry.BondType attribute) AtomId (class in molfoundry) atomId (molfoundry.Vertex property) Aut (class in molfoundry) aut() (molfoundry.Graph method) AutGroup (class in molfoundry) autInChI() (molfoundry.Graph method) B BondType (class in molfoundry) bondType (molfoundry.Edge property) build() (molfoundry.DG method) build_tracer() (molfoundry.atomtracing.TracerInputs method) by_element() (in module molfoundry.atomtracing) byId() (molfoundry.AtomId static method) bySymbol() (molfoundry.AtomId static method) C canonKey (molfoundry.Graph property) Charge (class in molfoundry) charge (molfoundry.Vertex property) clone() (molfoundry.Graph method) collapseHydrogens (molfoundry.GraphPrinter property) color (molfoundry.atomtracing.ReactionRule attribute) columnPhases (molfoundry.MultiPhaseStochsim.Trajectory attribute) columnVertexIds (molfoundry.MultiPhaseStochsim.Trajectory attribute) compose() (molfoundry.Aut method) concentration() (molfoundry.MultiPhaseStochsim method) (molfoundry.MultiPhaseStochsim.Phase method) Conformer (class in molfoundry) counts (molfoundry.MultiPhaseStochsim.Trajectory attribute) (molfoundry.Stochsim.Trajectory attribute) createdGraphs (molfoundry.DG property) D Default (molfoundry.GraphType attribute) degree (molfoundry.Vertex property) Derivation (class in molfoundry) Derivations (class in molfoundry) DG (class in molfoundry) dg (molfoundry.DG.Builder property) (molfoundry.DG.HyperEdge property) (molfoundry.DG.Vertex property) (molfoundry.MultiPhaseStochsim.Phase property) (molfoundry.Stochsim property) DG.Builder (class in molfoundry) DG.Builder.ExecuteResult (class in molfoundry) DG.HyperEdge (class in molfoundry) DG.Vertex (class in molfoundry) DGAtomTracing (class in molfoundry.atomtracing) DGStrat (class in molfoundry) DGVertexMapper (class in molfoundry) disable_post() (in module molfoundry) Double (molfoundry.BondType attribute) draw() (in module molfoundry.atomtracing) draw_filtered_source() (in module molfoundry.atomtracing) draw_filtered_source_target() (in module molfoundry.atomtracing) draw_filtered_target() (in module molfoundry.atomtracing) draw_reaction_network() (in module molfoundry.atomtracing) DrawLayout (in module molfoundry.atomtracing) drawMode (molfoundry.GraphPrinter property) drawRuleConditions (molfoundry.GraphPrinter property) DrawStyle (in module molfoundry.atomtracing) E Edge (class in molfoundry) EdgeRange (class in molfoundry) edges (molfoundry.DG property) (molfoundry.Graph property) educts (molfoundry.atomtracing.ReactionRule attribute) educts_product_indices (molfoundry.atomtracing.ReactionRule attribute) eLabelCount() (molfoundry.Graph method) Electron (molfoundry.GraphType attribute) electrons (molfoundry.AtomId property) embedRDKit() (molfoundry.Conformer method) enable_post() (in module molfoundry) entries() (molfoundry.VertexMap method) equals() (molfoundry.DG.HyperEdge method) eval() (molfoundry.RCEvaluator method) exactMass (molfoundry.Graph property) execute() (in module molfoundry) (molfoundry.DG.Builder method) externalId (molfoundry.Vertex property) F filterSubset() (in module molfoundry) filterUniverse() (in module molfoundry) findEdge() (molfoundry.DG method) findVertex() (molfoundry.DG method) from_dg() (molfoundry.atomtracing.DGAtomTracing static method) from_hyperedges() (molfoundry.atomtracing.DGAtomTracing static method) fromCycleNotation() (molfoundry.Aut static method) fromGens() (molfoundry.AutGroup static method) fromGMLFile() (molfoundry.Rule static method) fromGMLString() (molfoundry.Graph static method) (molfoundry.Rule static method) fromInChI() (molfoundry.Graph static method) fromMolfile() (molfoundry.Graph static method) fromMolFoundry() (molfoundry.Rule static method) fromRMG() (molfoundry.Graph static method) fromSMILES() (molfoundry.Graph static method) func (molfoundry.atomtracing.ReactionRule attribute) G generate() (molfoundry.AutGroup method) gens (molfoundry.AutGroup property) get_all_origin_id_positions() (molfoundry.atomtracing.SaturateTracer method) get_all_origin_species_targets() (molfoundry.atomtracing.SaturateTracer method) get_all_origin_target_labelings() (molfoundry.atomtracing.SaturateTracer method) get_all_position_id_labelings() (molfoundry.atomtracing.SaturateTracer method) get_all_species_labelings() (molfoundry.atomtracing.SaturateTracer method) get_origin_id_color_map() (in module molfoundry.atomtracing) getGMLString() (molfoundry.Graph method) (molfoundry.Rule method) getVertexCoordinate() (molfoundry.Conformer method) getVertexFromExternalId() (molfoundry.Graph method) Graph (class in molfoundry) graph (molfoundry.DG.Vertex property) (molfoundry.Edge property) (molfoundry.Vertex property) graphDatabase (molfoundry.DG property) graphGMLString() (in module molfoundry) GraphPrinter (class in molfoundry) GraphState (class in molfoundry) GraphType (class in molfoundry) H hasActiveBuilder (molfoundry.DG property) heavy_atoms() (in module molfoundry.atomtracing) hyperEdge (molfoundry.DGVertexMapper property) I id (molfoundry.AtomId property) (molfoundry.DG property) (molfoundry.DG.HyperEdge property) (molfoundry.DG.Vertex property) (molfoundry.Graph property) (molfoundry.Rule property) (molfoundry.Vertex property) identity_instance() (molfoundry.atomtracing.Template method) ids (molfoundry.atomtracing.LabelSet attribute) (molfoundry.atomtracing.Template attribute) inchi (molfoundry.Graph property) inchi() (in module molfoundry) inchiKey (molfoundry.Graph property) incidentEdges (molfoundry.Vertex property) inDegree (molfoundry.DG.Vertex property) index (molfoundry.MultiPhaseStochsim.Channel property) (molfoundry.MultiPhaseStochsim.Phase attribute) (molfoundry.Stochsim.StepInfo attribute) inEdges (molfoundry.DG.Vertex property) inputGraphs (in module molfoundry) inputRules (in module molfoundry) Invalid (molfoundry.BondType attribute) inverse (molfoundry.DG.HyperEdge property) inverse() (molfoundry.Aut method) isActive (molfoundry.DG.Builder property) isElectron() (molfoundry.Vertex method) isMolecule (molfoundry.Graph property) isNull() (molfoundry.DG.HyperEdge method) (molfoundry.DG.Vertex method) (molfoundry.Edge method) (molfoundry.Vertex method) Isomorphism (molfoundry.LabelRelation attribute) isomorphism() (molfoundry.Graph method) Isotope (class in molfoundry) isotope (molfoundry.Vertex property) isotopicMasses (molfoundry.AtomId property) iteration (molfoundry.MultiPhaseStochsim property) (molfoundry.Stochsim property) L label_set_of() (molfoundry.atomtracing.TracerInputs method) labeling_to_display_str() (molfoundry.atomtracing.SaturateTracer method) LabelRelation (class in molfoundry) LabelSet (class in molfoundry.atomtracing) LabelSettings (class in molfoundry) labelSettings (molfoundry.DG property) LabelType (class in molfoundry) labelType (molfoundry.Rule property) left (molfoundry.Derivation property) (molfoundry.Derivations property) leftPredicate (in module molfoundry) limit (molfoundry.DGVertexMapper property) locked (molfoundry.DG property) LogicError M makeAddDynamic() (molfoundry.DGStrat static method) makeAddStatic() (molfoundry.DGStrat static method) makeExecute() (molfoundry.DGStrat static method) makeFilter() (molfoundry.DGStrat static method) makeInverse() (molfoundry.Rule method) makeLeftPredicate() (molfoundry.DGStrat static method) makeParallel() (molfoundry.DGStrat static method) makeRepeat() (molfoundry.DGStrat static method) makeRevive() (molfoundry.DGStrat static method) makeRightPredicate() (molfoundry.DGStrat static method) makeRule() (molfoundry.DGStrat static method) makeSequence() (molfoundry.DGStrat static method) maxExternalId (molfoundry.Graph property) minExternalId (molfoundry.Graph property) module molfoundry.atomtracing molfile (molfoundry.Graph property) molfile() (in module molfoundry) molfoundry.atomtracing module molFoundryId (molfoundry.Rule property) mostAbundantIsotope (molfoundry.AtomId property) MultiPhaseStochsim (class in molfoundry) MultiPhaseStochsim.Channel (class in molfoundry) MultiPhaseStochsim.Phase (class in molfoundry) MultiPhaseStochsim.Trajectory (class in molfoundry) N name (molfoundry.atomtracing.LabelSet attribute) (molfoundry.atomtracing.ReactionRule attribute) (molfoundry.atomtracing.Template attribute) (molfoundry.Graph property) (molfoundry.MultiPhaseStochsim.Phase property) (molfoundry.Rule property) numEdges (molfoundry.DG property) (molfoundry.Graph property) numLeftComponents (molfoundry.Rule property) numRightComponents (molfoundry.Rule property) numSources (molfoundry.DG.HyperEdge property) numTargets (molfoundry.DG.HyperEdge property) numVertices (molfoundry.DG property) (molfoundry.Graph property) O optimizeXTB() (molfoundry.Conformer method) orbitalNames (molfoundry.AtomId property) orbitals (molfoundry.AtomId property) outDegree (molfoundry.DG.Vertex property) outEdges (molfoundry.DG.Vertex property) P phases (molfoundry.MultiPhaseStochsim property) position_id() (molfoundry.atomtracing.TracerInputs method) position_id_by_atom (molfoundry.atomtracing.TracerInputs attribute) postChapter() (in module molfoundry) postSection() (in module molfoundry) principalQuantumNumber (molfoundry.AtomId property) print() (molfoundry.DG method) (molfoundry.DG.HyperEdge method) (molfoundry.Graph method) (molfoundry.MultiPhaseStochsim method) (molfoundry.Rule method) (molfoundry.Stochsim method) products (molfoundry.atomtracing.ReactionRule attribute) protons (molfoundry.AtomId property) R rate (molfoundry.MultiPhaseStochsim.Channel property) rcCommon (in module molfoundry) RCEvaluator (class in molfoundry) RCExp (class in molfoundry) rcParallel (in module molfoundry) rcSub (in module molfoundry) rcSuper (in module molfoundry) reaction (molfoundry.Stochsim.StepInfo attribute) ReactionRule (class in molfoundry.atomtracing) reactionSMILES() (molfoundry.VertexMap method) relation (molfoundry.LabelSettings property) removeExternalId() (molfoundry.Vertex method) removeHydrogens() (molfoundry.Graph method) repeat (in module molfoundry) reverse() (molfoundry.atomtracing.ReactionRule method) revive() (in module molfoundry) right (molfoundry.Derivation property) (molfoundry.Derivations property) rightPredicate (in module molfoundry) Rule (class in molfoundry) rule (molfoundry.Derivation property) (molfoundry.VertexMap property) ruleGML() (in module molfoundry) ruleGMLString() (in module molfoundry) ruleMolFoundry() (in module molfoundry) ruleNodeId (molfoundry.VertexMapEntry attribute) rules (molfoundry.atomtracing.TracerInputs attribute) (molfoundry.Derivations property) (molfoundry.DG.HyperEdge property) run() (molfoundry.atomtracing.SaturateTracer method) S SaturateTracer (class in molfoundry.atomtracing) series() (molfoundry.MultiPhaseStochsim method) (molfoundry.MultiPhaseStochsim.Phase method) (molfoundry.MultiPhaseStochsim.Trajectory method) (molfoundry.Stochsim method) (molfoundry.Stochsim.Trajectory method) setDrawTime() (molfoundry.MultiPhaseStochsim method) (molfoundry.Stochsim method) setExternalId() (molfoundry.Vertex method) setInputRate() (molfoundry.MultiPhaseStochsim.Phase method) (molfoundry.Stochsim method) setOnStep() (molfoundry.MultiPhaseStochsim method) (molfoundry.Stochsim method) setOutputRate() (molfoundry.MultiPhaseStochsim.Phase method) (molfoundry.Stochsim method) setReactionRate() (molfoundry.MultiPhaseStochsim.Phase method) (molfoundry.Stochsim method) simulate() (molfoundry.MultiPhaseStochsim method) (molfoundry.Stochsim method) Single (molfoundry.BondType attribute) skipped_edges (molfoundry.atomtracing.TracerInputs attribute) smiles (molfoundry.atomtracing.Template attribute) (molfoundry.Graph property) smiles() (in module molfoundry) smilesWithExternalIds (molfoundry.Graph property) smilesWithIds (molfoundry.Graph property) source (molfoundry.Edge property) (molfoundry.VertexMapEntry attribute) sourceInstance (molfoundry.VertexMapEntry attribute) sources (molfoundry.DG.HyperEdge property) Specialisation (molfoundry.LabelRelation attribute) standardAtomicWeight (molfoundry.AtomId property) state() (molfoundry.MultiPhaseStochsim method) (molfoundry.MultiPhaseStochsim.Phase method) (molfoundry.Stochsim method) Stochsim (class in molfoundry) Stochsim.StepInfo (class in molfoundry) Stochsim.Trajectory (class in molfoundry) String (molfoundry.LabelType attribute) stringLabel (molfoundry.Edge property) (molfoundry.Vertex property) subset (molfoundry.GraphState property) subset() (molfoundry.DG.Builder.ExecuteResult method) symbol (molfoundry.AtomId property) T target (molfoundry.Edge property) (molfoundry.VertexMapEntry attribute) targetInstance (molfoundry.VertexMapEntry attribute) targets (molfoundry.DG.HyperEdge property) Template (class in molfoundry.atomtracing) template_by_graph_id (molfoundry.atomtracing.TracerInputs attribute) template_of() (molfoundry.atomtracing.TracerInputs method) TemplateInstance (in module molfoundry.atomtracing) templates (molfoundry.atomtracing.TracerInputs attribute) Term (molfoundry.LabelType attribute) time (molfoundry.MultiPhaseStochsim property) (molfoundry.Stochsim property) (molfoundry.Stochsim.StepInfo attribute) times (molfoundry.MultiPhaseStochsim.Trajectory attribute) (molfoundry.Stochsim.Trajectory attribute) times() (molfoundry.MultiPhaseStochsim method) total() (molfoundry.MultiPhaseStochsim method) totalSeries() (molfoundry.MultiPhaseStochsim method) TracerInputs (class in molfoundry.atomtracing) trajectory() (molfoundry.MultiPhaseStochsim method) (molfoundry.Stochsim method) transfer() (molfoundry.MultiPhaseStochsim method) Triple (molfoundry.BondType attribute) type (molfoundry.Graph property) (molfoundry.LabelSettings property) (molfoundry.Rule property) U Unification (molfoundry.LabelRelation attribute) universe (molfoundry.GraphState property) universe() (molfoundry.DG.Builder.ExecuteResult method) unlabeled_instance() (molfoundry.atomtracing.Template method) V valenceElectrons (molfoundry.AtomId property) valid (molfoundry.AtomId property) Vertex (class in molfoundry) VertexFilter (in module molfoundry) vertexIds (molfoundry.Stochsim.Trajectory attribute) VertexMap (class in molfoundry) VertexMapEntry (class in molfoundry) vertexMaps() (molfoundry.DG.HyperEdge method) VertexRange (class in molfoundry) vertices (molfoundry.DG property) (molfoundry.Graph property) vLabelCount() (molfoundry.Graph method) volume (molfoundry.MultiPhaseStochsim.Phase property) X xyz() (molfoundry.Conformer method)