Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X A add_in_flow() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) add_out_flow() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) addChannel() (molfoundry.MultiPhaseStochsim method) addCoupledChannel() (molfoundry.MultiPhaseStochsim method) addDerivation() (molfoundry.DG.Builder method) addHyperEdge() (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) addVertex() (molfoundry.DG.Builder method) AdjacencyConstraint (class in molfoundry) AllOf (class in molfoundry) AnyOf (class in molfoundry) apply() (molfoundry.DG.Builder method) applyMatch() (molfoundry.DG.Builder method) ApplyMode (class in molfoundry) applyPartialMatch() (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 Between (molfoundry.ConstraintOp attribute) BondType (class in molfoundry) bondType (molfoundry.Edge property) (molfoundry.RuleEdgeSide 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 canonIdentity (molfoundry.Species property) canonKey (molfoundry.Graph property) (molfoundry.Rule property) Changed (molfoundry.Membership attribute) changesLabel (molfoundry.RuleVertex property) Charge (class in molfoundry) charge (molfoundry.Vertex property) child (molfoundry.Not property) children (molfoundry.AdjacencyConstraint property) (molfoundry.AllOf property) (molfoundry.AnyOf property) (molfoundry.ConditionAnd property) (molfoundry.ConditionExists property) (molfoundry.ConditionNot property) (molfoundry.ConditionOr property) (molfoundry.ConditionTrue property) (molfoundry.LabelAnyConstraint property) (molfoundry.NoEdgeConstraint property) (molfoundry.ShortestPathConstraint property) Circle (molfoundry.OverlayShape attribute) Circles (molfoundry.DrawMode attribute) clone() (molfoundry.Graph method) collapseHydrogens (molfoundry.GraphPrinter property) color (molfoundry.atomtracing.ReactionRule attribute) columnKeys (molfoundry.Trajectory attribute) columnPhases (molfoundry.MultiPhaseStochsim.Trajectory attribute) columnVertexIds (molfoundry.MultiPhaseStochsim.Trajectory attribute) compileConditions() (molfoundry.Rule method) compose() (molfoundry.Aut method) CompositionEdge (class in molfoundry) CompositionGraph (class in molfoundry) CompositionVertex (class in molfoundry) concentration() (molfoundry.MultiPhaseStochsim method) (molfoundry.MultiPhaseStochsim.Phase method) Condition (in module molfoundry) condition (molfoundry.ConditionExists attribute) (molfoundry.ConditionNot attribute) (molfoundry.IncidenceConstraint property) ConditionAnd (class in molfoundry) ConditionEdge (class in molfoundry) ConditionExists (class in molfoundry) ConditionNot (class in molfoundry) ConditionOr (class in molfoundry) ConditionTrue (class in molfoundry) ConditionVertex (class in molfoundry) Conformer (class in molfoundry) Constraint (in module molfoundry) ConstraintOp (class in molfoundry) Context (molfoundry.Membership attribute) count (molfoundry.AdjacencyConstraint attribute) (molfoundry.IncidenceCount property) counts (molfoundry.MultiPhaseStochsim.Trajectory attribute) (molfoundry.Stochsim.Trajectory attribute) counts() (molfoundry.Trajectory method) Created (molfoundry.Membership attribute) createdGraphs (molfoundry.DG property) CWDPath (class in molfoundry) D DarkMode (class in molfoundry) darkMode (molfoundry.GraphPrinter property) Default (molfoundry.DrawStyle attribute) (molfoundry.GraphType attribute) degree (molfoundry.CompositionVertex property) (molfoundry.Vertex property) Deleted (molfoundry.Membership attribute) 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.DGPrintData property) (molfoundry.FlowSolution property) (molfoundry.FlowSolutionCertificate 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) DGPrintData (class in molfoundry) DGPrinter (class in molfoundry) DGStrat (class in molfoundry) DGVertexMapper (class in molfoundry) disable_post() (in module molfoundry) discovery (molfoundry.Species attribute) dispose() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) Dot (molfoundry.Layout attribute) Double (molfoundry.BondType attribute) dpoJumpClosure() (molfoundry.Rule method) 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) DrawMode (class in molfoundry) drawMode (molfoundry.GraphPrinter property) drawRuleConditions (molfoundry.GraphPrinter property) DrawStyle (class in molfoundry) drawStyle (molfoundry.GraphPrinter property) Dynamic (molfoundry.DarkMode attribute) E Edge (class in molfoundry) edge (molfoundry.MatchApplication attribute) edgeLabels (molfoundry.AdjacencyConstraint attribute) (molfoundry.IncidenceCount property) edgeLabelSep (molfoundry.DGPrinter property) EdgeRange (class in molfoundry) edges (molfoundry.CompositionGraph property) (molfoundry.ConditionExists attribute) (molfoundry.DG property) (molfoundry.FlowSolutionCertificate property) (molfoundry.Graph property) (molfoundry.Rule property) edgeWeights (molfoundry.IncidenceCount 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) enumerate_certificates() (molfoundry.FlowSolution method) enumerate_solutions() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) Equal (molfoundry.ConstraintOp attribute) 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) firstId (molfoundry.CompositionEdge property) (molfoundry.CompositionVertex property) flow (molfoundry.FlowSolution property) FlowModel (class in molfoundry) FlowModelSMT (class in molfoundry) FlowSolution (class in molfoundry) FlowSolutionCertificate (class in molfoundry) Force (molfoundry.GraphLayout attribute) from_dg() (molfoundry.atomtracing.DGAtomTracing static method) from_hyperedges() (molfoundry.atomtracing.DGAtomTracing static method) fromCycleNotation() (molfoundry.Aut static method) fromDFS() (molfoundry.Graph static method) (molfoundry.Rule 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) getEdge() (molfoundry.CompositionGraph method) (molfoundry.Rule method) getGMLString() (molfoundry.Graph method) (molfoundry.Rule method) getSBMLString() (molfoundry.DG method) getVertex() (molfoundry.CompositionGraph method) (molfoundry.Rule method) getVertexCoordinate() (molfoundry.Conformer method) getVertexFromExternalId() (molfoundry.Graph method) Graph (class in molfoundry) graph (molfoundry.CompositionEdge property) (molfoundry.CompositionVertex property) (molfoundry.DG.Vertex property) (molfoundry.Edge property) (molfoundry.Vertex property) graphDatabase (molfoundry.DG property) graphDFS() (in module molfoundry) graphGMLString() (in module molfoundry) GraphLayout (class in molfoundry) GraphPrinter (class in molfoundry) graphPrinter (molfoundry.DGPrinter property) GraphState (class in molfoundry) GraphType (class in molfoundry) GreaterThan (molfoundry.ConstraintOp attribute) GreaterThanOrEqual (molfoundry.ConstraintOp attribute) H hasActiveBuilder (molfoundry.DG property) heavy_atoms() (in module molfoundry.atomtracing) Hexagon (molfoundry.OverlayShape attribute) hyperEdge (molfoundry.DGVertexMapper property) I id (molfoundry.AdjacencyConstraint attribute) (molfoundry.AtomId property) (molfoundry.CompositionVertex property) (molfoundry.ConditionVertex attribute) (molfoundry.DG property) (molfoundry.DG.HyperEdge property) (molfoundry.DG.Vertex property) (molfoundry.Graph property) (molfoundry.Rule property) (molfoundry.RuleVertex property) (molfoundry.Vertex property) identity() (molfoundry.Rule static method) identity_instance() (molfoundry.atomtracing.Template method) ids (molfoundry.atomtracing.LabelSet attribute) (molfoundry.atomtracing.Template attribute) implied (molfoundry.NoEdgeConstraint attribute) in_flow (molfoundry.FlowSolution property) in_flow_var() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) inchi (molfoundry.Graph property) inchi() (in module molfoundry) inchiKey (molfoundry.Graph property) IncidenceConstraint (class in molfoundry) IncidenceCount (class in molfoundry) incidentEdges (molfoundry.CompositionVertex property) (molfoundry.Vertex property) include() (in module molfoundry) 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) is_realizable() (molfoundry.FlowSolution method) isActive (molfoundry.DG.Builder property) isChanged (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) isContext (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) isCreated (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) isDeleted (molfoundry.RuleEdge property) (molfoundry.RuleVertex 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) isPreserved (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) iterate() (molfoundry.RCEvaluator method) iteration (molfoundry.MultiPhaseStochsim property) (molfoundry.Stochsim property) K key (molfoundry.Species attribute) kind (molfoundry.Trajectory attribute) L label (molfoundry.ConditionEdge attribute) (molfoundry.ConditionVertex attribute) (molfoundry.LabelAnyConstraint attribute) (molfoundry.RuleEdgeSide property) (molfoundry.RuleVertexSide property) label_set_of() (molfoundry.atomtracing.TracerInputs method) LabelAnyConstraint (class in molfoundry) labeling_to_display_str() (molfoundry.atomtracing.SaturateTracer method) LabelRelation (class in molfoundry) labels (molfoundry.LabelAnyConstraint attribute) LabelSet (class in molfoundry.atomtracing) LabelSettings (class in molfoundry) labelSettings (molfoundry.DG property) LabelType (class in molfoundry) labelType (molfoundry.Rule property) Layout (class in molfoundry) layout (molfoundry.DGPrinter property) (molfoundry.GraphPrinter property) layoutRankDir (molfoundry.DGPrinter property) left (molfoundry.Derivation property) (molfoundry.Derivations property) (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) leftLabel (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) leftPredicate (in module molfoundry) length (molfoundry.ShortestPathConstraint attribute) LessThan (molfoundry.ConstraintOp attribute) LessThanOrEqual (molfoundry.ConstraintOp attribute) limit (molfoundry.DGVertexMapper property) load() (molfoundry.Trajectory static method) load_config() (molfoundry.atomtracing.SaturateTracer class method) load_trajectory() (in module molfoundry) locked (molfoundry.DG property) LogicError M makeAddDynamic() (molfoundry.DGStrat static method) makeAddStatic() (molfoundry.DGStrat static method) makeDuplicate() (molfoundry.DGPrintData 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) MatchApplication (class in molfoundry) matchCondition (molfoundry.Rule property) matchConstraintsAdjacency (molfoundry.Rule property) matchConstraintsLabelAny (molfoundry.Rule property) matchConstraintsNoEdge (molfoundry.Rule property) matchConstraintsShortestPath (molfoundry.Rule property) matches() (molfoundry.Rule method) maxExternalId (molfoundry.Graph property) MAXIMIZE (molfoundry.ObjectiveSense attribute) maxLength (molfoundry.ShortestPathConstraint attribute) Membership (class in molfoundry) membership (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) minExternalId (molfoundry.Graph property) MINIMIZE (molfoundry.ObjectiveSense attribute) model (molfoundry.FlowModel property) (molfoundry.FlowModelSMT property) module molfoundry.atomtracing Mol (molfoundry.DrawMode attribute) (molfoundry.GraphLayout attribute) molfile (molfoundry.Graph property) molfile() (in module molfoundry) molfoundry.atomtracing module molFoundryId (molfoundry.Rule property) monomorphism() (molfoundry.Graph method) 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) nodeLabels (molfoundry.AdjacencyConstraint attribute) (molfoundry.IncidenceCount property) NoEdgeConstraint (class in molfoundry) none (molfoundry.OverlayShape attribute) Not (class in molfoundry) numEdges (molfoundry.CompositionGraph property) (molfoundry.DG property) (molfoundry.Graph property) (molfoundry.Rule property) numLeftComponents (molfoundry.Rule property) numMatches() (molfoundry.DG.HyperEdge method) (molfoundry.Rule method) numRightComponents (molfoundry.Rule property) numSources (molfoundry.DG.HyperEdge property) numTargets (molfoundry.DG.HyperEdge property) numVertices (molfoundry.CompositionGraph property) (molfoundry.DG property) (molfoundry.Graph property) (molfoundry.Rule property) O obj_value (molfoundry.FlowSolution property) ObjectiveSense (class in molfoundry) Off (molfoundry.DarkMode attribute) On (molfoundry.DarkMode attribute) op (molfoundry.AdjacencyConstraint attribute) (molfoundry.IncidenceCount property) (molfoundry.ShortestPathConstraint attribute) operands (molfoundry.ConditionAnd attribute) (molfoundry.ConditionOr attribute) optimize() (molfoundry.Rule method) optimizeXTB() (molfoundry.Conformer method) optimum() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) orbitalNames (molfoundry.AtomId property) orbitals (molfoundry.AtomId property) out_flow (molfoundry.FlowSolution property) out_flow_var() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) outDegree (molfoundry.DG.Vertex property) outEdges (molfoundry.DG.Vertex property) OverlayShape (class in molfoundry) P phases (molfoundry.MultiPhaseStochsim property) popEdgeColor() (molfoundry.DGPrinter method) popEdgeLabel() (molfoundry.DGPrinter method) popEdgeVisible() (molfoundry.DGPrinter method) popFilePrefix() (in module molfoundry) popVertexColor() (molfoundry.DGPrinter method) popVertexLabel() (molfoundry.DGPrinter method) popVertexOverlay() (molfoundry.GraphPrinter method) popVertexVisible() (molfoundry.DGPrinter method) position_id() (molfoundry.atomtracing.TracerInputs method) position_id_by_atom (molfoundry.atomtracing.TracerInputs attribute) postChapter() (in module molfoundry) postSection() (in module molfoundry) prefixFilename() (in module molfoundry) principalQuantumNumber (molfoundry.AtomId property) print() (molfoundry.DG method) (molfoundry.DG.HyperEdge method) (molfoundry.FlowSolution method) (molfoundry.FlowSolutionCertificate method) (molfoundry.Graph method) (molfoundry.MultiPhaseStochsim method) (molfoundry.Rule method) (molfoundry.Stochsim method) products (molfoundry.atomtracing.ReactionRule attribute) protons (molfoundry.AtomId property) pushEdgeColor() (molfoundry.DGPrinter method) pushEdgeLabel() (molfoundry.DGPrinter method) pushEdgeVisible() (molfoundry.DGPrinter method) pushFilePrefix() (in module molfoundry) pushVertexColor() (molfoundry.DGPrinter method) pushVertexLabel() (molfoundry.DGPrinter method) pushVertexOverlay() (molfoundry.GraphPrinter method) pushVertexVisible() (molfoundry.DGPrinter method) 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) reaction_var() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT method) ReactionRule (class in molfoundry.atomtracing) reactions (molfoundry.Trajectory attribute) reactionSMILES() (molfoundry.VertexMap method) reconnectSource() (molfoundry.DGPrintData method) reconnectTarget() (molfoundry.DGPrintData method) relation (molfoundry.LabelSettings property) removeDuplicate() (molfoundry.DGPrintData method) removeExternalId() (molfoundry.Vertex method) removeHydrogens() (molfoundry.Graph method) removeHyperEdge() (molfoundry.DG.Builder method) removeVertex() (molfoundry.DG.Builder method) repeat (in module molfoundry) reverse() (molfoundry.atomtracing.ReactionRule method) revive() (in module molfoundry) right (molfoundry.Derivation property) (molfoundry.Derivations property) (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) rightLabel (molfoundry.RuleEdge property) (molfoundry.RuleVertex property) rightPredicate (in module molfoundry) Rule (class in molfoundry) rule (molfoundry.Derivation property) (molfoundry.VertexMap property) ruleDFS() (in module molfoundry) RuleEdge (class in molfoundry) RuleEdgeSide (class in molfoundry) 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) RuleVertex (class in molfoundry) RuleVertexSide (class in molfoundry) run() (molfoundry.atomtracing.SaturateTracer method) S SaturateTracer (class in molfoundry.atomtracing) save_config() (molfoundry.atomtracing.SaturateTracer method) secondId (molfoundry.CompositionEdge property) (molfoundry.CompositionVertex property) series() (molfoundry.MultiPhaseStochsim method) (molfoundry.MultiPhaseStochsim.Phase method) (molfoundry.MultiPhaseStochsim.Trajectory method) (molfoundry.Stochsim method) (molfoundry.Stochsim.Trajectory method) (molfoundry.Trajectory method) seriesByCanon() (molfoundry.Trajectory method) set_objective() (molfoundry.FlowModel method) (molfoundry.FlowModelSMT 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) ShortestPathConstraint (class in molfoundry) 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) solution (molfoundry.FlowSolutionCertificate property) source (molfoundry.CompositionEdge property) (molfoundry.ConditionEdge attribute) (molfoundry.Edge property) (molfoundry.NoEdgeConstraint attribute) (molfoundry.RuleEdge property) (molfoundry.ShortestPathConstraint attribute) (molfoundry.VertexMapEntry attribute) sourceInstance (molfoundry.VertexMapEntry attribute) sources (molfoundry.DG.HyperEdge property) Specialisation (molfoundry.LabelRelation attribute) Species (class in molfoundry) species (molfoundry.Trajectory attribute) sqpoJumpClosure() (molfoundry.Rule method) Square (molfoundry.OverlayShape attribute) standardAtomicWeight (molfoundry.AtomId property) state() (molfoundry.MultiPhaseStochsim method) (molfoundry.MultiPhaseStochsim.Phase method) (molfoundry.Stochsim method) stepReactions (molfoundry.Trajectory attribute) stereo (molfoundry.RuleVertexSide property) Stochsim (class in molfoundry) Stochsim.StepInfo (class in molfoundry) Stochsim.Trajectory (class in molfoundry) Stress (molfoundry.Layout attribute) String (molfoundry.LabelType attribute) stringLabel (molfoundry.CompositionEdge property) (molfoundry.CompositionVertex property) (molfoundry.Edge property) (molfoundry.Vertex property) subset (molfoundry.GraphState property) subset() (molfoundry.DG.Builder.ExecuteResult method) svg() (molfoundry.DG method) (molfoundry.DG.HyperEdge method) (molfoundry.FlowSolution method) (molfoundry.FlowSolutionCertificate method) (molfoundry.Graph method) (molfoundry.Rule method) symbol (molfoundry.AtomId property) T target (molfoundry.CompositionEdge property) (molfoundry.ConditionEdge attribute) (molfoundry.Edge property) (molfoundry.NoEdgeConstraint attribute) (molfoundry.RuleEdge property) (molfoundry.ShortestPathConstraint attribute) (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) 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) (molfoundry.Trajectory attribute) times() (molfoundry.MultiPhaseStochsim method) title (molfoundry.Trajectory attribute) total() (molfoundry.MultiPhaseStochsim method) totalSeries() (molfoundry.MultiPhaseStochsim method) TracerInputs (class in molfoundry.atomtracing) Trajectory (class in molfoundry) trajectory() (molfoundry.MultiPhaseStochsim method) (molfoundry.Stochsim method) trajectoryTable() (molfoundry.FlowSolutionCertificate method) transfer() (molfoundry.MultiPhaseStochsim method) TriangleDown (molfoundry.OverlayShape attribute) TriangleLeft (molfoundry.OverlayShape attribute) TriangleRight (molfoundry.OverlayShape attribute) TriangleUp (molfoundry.OverlayShape attribute) 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) UseAll (molfoundry.ApplyMode attribute) UseAny (molfoundry.ApplyMode attribute) UseAnyMultiplicity (molfoundry.ApplyMode attribute) V valenceElectrons (molfoundry.AtomId property) valid (molfoundry.AtomId property) version (molfoundry.Trajectory attribute) Vertex (class in molfoundry) VertexFilter (in module molfoundry) vertexIds (molfoundry.Stochsim.Trajectory attribute) vertexLabels (molfoundry.IncidenceConstraint property) vertexLabelSep (molfoundry.DGPrinter property) VertexMap (class in molfoundry) vertexMap (molfoundry.MatchApplication attribute) VertexMapEntry (class in molfoundry) vertexMaps() (molfoundry.DG.HyperEdge method) VertexOverlay (class in molfoundry) VertexRange (class in molfoundry) vertices (molfoundry.CompositionGraph property) (molfoundry.ConditionExists attribute) (molfoundry.DG property) (molfoundry.Graph property) (molfoundry.Rule property) vLabelCount() (molfoundry.Graph method) volume (molfoundry.MultiPhaseStochsim.Phase property) W withExternalId (molfoundry.GraphPrinter property) withGraphName (molfoundry.DGPrinter property) withIndex (molfoundry.GraphPrinter property) withRuleId (molfoundry.DGPrinter property) withRuleName (molfoundry.DGPrinter property) withShortcutEdges (molfoundry.DGPrinter property) withShortcutEdgesAfterVisibility (molfoundry.DGPrinter property) X xkcd (molfoundry.DrawStyle attribute) xyz() (molfoundry.Conformer method)
