Index

Symbols

--debug mod command line option --help mod command line option mod_post command line option --install-format mod_post command line option --install-format-sudo mod_post command line option --memcheck mod command line option --nopost mod command line option --profile mod command line option --version mod command line option

--vgArgs mod command line option -e mod command line option -f mod command line option -h mod command line option mod_post command line option -i mod command line option -j mod command line option mod_post command line option -q mod command line option -v mod command line option

_

__bool__() (mod.protocols.Graph.Edge method) __call__() (mod.stochsim.DrawMassAction method) (mod.stochsim.DrawTimeExponential method) __eq__() (mod.causality.EventTrace method) (mod.causality.Marking method) (mod.DGPetriNetMarking method) __getitem__() (mod.causality.EventTrace method) (mod.causality.Marking method) (mod.causality.RealisabilityQuery method) (mod.CausalityFlowQuery method) (mod.DGPetriNetMarking method) (mod.DGVertexMapper method) (mod.FlowSolutionRange method) (mod.FlowVarSumCustom method) (mod.FlowVarSumEdge method) (mod.FlowVarSumVertex method) (mod.Graph.Aut method) (mod.Graph.VertexRange method) (mod.hyperflow.SolutionRange method) (mod.hyperflow.VarSumCustom method) (mod.hyperflow.VarSumEdge method) (mod.hyperflow.VarSumVertex method) (mod.protocols.VertexMap method) (mod.RCMatch method) (mod.Rule.VertexRange method) (mod.UnionGraph method) (mod.UnionGraph.VertexRange method) __init__() (mod.AtomData method) (mod.AtomId method) (mod.causality.EdgeAction method) (mod.causality.EventTrace method) (mod.causality.InputAction method) (mod.causality.Marking method) (mod.causality.MassActionKinetics method) (mod.causality.Net method) (mod.causality.OutputAction method) (mod.causality.RealisabilityQuery method) (mod.CausalityFlowQuery method) (mod.Charge method) (mod.CWDPath method) (mod.DG method) (mod.DG.HyperEdge method) (mod.DG.Vertex method) (mod.DGPetriNet method) (mod.DGPetriNetMarking method) (mod.DGPrintData method) (mod.DGVertexMapper method) (mod.Flow method) (mod.FlowVarCustom method) (mod.FlowVarEdge method) (mod.FlowVarSumCustom method) (mod.FlowVarSumEdge method) (mod.FlowVarSumVertex method) (mod.FlowVarVertex method) (mod.FlowVarVertexGraph method) (mod.GraphPrinter method) (mod.hyperflow.Model method) (mod.hyperflow.VarCustom method) (mod.hyperflow.VarEdge method) (mod.hyperflow.VarSumCustom method) (mod.hyperflow.VarSumEdge method) (mod.hyperflow.VarSumVertex method) (mod.hyperflow.VarVertex method) (mod.hyperflow.VarVertexGraph method) (mod.Isotope method) (mod.LabelSettings method) (mod.protocols.Graph.Edge method) (mod.protocols.Graph.Vertex method) (mod.RCEvaluator method) (mod.RCMatch method) (mod.UnionGraph method)

__int__() (mod.AtomId method) (mod.Charge method) (mod.Isotope method) __iter__() (mod.DGVertexMapper method) (mod.FlowSolutionRange method) (mod.hyperflow.SolutionRange method) (mod.UnionGraph method) __len__() (mod.causality.EventTrace method) (mod.DGVertexMapper method) (mod.FlowSolutionRange method) (mod.hyperflow.SolutionRange method) (mod.UnionGraph method) __setitem__() (mod.causality.RealisabilityQuery method) (mod.CausalityFlowQuery method) __str__() (mod.BondType method) (mod.FlowVarCustom method) (mod.FlowVarEdge method) (mod.FlowVarSumCustom method) (mod.FlowVarSumEdge method) (mod.FlowVarSumVertex method) (mod.FlowVarVertex method) (mod.FlowVarVertexGraph method)

A

absGap (mod.Flow attribute) (mod.hyperflow.Model attribute) Action (C++ enum) (class in mod) action (mod.causality.EventTrace.Event attribute) Action::Error (C++ enumerator) Action::Ignore (C++ enumerator) Action::Warn (C++ enumerator) add() (mod.causality.EventTrace method) (mod.causality.Marking method) (mod.DGPetriNetMarking method) addAbstract() (mod.DG.Builder method) addBoolVariable() (mod.hyperflow.Model method) addConstraint() (mod.Flow method) (mod.hyperflow.Model method) addDerivation() (mod.DG.Builder method) addEnumerationVar() (mod.Flow method) (mod.hyperflow.Model method) addFloatVariable() (mod.hyperflow.Model method) addHyperEdge() (mod.DG.Builder method) addIntVariable() (mod.Flow method) (mod.hyperflow.Model method) addSink() (mod.Flow method) (mod.hyperflow.Model method) addSource() (mod.Flow method) (mod.hyperflow.Model method) addSubset() (in module mod) addTransitEnumeration() (mod.Flow method) (mod.hyperflow.Model method)

addUniverse() (in module mod) allowHyperLoops (mod.Flow attribute) (mod.hyperflow.Model attribute) allowIOReversal (mod.Flow attribute) (mod.hyperflow.Model attribute) allowReversal (mod.Flow attribute) (mod.hyperflow.Model attribute) apply() (mod.DG.Builder method) Aromatic (mod.BondType attribute) AtomData (C++ class) (class in mod) AtomData::AtomData (C++ function), [1], [2], [3] AtomData::getAtomId (C++ function) AtomData::getCharge (C++ function) AtomData::getIsotope (C++ function) AtomData::getRadical (C++ function) AtomData::operator<< (C++ function) AtomId (C++ class) (class in mod) atomId (mod.AtomData attribute) (mod.protocols.LabelledGraph.Vertex attribute) AtomId::AtomId (C++ function), [1] AtomId::operator unsigned char (C++ function) AtomId::operator<< (C++ function) AtomId::symbol (C++ function) AtomIds (class in mod) AtomIds::Invalid (C++ member) AtomIds::Max (C++ member) aut() (mod.Graph method)

B

bfsExclusive (mod.FlowOverallAutocatalysis attribute) (mod.hyperflow.Model.OverallAutocatalysis attribute) BondType (C++ enum) (class in mod) bondType (mod.protocols.LabelledGraph.Edge attribute)

BondType::Aromatic (C++ enumerator) BondType::Double (C++ enumerator) BondType::Invalid (C++ enumerator) BondType::Single (C++ enumerator) BondType::Triple (C++ enumerator) build() (mod.DG method)

C

cacheEnergy() (mod.Graph method) causality.DAG (class in mod) causality.EdgeAction (class in mod) causality.EventTrace (class in mod) causality.EventTrace.Event (class in mod) causality.EventTracePrinter (class in mod) causality.InputAction (class in mod) causality.Marking (class in mod) causality.MassActionKinetics (class in mod) causality.Net (class in mod) causality.OutputAction (class in mod) causality.RealisabilityQuery (class in mod) causality::Action (C++ type) causality::DAG (C++ class) causality::DAG::getDG (C++ function) causality::DAG::getPrintData (C++ function) causality::DGPetriNet (C++ class) causality::DGPetriNet::getDG (C++ function) causality::DGPetriNet::getPostPlaces (C++ function) causality::DGPetriNet::make (C++ function) causality::DGPetriNet::operator<< (C++ function) causality::DGPetriNet::syncSize (C++ function) causality::DGPetriNetMarking (C++ class) causality::DGPetriNetMarking::add (C++ function) causality::DGPetriNetMarking::DGPetriNetMarking (C++ function) causality::DGPetriNetMarking::fire (C++ function) causality::DGPetriNetMarking::getAllEnabled (C++ function) causality::DGPetriNetMarking::getEmptyPostPlaces (C++ function) causality::DGPetriNetMarking::getNet (C++ function) causality::DGPetriNetMarking::getNonZeroPlaces (C++ function) causality::DGPetriNetMarking::getNumTokens (C++ function) causality::DGPetriNetMarking::isEnabled (C++ function) causality::DGPetriNetMarking::operator!= (C++ function) causality::DGPetriNetMarking::operator<< (C++ function) causality::DGPetriNetMarking::operator== (C++ function) causality::DGPetriNetMarking::operator[] (C++ function) causality::DGPetriNetMarking::remove (C++ function) causality::DGPetriNetMarking::syncSize (C++ function) causality::EdgeAction (C++ class) causality::EdgeAction::applyTo (C++ function) causality::EdgeAction::edge (C++ member) causality::EdgeAction::EdgeAction (C++ function), [1] causality::EventTrace (C++ class) causality::EventTrace::add (C++ function) causality::EventTrace::begin (C++ function) causality::EventTrace::const_iterator (C++ type) causality::EventTrace::dump (C++ function), [1] causality::EventTrace::end (C++ function) causality::EventTrace::Event (C++ class) causality::EventTrace::Event::action (C++ member) causality::EventTrace::Event::time (C++ member) causality::EventTrace::EventTrace (C++ function) causality::EventTrace::getInitialState (C++ function) causality::EventTrace::getTime (C++ function) causality::EventTrace::iterator (C++ type) causality::EventTrace::load (C++ function), [1] causality::EventTrace::operator<< (C++ function) causality::EventTrace::operator== (C++ function) causality::EventTrace::operator[] (C++ function) causality::EventTrace::print (C++ function), [1] causality::EventTrace::size (C++ function) causality::EventTracePrinter (C++ class) causality::EventTracePrinter::getLogCount (C++ function) causality::EventTracePrinter::getLogTime (C++ function) causality::EventTracePrinter::getMaxPointsPerVertex (C++ function) causality::EventTracePrinter::popOptions (C++ function) causality::EventTracePrinter::popVertexOptions (C++ function) causality::EventTracePrinter::popVertexVisible (C++ function) causality::EventTracePrinter::pushOptions (C++ function) causality::EventTracePrinter::pushVertexOptions (C++ function) causality::EventTracePrinter::pushVertexVisible (C++ function) causality::EventTracePrinter::setLogCount (C++ function) causality::EventTracePrinter::setLogTime (C++ function) causality::EventTracePrinter::setMaxPointsPerVertex (C++ function) causality::EventTracePrinter::setPostContent (C++ function) causality::EventTracePrinter::setPreContent (C++ function) causality::FlowQuery (C++ class) causality::FlowQuery::findDAG (C++ function) causality::FlowQuery::FlowQuery (C++ function) causality::FlowQuery::getBorrow (C++ function), [1] causality::FlowQuery::getConstrainRouting (C++ function) causality::FlowQuery::getDG (C++ function) causality::FlowQuery::getMultiplicity (C++ function)

causality::FlowQuery::setBorrow (C++ function), [1] causality::FlowQuery::setConstrainRouting (C++ function) causality::FlowQuery::setMultiplicity (C++ function) causality::InputAction (C++ class) causality::InputAction::applyTo (C++ function) causality::InputAction::InputAction (C++ function), [1] causality::InputAction::vertex (C++ member) causality::Marking (C++ class) causality::Marking::add (C++ function), [1] causality::Marking::fire (C++ function) causality::Marking::getAllEnabled (C++ function) causality::Marking::getEmptyPostPlaces (C++ function) causality::Marking::getNet (C++ function) causality::Marking::getNonZeroPlaces (C++ function) causality::Marking::getNumTokens (C++ function) causality::Marking::isEnabled (C++ function) causality::Marking::Marking (C++ function) causality::Marking::operator!= (C++ function) causality::Marking::operator<< (C++ function) causality::Marking::operator== (C++ function) causality::Marking::operator[] (C++ function), [1] causality::Marking::remove (C++ function), [1] causality::Marking::syncSize (C++ function) causality::MassActionKinetics (C++ class) causality::MassActionKinetics::draw (C++ function) causality::MassActionKinetics::MassActionKinetics (C++ function) causality::MassActionKinetics::syncSize (C++ function) causality::Net (C++ class) causality::Net::getDG (C++ function) causality::Net::getPostPlaces (C++ function) causality::Net::make (C++ function) causality::Net::operator<< (C++ function) causality::Net::syncSize (C++ function) causality::OutputAction (C++ class) causality::OutputAction::applyTo (C++ function) causality::OutputAction::OutputAction (C++ function), [1] causality::OutputAction::vertex (C++ member) causality::RealisabilityQuery (C++ class) causality::RealisabilityQuery::findDAG (C++ function) causality::RealisabilityQuery::getBorrow (C++ function), [1] causality::RealisabilityQuery::getDG (C++ function) causality::RealisabilityQuery::getMultiplicity (C++ function) causality::RealisabilityQuery::getRespectTransit (C++ function) causality::RealisabilityQuery::RealisabilityQuery (C++ function) causality::RealisabilityQuery::setBorrow (C++ function), [1] causality::RealisabilityQuery::setMultiplicity (C++ function) causality::RealisabilityQuery::setRespectTransit (C++ function) CausalityFlowQuery (class in mod) Charge (C++ class) (class in mod) charge (mod.AtomData attribute) (mod.protocols.LabelledGraph.Vertex attribute) Charge::Charge (C++ function), [1] Charge::operator signed char (C++ function) Charge::operator<< (C++ function) Check (mod.IsomorphismPolicy attribute) clean mod command line option codomain (mod.protocols.VertexMap attribute) collapseHydrogens (mod.GraphPrinter attribute) comatch (mod.DGVertexMapper.Result attribute) command() (in module post) compose() (mod.RCMatch method) composeAll() (mod.RCMatch method) Config (C++ class) (class in mod) config (in module mod) constrainRouting (mod.CausalityFlowQuery attribute) context (mod.Rule attribute) (mod.Rule.Edge attribute) (mod.Rule.Vertex attribute) core (mod.Rule.ContextGraph.Edge attribute) (mod.Rule.ContextGraph.Vertex attribute) (mod.Rule.LeftGraph.Edge attribute) (mod.Rule.LeftGraph.Vertex attribute) (mod.Rule.RightGraph.Edge attribute) (mod.Rule.RightGraph.Vertex attribute) createdGraphs (mod.DG attribute) createdRules (mod.RCEvaluator attribute) customBoolVariables (mod.hyperflow.Model attribute) customFloatVariables (mod.hyperflow.Model attribute) customIntVariables (mod.Flow attribute) (mod.hyperflow.Model attribute) CWDPath (class in mod)

D

degree (mod.protocols.Graph.Vertex attribute) deltaEnergy (in module mod) Derivation (C++ class) (class in mod) Derivation::GraphList (C++ type) Derivation::left (C++ member) Derivation::operator Derivations (C++ function) Derivation::r (C++ member) Derivation::right (C++ member) Derivations (C++ class) (class in mod) Derivations::GraphList (C++ type) Derivations::left (C++ member) Derivations::right (C++ member) Derivations::rules (C++ member) DG (class in mod) dg (mod.causality.DAG attribute) (mod.causality.Net attribute) (mod.causality.RealisabilityQuery attribute) (mod.CausalityFlowQuery attribute) (mod.DG.Builder attribute) (mod.DG.HyperEdge attribute) (mod.DG.Vertex attribute) (mod.DGPetriNet attribute) (mod.DGPrintData attribute) (mod.Flow attribute) (mod.hyperflow.Model attribute) (mod.stochsim.Simulator property) DG.Builder (class in mod) DG.Builder.AddAbstractResult (class in mod) DG.Builder.ExecuteResult (class in mod) DG.HyperEdge (class in mod) DG.Vertex (class in mod) dg::AddAbstractResult (C++ class) dg::AddAbstractResult::getEdge (C++ function) dg::AddAbstractResult::getGraph (C++ function) dg::Builder (C++ class) dg::Builder::addAbstract (C++ function) dg::Builder::addDerivation (C++ function), [1] dg::Builder::addHyperEdge (C++ function), [1] dg::Builder::apply (C++ function), [1], [2] dg::Builder::execute (C++ function), [1], [2] dg::Builder::getDG (C++ function) dg::Builder::isActive (C++ function) dg::Builder::load (C++ function) dg::DG (C++ class) dg::DG::build (C++ function), [1] dg::DG::diff (C++ function) dg::DG::dump (C++ function), [1] dg::DG::EdgeIterator (C++ class) dg::DG::EdgeIterator::EdgeIterator (C++ function) dg::DG::EdgeRange (C++ class) dg::DG::edges (C++ function) dg::DG::findEdge (C++ function), [1] dg::DG::findVertex (C++ function) dg::DG::getCreatedGraphs (C++ function) dg::DG::getGraphDatabase (C++ function) dg::DG::getHyper (C++ function) dg::DG::getId (C++ function) dg::DG::getLabelSettings (C++ function) dg::DG::getNonHyper (C++ function) dg::DG::hasActiveBuilder (C++ function) dg::DG::HyperEdge (C++ class) dg::DG::HyperEdge::getDG (C++ function) dg::DG::HyperEdge::getId (C++ function) dg::DG::HyperEdge::getInverse (C++ function) dg::DG::HyperEdge::HyperEdge (C++ function) dg::DG::HyperEdge::isNull (C++ function) dg::DG::HyperEdge::numSources (C++ function) dg::DG::HyperEdge::numTargets (C++ function) dg::DG::HyperEdge::operator bool (C++ function) dg::DG::HyperEdge::print (C++ function) dg::DG::HyperEdge::rules (C++ function) dg::DG::HyperEdge::sources (C++ function) dg::DG::HyperEdge::targets (C++ function) dg::DG::InEdgeIterator (C++ class) dg::DG::InEdgeIterator::InEdgeIterator (C++ function) dg::DG::InEdgeRange (C++ class) dg::DG::isLocked (C++ function) dg::DG::listStats (C++ function) dg::DG::load (C++ function), [1] dg::DG::make (C++ function) dg::DG::numEdges (C++ function) dg::DG::numVertices (C++ function) dg::DG::operator<< (C++ function) dg::DG::OutEdgeIterator (C++ class) dg::DG::OutEdgeIterator::OutEdgeIterator (C++ function) dg::DG::OutEdgeRange (C++ class) dg::DG::print (C++ function) dg::DG::printNonHyper (C++ function) dg::DG::RuleIterator (C++ class) dg::DG::RuleIterator::RuleIterator (C++ function) dg::DG::RuleRange (C++ class) dg::DG::SourceIterator (C++ class) dg::DG::SourceIterator::SourceIterator (C++ function) dg::DG::SourceRange (C++ class) dg::DG::TargetIterator (C++ class) dg::DG::TargetIterator::TargetIterator (C++ function) dg::DG::TargetRange (C++ class) dg::DG::Vertex (C++ class) dg::DG::Vertex::getDG (C++ function) dg::DG::Vertex::getGraph (C++ function) dg::DG::Vertex::getId (C++ function) dg::DG::Vertex::getOutDegree (C++ function) dg::DG::Vertex::inDegree (C++ function) dg::DG::Vertex::inEdges (C++ function) dg::DG::Vertex::isNull (C++ function) dg::DG::Vertex::operator bool (C++ function) dg::DG::Vertex::outEdges (C++ function) dg::DG::Vertex::Vertex (C++ function) dg::DG::VertexIterator (C++ class) dg::DG::VertexIterator::VertexIterator (C++ function) dg::DG::VertexRange (C++ class)

dg::DG::vertices (C++ function) dg::ExecuteResult (C++ class) dg::ExecuteResult::getSubset (C++ function) dg::ExecuteResult::getUniverse (C++ function) dg::ExecuteResult::list (C++ function) dg::PrintData (C++ class) dg::PrintData::getDG (C++ function) dg::PrintData::makeDuplicate (C++ function) dg::PrintData::PrintData (C++ function) dg::PrintData::reconnectSource (C++ function) dg::PrintData::reconnectTarget (C++ function) dg::PrintData::removeDuplicate (C++ function) dg::Printer (C++ class) dg::Printer::getEdgeLabelSep (C++ function) dg::Printer::getGraphPrinter (C++ function), [1] dg::Printer::getGraphvizPrefix (C++ function) dg::Printer::getLabelsAsLatexMath (C++ function) dg::Printer::getTikzpictureOption (C++ function) dg::Printer::getVertexLabelSep (C++ function) dg::Printer::getWithGraphImages (C++ function) dg::Printer::getWithGraphName (C++ function) dg::Printer::getWithInlineGraphs (C++ function) dg::Printer::getWithRuleId (C++ function) dg::Printer::getWithRuleName (C++ function) dg::Printer::getWithShortcutEdges (C++ function) dg::Printer::getWithShortcutEdgesAfterVisibility (C++ function) dg::Printer::popEdgeColour (C++ function) dg::Printer::popEdgeLabel (C++ function) dg::Printer::popEdgeVisible (C++ function) dg::Printer::popVertexColour (C++ function) dg::Printer::popVertexLabel (C++ function) dg::Printer::popVertexVisible (C++ function) dg::Printer::pushEdgeColour (C++ function) dg::Printer::pushEdgeLabel (C++ function) dg::Printer::pushEdgeVisible (C++ function) dg::Printer::pushVertexColour (C++ function) dg::Printer::pushVertexLabel (C++ function) dg::Printer::pushVertexVisible (C++ function) dg::Printer::setEdgeLabelSep (C++ function) dg::Printer::setGraphvizPrefix (C++ function) dg::Printer::setImageOverwrite (C++ function) dg::Printer::setLabelsAsLatexMath (C++ function) dg::Printer::setMirrorOverwrite (C++ function) dg::Printer::setRotationOverwrite (C++ function) dg::Printer::setTikzpictureOption (C++ function) dg::Printer::setVertexLabelSep (C++ function) dg::Printer::setWithGraphImages (C++ function) dg::Printer::setWithGraphName (C++ function) dg::Printer::setWithInlineGraphs (C++ function) dg::Printer::setWithRuleId (C++ function) dg::Printer::setWithRuleName (C++ function) dg::Printer::setWithShortcutEdges (C++ function) dg::Printer::setWithShortcutEdgesAfterVisibility (C++ function) dg::Strategy (C++ class) dg::Strategy::GraphState (C++ class) dg::Strategy::GraphState::getSubset (C++ function) dg::Strategy::GraphState::getUniverse (C++ function) dg::Strategy::makeAdd (C++ function), [1] dg::Strategy::makeExecute (C++ function) dg::Strategy::makeFilter (C++ function) dg::Strategy::makeLeftPredicate (C++ function) dg::Strategy::makeParallel (C++ function) dg::Strategy::makeRepeat (C++ function) dg::Strategy::makeRevive (C++ function) dg::Strategy::makeRightPredicate (C++ function) dg::Strategy::makeRule (C++ function) dg::Strategy::makeSequence (C++ function) dg::VertexMapper (C++ class) dg::VertexMapper::begin (C++ function) dg::VertexMapper::Comatch (C++ type) dg::VertexMapper::const_iterator (C++ type) dg::VertexMapper::end (C++ function) dg::VertexMapper::getEdge (C++ function) dg::VertexMapper::getLeft (C++ function) dg::VertexMapper::getRight (C++ function) dg::VertexMapper::iterator (C++ class) dg::VertexMapper::Map (C++ type) dg::VertexMapper::Match (C++ type) dg::VertexMapper::operator[] (C++ function) dg::VertexMapper::Result (C++ class) dg::VertexMapper::Result::comatch (C++ member) dg::VertexMapper::Result::map (C++ member) dg::VertexMapper::Result::match (C++ member) dg::VertexMapper::Result::r (C++ member) dg::VertexMapper::size (C++ function) dg::VertexMapper::VertexMapper (C++ function), [1] dgFlow (mod.FlowSolutionSet attribute) DGPetriNet (class in mod) DGPetriNetMarking (class in mod) DGPrintData (class in mod) DGPrinter (class in mod) dgPrinter (mod.FlowPrinter attribute) (mod.hyperflow.Printer attribute) DGStrat (class in mod) DGStrat.GraphState (class in mod) DGVertexMapper (class in mod) DGVertexMapper.Result (class in mod) diffDGs() (in module mod) disableAll() (mod.GraphPrinter method) disableCommands() (in module post) disableCompileSummary() (in module post) disableInvokeMake() (in module post) domain (mod.protocols.VertexMap attribute) Double (mod.BondType attribute) draw() (mod.causality.MassActionKinetics method) (mod.stochsim.DrawFunction method) DrawFunction (class in mod.stochsim) DrawMassAction (class in mod.stochsim) DrawTimeExponential (class in mod.stochsim) dump() (mod.causality.EventTrace method) (mod.DG method) (mod.Flow method) (mod.hyperflow.Model method)

E

edge (mod.causality.EdgeAction attribute) (mod.DGVertexMapper attribute) (mod.FlowVarEdge attribute) (mod.hyperflow.VarEdge attribute) (mod.UnionGraph.Edge attribute) edgeFlow (in module mod) edgeLabelSep (mod.DGPrinter attribute) edges (mod.DG attribute) (mod.protocols.Graph attribute) edgesAsBonds (mod.GraphPrinter attribute) eLabelCount() (mod.Graph method) enable() (mod.FlowOverallAutocatalysis method) (mod.FlowOverallCatalysis method) (mod.FlowThermodynamics method) (mod.hyperflow.Model.OverallAutocatalysis method) (mod.hyperflow.Model.OverallCatalysis method) (mod.hyperflow.Model.Thermodynamics method) enableAll() (mod.GraphPrinter method) enableCommands() (in module post) enableCompileSummary() (in module post) enableInvokeMake() (in module post) energy (in module mod) (mod.Graph attribute) enumerateIsomorphisms() (mod.Graph method) enumerateMonomorphisms() (mod.Graph method) enumerationVars (mod.Flow attribute) (mod.hyperflow.Model attribute)

environment variable MOD_DEBUGGER, [1], [2] MOD_ILP_SOLVER MOD_IPYTHON, [1], [2] MOD_NO_DEPRECATED, [1] MOD_NUM_POST_THREADS, [1] MOD_PLUGIN_PATH MOD_PYTHON, [1], [2], [3] Error (mod.Action attribute) eval() (mod.FlowSolution method) (mod.FlowSolutionOld method) (mod.hyperflow.Solution method) (mod.RCEvaluator method) exactMass (mod.Graph attribute) Exception (C++ class) Exception::append (C++ function) Exception::getName (C++ function) Exception::printStacktrace (C++ function) Exception::what (C++ function) exclude() (mod.Flow method) (mod.hyperflow.Model method) excluded (mod.Flow attribute) (mod.hyperflow.Model attribute) execute() (in module mod) (mod.DG.Builder method) ExpandByStrategy (class in mod.stochsim)

F

FatalError (C++ class) filterSubset() (in module mod) filterUniverse() (in module mod) findDAG() (mod.causality.RealisabilityQuery method) (mod.CausalityFlowQuery method) findEdge() (mod.DG method) findSolutions() (mod.Flow method) (mod.hyperflow.Model method) findVertex() (mod.DG method) fire() (mod.causality.Marking method) (mod.DGPetriNetMarking method) first (mod.RCMatch attribute) Flow (class in mod) flow (mod.FlowSolution attribute) (mod.FlowSolutionOld attribute) (mod.FlowSolutionRange attribute) flow::Flow (C++ class) flow::Flow::addConstraint (C++ function) flow::Flow::addEnumerationVar (C++ function) flow::Flow::addIntVariable (C++ function) flow::Flow::addSink (C++ function), [1] flow::Flow::addSource (C++ function), [1] flow::Flow::addTransitEnumeration (C++ function), [1] flow::Flow::dump (C++ function), [1] flow::Flow::exclude (C++ function), [1] flow::Flow::findSolutions (C++ function), [1], [2] flow::Flow::getAbsGap (C++ function) flow::Flow::getAllowHyperLoops (C++ function) flow::Flow::getAllowIOReversal (C++ function) flow::Flow::getAllowReversal (C++ function) flow::Flow::getCustomIntVariables (C++ function) flow::Flow::getDG (C++ function) flow::Flow::getEnumerationVars (C++ function) flow::Flow::getExcluded (C++ function) flow::Flow::getFlow (C++ function), [1] flow::Flow::getId (C++ function) flow::Flow::getOldSolutions (C++ function) flow::Flow::getRelaxed (C++ function) flow::Flow::getSeparatedIOInternalTransit (C++ function) flow::Flow::getSinks (C++ function) flow::Flow::getSolutions (C++ function) flow::Flow::getSources (C++ function) flow::Flow::getTransitEnumeration (C++ function) flow::Flow::isSpecificationLocked (C++ function) flow::Flow::listSpecification (C++ function) flow::Flow::load (C++ function), [1] flow::Flow::loadString (C++ function), [1] flow::Flow::make (C++ function), [1] flow::Flow::OverallAutocatalysis (C++ class) flow::Flow::overallAutocatalysis (C++ member) flow::Flow::OverallAutocatalysis::enable (C++ function) flow::Flow::OverallAutocatalysis::getBFSExclusive (C++ function) flow::Flow::OverallAutocatalysis::getForceExistence (C++ function) flow::Flow::OverallAutocatalysis::getStrictTransit (C++ function) flow::Flow::OverallAutocatalysis::setBFSExclusive (C++ function) flow::Flow::OverallAutocatalysis::setForceExistence (C++ function) flow::Flow::OverallAutocatalysis::setStrictTransit (C++ function) flow::Flow::OverallCatalysis (C++ class) flow::Flow::overallCatalysis (C++ member) flow::Flow::OverallCatalysis::enable (C++ function) flow::Flow::OverallCatalysis::getForceExistence (C++ function) flow::Flow::OverallCatalysis::getStrictTransit (C++ function) flow::Flow::OverallCatalysis::setForceExistence (C++ function) flow::Flow::OverallCatalysis::setStrictTransit (C++ function) flow::Flow::printEnumerationTree (C++ function) flow::Flow::printExpanded (C++ function) flow::Flow::printExpandedVertex (C++ function), [1] flow::Flow::separateIOInternalTransit (C++ function), [1] flow::Flow::setAbsGap (C++ function) flow::Flow::setAllowHyperLoops (C++ function) flow::Flow::setAllowIOReversal (C++ function) flow::Flow::setAllowReversal (C++ function) flow::Flow::setObjectiveFunction (C++ function) flow::Flow::setRelaxed (C++ function) flow::Flow::Thermodynamics (C++ class) flow::Flow::thermodynamics (C++ member) flow::Flow::Thermodynamics::enable (C++ function) flow::Flow::Thermodynamics::getEnergyBounds (C++ function), [1] flow::Flow::Thermodynamics::getTemperature (C++ function) flow::Flow::Thermodynamics::setEnergyBounds (C++ function), [1] flow::Flow::Thermodynamics::setTemperature (C++ function) flow::LinConstraint (C++ class) flow::LinConstraint::bound (C++ member) flow::LinConstraint::exp (C++ member) flow::LinConstraint::LinConstraint (C++ function) flow::LinConstraint::operator<< (C++ function) flow::LinConstraint::Relation (C++ enum) flow::LinConstraint::relation (C++ member) flow::LinExp (C++ class) flow::LinExp::FloatElement (C++ type) flow::LinExp::getFloatElements (C++ function) flow::LinExp::getIntElements (C++ function) flow::LinExp::IntElement (C++ type) flow::LinExp::LinExp (C++ function), [1] flow::LinExp::operator<< (C++ function) flow::Printer (C++ class) flow::Printer::getDGPrinter (C++ function), [1] flow::Printer::getPrintFiltered (C++ function) flow::Printer::getPrintUnfiltered (C++ function) flow::Printer::getUnfilteredFlowColour (C++ function) flow::Printer::popInEdgeLabel (C++ function) flow::Printer::popInOutEdgeLabel (C++ function) flow::Printer::pushInEdgeLabel (C++ function) flow::Printer::pushOutEdgeLabel (C++ function) flow::Printer::setPrintFiltered (C++ function) flow::Printer::setPrintUnfiltered (C++ function) flow::Printer::setUnfilteredFlowColour (C++ function) flow::Solution (C++ class) flow::Solution::eval (C++ function) flow::Solution::getFlow (C++ function) flow::Solution::getId (C++ function) flow::Solution::list (C++ function) flow::Solution::operator!= (C++ function) flow::Solution::operator< (C++ function) flow::Solution::operator<< (C++ function) flow::Solution::operator== (C++ function) flow::Solution::print (C++ function), [1] flow::SolutionOld (C++ class) flow::SolutionOld::eval (C++ function)

flow::SolutionOld::getFlow (C++ function) flow::SolutionOld::getId (C++ function) flow::SolutionOld::haxListDerivations (C++ function) flow::SolutionOld::print (C++ function) flow::SolutionRange (C++ class) flow::SolutionRange::begin (C++ function) flow::SolutionRange::const_iterator (C++ type) flow::SolutionRange::end (C++ function) flow::SolutionRange::getFlow (C++ function) flow::SolutionRange::iterator (C++ type) flow::SolutionRange::list (C++ function) flow::SolutionRange::operator<< (C++ function) flow::SolutionRange::operator[] (C++ function) flow::SolutionRange::print (C++ function), [1] flow::SolutionRange::size (C++ function) flow::SolutionSet (C++ class) flow::SolutionSet::begin (C++ function) flow::SolutionSet::end (C++ function) flow::SolutionSet::getFlow (C++ function) flow::SolutionSet::list (C++ function) flow::SolutionSet::operator[] (C++ function) flow::SolutionSet::print (C++ function) flow::SolutionSet::size (C++ function) flow::SolutionSet::SolutionSet (C++ function) flow::Var (C++ class) flow::Var::applyVisitor (C++ function), [1] flow::Var::get (C++ function) flow::Var::operator<< (C++ function) flow::Var::operator== (C++ function) flow::Var::v (C++ member) flow::Var::Var (C++ function) flow::Var::VarImpl (C++ type) flow::VarCustom (C++ class) flow::VarCustom::id (C++ member) flow::VarCustom::name (C++ member) flow::VarCustom::operator<< (C++ function) flow::VarCustom::operator== (C++ function) flow::VarCustom::VarCustom (C++ function) flow::VarEdge (C++ class) flow::VarEdge::edge (C++ member) flow::VarEdge::id (C++ member) flow::VarEdge::operator<< (C++ function) flow::VarEdge::operator== (C++ function) flow::VarEdge::VarEdge (C++ function) flow::VarSumCustom (C++ class) flow::VarSumCustom::id (C++ member) flow::VarSumCustom::operator<< (C++ function) flow::VarSumCustom::operator== (C++ function) flow::VarSumCustom::operator[] (C++ function) flow::VarSumCustom::VarSumCustom (C++ function) flow::VarSumEdge (C++ class) flow::VarSumEdge::id (C++ member) flow::VarSumEdge::operator<< (C++ function) flow::VarSumEdge::operator== (C++ function) flow::VarSumEdge::operator[] (C++ function) flow::VarSumEdge::VarSumEdge (C++ function) flow::VarSumVertex (C++ class) flow::VarSumVertex::id (C++ member) flow::VarSumVertex::operator<< (C++ function) flow::VarSumVertex::operator== (C++ function) flow::VarSumVertex::operator[] (C++ function), [1] flow::VarSumVertex::VarSumVertex (C++ function) flow::VarVertex (C++ class) flow::VarVertex::id (C++ member) flow::VarVertex::operator<< (C++ function) flow::VarVertex::operator== (C++ function) flow::VarVertex::v (C++ member) flow::VarVertex::VarVertex (C++ function) flow::VarVertexGraph (C++ class) flow::VarVertexGraph::g (C++ member) flow::VarVertexGraph::id (C++ member) flow::VarVertexGraph::operator<< (C++ function) flow::VarVertexGraph::operator== (C++ function) flow::VarVertexGraph::VarVertexGraph (C++ function) FlowLinConstraint (class in mod) FlowLinExp (class in mod) FlowOverallAutocatalysis (class in mod) FlowOverallCatalysis (class in mod) FlowPrinter (class in mod) FlowSolution (class in mod) FlowSolutionOld (class in mod) FlowSolutionRange (class in mod) FlowSolutionSet (class in mod) FlowThermodynamics (class in mod) FlowVar (class in mod) FlowVarCustom (class in mod) FlowVarEdge (class in mod) FlowVarSumCustom (class in mod) FlowVarSumEdge (class in mod) FlowVarSumVertex (class in mod) FlowVarVertex (class in mod) FlowVarVertexGraph (class in mod) flushCommands() (in module post) forceExistence (mod.FlowOverallAutocatalysis attribute) (mod.FlowOverallCatalysis attribute) (mod.hyperflow.Model.OverallAutocatalysis attribute) (mod.hyperflow.Model.OverallCatalysis attribute) fromDFS() (mod.Graph static method) (mod.Rule static method) fromDFSMulti() (mod.Graph static method) fromGMLFile() (mod.Graph static method) (mod.Rule static method) fromGMLFileMulti() (mod.Graph static method) fromGMLString() (mod.Graph static method) (mod.Rule static method) fromGMLStringMulti() (mod.Graph static method) fromMOLFile() (mod.Graph static method) fromMOLFileMulti() (mod.Graph static method) fromMOLString() (mod.Graph static method) fromMOLStringMulti() (mod.Graph static method) fromSDFile() (mod.Graph static method) fromSDFileMulti() (mod.Graph static method) fromSDString() (mod.Graph static method) fromSDStringMulti() (mod.Graph static method) fromSMILES() (mod.Graph static method) fromSMILESMulti() (mod.Graph static method) Function (C++ class) Function<R(Args...)> (C++ class) Function<R(Args...)>::clone (C++ function) Function<R(Args...)>::operator() (C++ function) Function<R(Args...)>::print (C++ function)

G

gens (mod.Graph.AutGroup attribute) get2DX() (mod.Rule.Vertex method) get2DY() (mod.Rule.Vertex method) getAllEnabled() (mod.causality.Marking method) (mod.DGPetriNetMarking method) getAvailableILPSolvers (C++ function) getAvailableILPSolvers() (in module mod) getConfig (C++ function) getConfig() (in module mod) getEdge() (mod.DG.Builder.AddAbstractResult method) getEmptyPostPlaces() (mod.causality.Marking method) (mod.DGPetriNetMarking method) getEnergyBounds() (mod.FlowThermodynamics method) (mod.hyperflow.Model.Thermodynamics method) getGMLString() (mod.Graph method) (mod.Rule method) getGraph() (mod.DG.Builder.AddAbstractResult method) getNonZeroPlaces() (mod.causality.Marking method) (mod.DGPetriNetMarking method) getPostPlaces() (mod.causality.Net method) (mod.DGPetriNet method) getVertexFromExternalId() (mod.Graph method) (mod.Rule method) Graph (class in mod) (class in mod.protocols) graph (mod.DG.Vertex attribute) (mod.FlowVarVertexGraph attribute) (mod.hyperflow.VarVertexGraph attribute) (mod.protocols.Graph.Edge attribute) (mod.protocols.Graph.Vertex attribute) (mod.Rule.ContextGraph.Edge attribute) Graph.Aut (class in mod) Graph.AutGroup (class in mod) Graph.AutGroupGensRange (class in mod) Graph.Edge (class in mod) (class in mod.protocols) Graph.EdgeRange (class in mod) (class in mod.protocols) Graph.IncidentEdgeRange (class in mod) (class in mod.protocols) Graph.Vertex (class in mod) (class in mod.protocols) Graph.VertexRange (class in mod) (class in mod.protocols) graph::Graph (C++ class) graph::Graph::Aut (C++ class) graph::Graph::aut (C++ function) graph::Graph::Aut::operator[] (C++ function) graph::Graph::AutGroup (C++ class) graph::Graph::AutGroup::AutGroup (C++ function) graph::Graph::AutGroup::Gens (C++ class) graph::Graph::AutGroup::gens (C++ function) graph::Graph::cacheEnergy (C++ function) graph::Graph::create (C++ function), [1] graph::Graph::Edge (C++ class) graph::Graph::Edge::Edge (C++ function) graph::Graph::Edge::getBondType (C++ function) graph::Graph::Edge::getGraph (C++ function) graph::Graph::Edge::getStringLabel (C++ function) graph::Graph::Edge::isNull (C++ function) graph::Graph::Edge::operator bool (C++ function) graph::Graph::Edge::source (C++ function) graph::Graph::Edge::target (C++ function) graph::Graph::EdgeIterator (C++ class) graph::Graph::EdgeIterator::EdgeIterator (C++ function) graph::Graph::EdgeRange (C++ class) graph::Graph::edges (C++ function) graph::Graph::eLabelCount (C++ function) graph::Graph::enumerateIsomorphisms (C++ function) graph::Graph::enumerateMonomorphisms (C++ function) graph::Graph::fromDFS (C++ function) graph::Graph::fromDFSMulti (C++ function) graph::Graph::fromGMLFile (C++ function) graph::Graph::fromGMLFileMulti (C++ function) graph::Graph::fromGMLString (C++ function) graph::Graph::fromGMLStringMulti (C++ function) graph::Graph::fromMOLFile (C++ function) graph::Graph::fromMOLFileMulti (C++ function) graph::Graph::fromMOLString (C++ function) graph::Graph::fromMOLStringMulti (C++ function) graph::Graph::fromSDFile (C++ function) graph::Graph::fromSDFileMulti (C++ function) graph::Graph::fromSDString (C++ function) graph::Graph::fromSDStringMulti (C++ function) graph::Graph::fromSMILES (C++ function), [1] graph::Graph::fromSMILESMulti (C++ function), [1] graph::Graph::getEnergy (C++ function) graph::Graph::getExactMass (C++ function) graph::Graph::getGMLString (C++ function) graph::Graph::getGraphDFS (C++ function) graph::Graph::getGraphDFSWithIds (C++ function) graph::Graph::getId (C++ function) graph::Graph::getImage (C++ function) graph::Graph::getImageCommand (C++ function) graph::Graph::getIsMolecule (C++ function) graph::Graph::getLinearEncoding (C++ function) graph::Graph::getLoadingWarnings (C++ function) graph::Graph::getMaxExternalId (C++ function) graph::Graph::getMinExternalId (C++ function) graph::Graph::getName (C++ function) graph::Graph::getSmiles (C++ function) graph::Graph::getSmilesWithIds (C++ function) graph::Graph::getVertexFromExternalId (C++ function) graph::Graph::IncidentEdgeIterator (C++ class) graph::Graph::IncidentEdgeIterator::IncidentEdgeIterator (C++ function) graph::Graph::IncidentEdgeRange (C++ class) graph::Graph::instantiateStereo (C++ function) graph::Graph::isomorphism (C++ function) graph::Graph::makePermutation (C++ function) graph::Graph::monomorphism (C++ function) graph::Graph::numEdges (C++ function) graph::Graph::numVertices (C++ function) graph::Graph::print (C++ function), [1] graph::Graph::printGML (C++ function) graph::Graph::printTermState (C++ function) graph::Graph::setImage (C++ function) graph::Graph::setImageCommand (C++ function) graph::Graph::setName (C++ function)

graph::Graph::Vertex (C++ class) graph::Graph::Vertex::getAtomId (C++ function) graph::Graph::Vertex::getCharge (C++ function) graph::Graph::Vertex::getDegree (C++ function) graph::Graph::Vertex::getGraph (C++ function) graph::Graph::Vertex::getId (C++ function) graph::Graph::Vertex::getIsotope (C++ function) graph::Graph::Vertex::getRadical (C++ function) graph::Graph::Vertex::getStringLabel (C++ function) graph::Graph::Vertex::incidentEdges (C++ function) graph::Graph::Vertex::isNull (C++ function) graph::Graph::Vertex::operator bool (C++ function) graph::Graph::Vertex::printStereo (C++ function), [1] graph::Graph::Vertex::Vertex (C++ function) graph::Graph::VertexIterator (C++ class) graph::Graph::VertexIterator::VertexIterator (C++ function) graph::Graph::VertexRange (C++ class) graph::Graph::vertices (C++ function) graph::Graph::vLabelCount (C++ function) graph::Printer (C++ class) graph::Printer::disableAll (C++ function) graph::Printer::enableAll (C++ function) graph::Printer::getCollapseHydrogens (C++ function) graph::Printer::getEdgesAsBonds (C++ function) graph::Printer::getGraphvizPrefix (C++ function) graph::Printer::getMirror (C++ function) graph::Printer::getRaiseCharges (C++ function) graph::Printer::getRaiseIsotopes (C++ function) graph::Printer::getRotation (C++ function) graph::Printer::getSimpleCarbons (C++ function) graph::Printer::getThick (C++ function) graph::Printer::getWithColour (C++ function) graph::Printer::getWithGraphvizCoords (C++ function) graph::Printer::getWithIndex (C++ function) graph::Printer::getWithPrettyStereo (C++ function) graph::Printer::getWithRawStereo (C++ function) graph::Printer::getWithTexttt (C++ function) graph::Printer::operator!= (C++ function) graph::Printer::operator== (C++ function) graph::Printer::setCollapseHydrogens (C++ function) graph::Printer::setEdgesAsBonds (C++ function) graph::Printer::setGraphvizPrefix (C++ function) graph::Printer::setMirror (C++ function) graph::Printer::setMolDefault (C++ function) graph::Printer::setRaiseCharges (C++ function) graph::Printer::setRaiseIsotopes (C++ function) graph::Printer::setReactionDefault (C++ function) graph::Printer::setRotation (C++ function) graph::Printer::setSimpleCarbons (C++ function) graph::Printer::setThick (C++ function) graph::Printer::setWithColour (C++ function) graph::Printer::setWithGraphvizCoords (C++ function) graph::Printer::setWithIndex (C++ function) graph::Printer::setWithPrettyStereo (C++ function) graph::Printer::setWithRawStereo (C++ function) graph::Printer::setWithTexttt (C++ function) graph::Union (C++ class) graph::Union::begin (C++ function) graph::Union::const_iterator (C++ type) graph::Union::Edge (C++ class) graph::Union::Edge::Edge (C++ function) graph::Union::Edge::getBondType (C++ function) graph::Union::Edge::getEdge (C++ function) graph::Union::Edge::getGraph (C++ function) graph::Union::Edge::getGraphIndex (C++ function) graph::Union::Edge::getStringLabel (C++ function) graph::Union::Edge::isNull (C++ function) graph::Union::Edge::operator bool (C++ function) graph::Union::Edge::source (C++ function) graph::Union::Edge::target (C++ function) graph::Union::EdgeIterator (C++ class) graph::Union::EdgeIterator::EdgeIterator (C++ function) graph::Union::EdgeRange (C++ class) graph::Union::edges (C++ function) graph::Union::end (C++ function) graph::Union::IncidentEdgeIterator (C++ class) graph::Union::IncidentEdgeIterator::IncidentEdgeIterator (C++ function) graph::Union::IncidentEdgeRange (C++ class) graph::Union::iterator (C++ type) graph::Union::numEdges (C++ function) graph::Union::numVertices (C++ function) graph::Union::operator<< (C++ function) graph::Union::operator[] (C++ function) graph::Union::printTermState (C++ function) graph::Union::size (C++ function) graph::Union::Union (C++ function), [1] graph::Union::Vertex (C++ class) graph::Union::Vertex::getAtomId (C++ function) graph::Union::Vertex::getCharge (C++ function) graph::Union::Vertex::getDegree (C++ function) graph::Union::Vertex::getGraph (C++ function) graph::Union::Vertex::getGraphIndex (C++ function) graph::Union::Vertex::getId (C++ function) graph::Union::Vertex::getIsotope (C++ function) graph::Union::Vertex::getRadical (C++ function) graph::Union::Vertex::getStringLabel (C++ function) graph::Union::Vertex::getVertex (C++ function) graph::Union::Vertex::incidentEdges (C++ function) graph::Union::Vertex::isNull (C++ function) graph::Union::Vertex::operator bool (C++ function) graph::Union::Vertex::printStereo (C++ function), [1] graph::Union::Vertex::Vertex (C++ function) graph::Union::VertexIterator (C++ class) graph::Union::VertexIterator::VertexIterator (C++ function) graph::Union::VertexRange (C++ class) graph::Union::vertices (C++ function) graphDatabase (mod.DG attribute) graphDFS (mod.Graph attribute) graphDFS() (in module mod) graphDFSWithIds (mod.Graph attribute) graphGML() (in module mod) graphGMLString() (in module mod) GraphHandle (C++ type) graphIndex (mod.UnionGraph.Edge attribute) (mod.UnionGraph.Vertex attribute) GraphPrinter (class in mod) graphPrinter (mod.DGPrinter attribute) graphvizPrefix (mod.DGPrinter attribute) (mod.GraphPrinter attribute)

H

hasActiveBuilder (mod.DG attribute) haxListDerivations() (mod.FlowSolutionOld method) hyperflow.LinConstraint (class in mod) hyperflow.LinExp (class in mod) hyperflow.Model (class in mod) hyperflow.Model.OverallAutocatalysis (class in mod) hyperflow.Model.OverallCatalysis (class in mod) hyperflow.Model.Thermodynamics (class in mod) hyperflow.Printer (class in mod) hyperflow.Solution (class in mod) hyperflow.SolutionRange (class in mod) hyperflow.Var (class in mod) hyperflow.VarCustom (class in mod) hyperflow.VarEdge (class in mod) hyperflow.vars.deltaEnergy (in module mod) hyperflow.vars.edgeFlow (in module mod) hyperflow.vars.energy (in module mod) hyperflow.vars.inFlow (in module mod) hyperflow.vars.isBothReverseUsed (in module mod) hyperflow.vars.isEdgeUsed (in module mod) hyperflow.vars.isInGreaterOut (in module mod) hyperflow.vars.isInLessOut (in module mod) hyperflow.vars.isInOutZero (in module mod) hyperflow.vars.isInUsed (in module mod) hyperflow.vars.isOutUsed (in module mod) hyperflow.vars.isOverallAutocata (in module mod) hyperflow.vars.isOverallCata (in module mod) hyperflow.vars.isVertexUsed (in module mod) hyperflow.vars.logConcentration (in module mod) hyperflow.vars.outFlow (in module mod) hyperflow.vars.transitInternalFlow (in module mod) hyperflow.vars.vertexFlow (in module mod) hyperflow.VarSumCustom (class in mod) hyperflow.VarSumEdge (class in mod) hyperflow.VarSumVertex (class in mod) hyperflow.VarVertex (class in mod) hyperflow.VarVertexGraph (class in mod) hyperflow::LinConstraint (C++ class) hyperflow::LinConstraint::bound (C++ member) hyperflow::LinConstraint::exp (C++ member) hyperflow::LinConstraint::LinConstraint (C++ function) hyperflow::LinConstraint::operator<< (C++ function) hyperflow::LinConstraint::Relation (C++ enum) hyperflow::LinConstraint::relation (C++ member) hyperflow::LinExp (C++ class) hyperflow::LinExp::FloatElement (C++ type) hyperflow::LinExp::getFloatElements (C++ function) hyperflow::LinExp::getIntElements (C++ function) hyperflow::LinExp::IntElement (C++ type) hyperflow::LinExp::LinExp (C++ function), [1], [2] hyperflow::LinExp::operator*= (C++ function), [1] hyperflow::LinExp::operator+= (C++ function) hyperflow::LinExp::operator-= (C++ function) hyperflow::LinExp::operator<< (C++ function) hyperflow::Model (C++ class) hyperflow::Model::addBoolVariable (C++ function) hyperflow::Model::addConstraint (C++ function) hyperflow::Model::addEnumerationVar (C++ function) hyperflow::Model::addFloatVariable (C++ function) hyperflow::Model::addIntVariable (C++ function) hyperflow::Model::addSink (C++ function), [1] hyperflow::Model::addSource (C++ function), [1] hyperflow::Model::addTransitEnumeration (C++ function), [1] hyperflow::Model::copy (C++ function) hyperflow::Model::dump (C++ function), [1] hyperflow::Model::exclude (C++ function), [1] hyperflow::Model::findSolutions (C++ function), [1], [2] hyperflow::Model::getAbsGap (C++ function) hyperflow::Model::getAllowHyperLoops (C++ function) hyperflow::Model::getAllowIOReversal (C++ function) hyperflow::Model::getAllowReversal (C++ function) hyperflow::Model::getCustomBoolVariables (C++ function) hyperflow::Model::getCustomFloatVariables (C++ function) hyperflow::Model::getCustomIntVariables (C++ function) hyperflow::Model::getDG (C++ function) hyperflow::Model::getEnumerationVars (C++ function) hyperflow::Model::getExcluded (C++ function) hyperflow::Model::getId (C++ function) hyperflow::Model::getRelaxed (C++ function) hyperflow::Model::getSeparatedIOInternalTransit (C++ function) hyperflow::Model::getSinks (C++ function) hyperflow::Model::getSolutions (C++ function) hyperflow::Model::getSources (C++ function) hyperflow::Model::getTransitEnumeration (C++ function) hyperflow::Model::isSpecificationLocked (C++ function) hyperflow::Model::listSpecification (C++ function) hyperflow::Model::load (C++ function), [1] hyperflow::Model::loadString (C++ function), [1] hyperflow::Model::make (C++ function), [1] hyperflow::Model::OverallAutocatalysis (C++ class) hyperflow::Model::overallAutocatalysis (C++ member) hyperflow::Model::OverallAutocatalysis::enable (C++ function) hyperflow::Model::OverallAutocatalysis::getBFSExclusive (C++ function) hyperflow::Model::OverallAutocatalysis::getForceExistence (C++ function) hyperflow::Model::OverallAutocatalysis::getStrictTransit (C++ function) hyperflow::Model::OverallAutocatalysis::isEnabled (C++ function) hyperflow::Model::OverallAutocatalysis::setBFSExclusive (C++ function) hyperflow::Model::OverallAutocatalysis::setForceExistence (C++ function) hyperflow::Model::OverallAutocatalysis::setStrictTransit (C++ function) hyperflow::Model::OverallCatalysis (C++ class) hyperflow::Model::overallCatalysis (C++ member) hyperflow::Model::OverallCatalysis::enable (C++ function) hyperflow::Model::OverallCatalysis::getForceExistence (C++ function) hyperflow::Model::OverallCatalysis::getStrictTransit (C++ function) hyperflow::Model::OverallCatalysis::isEnabled (C++ function) hyperflow::Model::OverallCatalysis::setForceExistence (C++ function) hyperflow::Model::OverallCatalysis::setStrictTransit (C++ function) hyperflow::Model::printEnumerationTree (C++ function) hyperflow::Model::printExpanded (C++ function) hyperflow::Model::printExpandedVertex (C++ function), [1] hyperflow::Model::separateIOInternalTransit (C++ function), [1] hyperflow::Model::setAbsGap (C++ function) hyperflow::Model::setAllowHyperLoops (C++ function) hyperflow::Model::setAllowIOReversal (C++ function) hyperflow::Model::setAllowReversal (C++ function) hyperflow::Model::setObjectiveFunction (C++ function)

hyperflow::Model::setRelaxed (C++ function) hyperflow::Model::Thermodynamics (C++ class) hyperflow::Model::thermodynamics (C++ member) hyperflow::Model::Thermodynamics::enable (C++ function) hyperflow::Model::Thermodynamics::getEnergyBounds (C++ function), [1] hyperflow::Model::Thermodynamics::getTemperature (C++ function) hyperflow::Model::Thermodynamics::isEnabled (C++ function) hyperflow::Model::Thermodynamics::setEnergyBounds (C++ function), [1] hyperflow::Model::Thermodynamics::setTemperature (C++ function) hyperflow::operator* (C++ function), [1], [2], [3] hyperflow::operator+ (C++ function) hyperflow::operator- (C++ function) hyperflow::operator<= (C++ function), [1] hyperflow::operator== (C++ function), [1] hyperflow::operator>= (C++ function), [1] hyperflow::Printer (C++ class) hyperflow::Printer::getDGPrinter (C++ function), [1] hyperflow::Printer::getPrintFiltered (C++ function) hyperflow::Printer::getPrintUnfiltered (C++ function) hyperflow::Printer::getUnfilteredFlowColour (C++ function) hyperflow::Printer::popInEdgeLabel (C++ function) hyperflow::Printer::popInOutEdgeLabel (C++ function) hyperflow::Printer::pushInEdgeLabel (C++ function) hyperflow::Printer::pushOutEdgeLabel (C++ function) hyperflow::Printer::setPrintFiltered (C++ function) hyperflow::Printer::setPrintUnfiltered (C++ function) hyperflow::Printer::setUnfilteredFlowColour (C++ function) hyperflow::Solution (C++ class) hyperflow::Solution::eval (C++ function) hyperflow::Solution::getId (C++ function) hyperflow::Solution::getModel (C++ function) hyperflow::Solution::getObjectiveValue (C++ function) hyperflow::Solution::list (C++ function) hyperflow::Solution::operator!= (C++ function) hyperflow::Solution::operator< (C++ function) hyperflow::Solution::operator<< (C++ function) hyperflow::Solution::operator== (C++ function) hyperflow::Solution::print (C++ function), [1] hyperflow::SolutionRange (C++ class) hyperflow::SolutionRange::begin (C++ function) hyperflow::SolutionRange::const_iterator (C++ type) hyperflow::SolutionRange::end (C++ function) hyperflow::SolutionRange::getModel (C++ function) hyperflow::SolutionRange::iterator (C++ type) hyperflow::SolutionRange::list (C++ function) hyperflow::SolutionRange::operator<< (C++ function) hyperflow::SolutionRange::operator[] (C++ function) hyperflow::SolutionRange::print (C++ function), [1] hyperflow::SolutionRange::size (C++ function) hyperflow::Var (C++ class) hyperflow::Var::applyVisitor (C++ function), [1] hyperflow::Var::get (C++ function) hyperflow::Var::operator<< (C++ function) hyperflow::Var::operator== (C++ function) hyperflow::Var::v (C++ member) hyperflow::Var::Var (C++ function) hyperflow::Var::VarImpl (C++ type) hyperflow::VarCustom (C++ class) hyperflow::VarCustom::id (C++ member) hyperflow::VarCustom::name (C++ member) hyperflow::VarCustom::operator<< (C++ function) hyperflow::VarCustom::operator== (C++ function) hyperflow::VarCustom::VarCustom (C++ function) hyperflow::VarEdge (C++ class) hyperflow::VarEdge::edge (C++ member) hyperflow::VarEdge::id (C++ member) hyperflow::VarEdge::operator<< (C++ function) hyperflow::VarEdge::operator== (C++ function) hyperflow::VarEdge::VarEdge (C++ function) hyperflow::vars::deltaEnergy (C++ member) hyperflow::vars::edgeFlow (C++ member) hyperflow::vars::energy (C++ member) hyperflow::vars::inFlow (C++ member) hyperflow::vars::isBothReverseUsed (C++ member) hyperflow::vars::isEdgeUsed (C++ member) hyperflow::vars::isInGreaterOut (C++ member) hyperflow::vars::isInLessOut (C++ member) hyperflow::vars::isInOutZero (C++ member) hyperflow::vars::isInUsed (C++ member) hyperflow::vars::isOutUsed (C++ member) hyperflow::vars::isOverallAutocata (C++ member) hyperflow::vars::isOverallCata (C++ member) hyperflow::vars::isVertexUsed (C++ member) hyperflow::vars::logConcentration (C++ member) hyperflow::vars::outFlow (C++ member) hyperflow::vars::transitInternalFlow (C++ member) hyperflow::vars::vertexFlow (C++ member) hyperflow::VarSumCustom (C++ class) hyperflow::VarSumCustom::id (C++ member) hyperflow::VarSumCustom::operator<< (C++ function) hyperflow::VarSumCustom::operator== (C++ function) hyperflow::VarSumCustom::operator[] (C++ function) hyperflow::VarSumCustom::VarSumCustom (C++ function) hyperflow::VarSumEdge (C++ class) hyperflow::VarSumEdge::id (C++ member) hyperflow::VarSumEdge::operator<< (C++ function) hyperflow::VarSumEdge::operator== (C++ function) hyperflow::VarSumEdge::operator[] (C++ function) hyperflow::VarSumEdge::VarSumEdge (C++ function) hyperflow::VarSumVertex (C++ class) hyperflow::VarSumVertex::id (C++ member) hyperflow::VarSumVertex::operator<< (C++ function) hyperflow::VarSumVertex::operator== (C++ function) hyperflow::VarSumVertex::operator[] (C++ function), [1] hyperflow::VarSumVertex::VarSumVertex (C++ function) hyperflow::VarVertex (C++ class) hyperflow::VarVertex::id (C++ member) hyperflow::VarVertex::operator<< (C++ function) hyperflow::VarVertex::operator== (C++ function) hyperflow::VarVertex::v (C++ member) hyperflow::VarVertex::VarVertex (C++ function) hyperflow::VarVertexGraph (C++ class) hyperflow::VarVertexGraph::g (C++ member) hyperflow::VarVertexGraph::id (C++ member) hyperflow::VarVertexGraph::operator<< (C++ function) hyperflow::VarVertexGraph::operator== (C++ function) hyperflow::VarVertexGraph::VarVertexGraph (C++ function)

I

id (mod.DG attribute) (mod.DG.HyperEdge attribute) (mod.DG.Vertex attribute) (mod.Flow attribute) (mod.FlowSolution attribute) (mod.FlowSolutionOld attribute) (mod.FlowVarCustom attribute) (mod.FlowVarEdge attribute) (mod.FlowVarSumCustom attribute) (mod.FlowVarSumEdge attribute) (mod.FlowVarSumVertex attribute) (mod.FlowVarVertex attribute) (mod.FlowVarVertexGraph attribute) (mod.Graph attribute) (mod.hyperflow.Model attribute) (mod.hyperflow.Solution attribute) (mod.hyperflow.VarCustom attribute) (mod.hyperflow.VarEdge attribute) (mod.hyperflow.VarSumCustom attribute) (mod.hyperflow.VarSumEdge attribute) (mod.hyperflow.VarSumVertex attribute) (mod.hyperflow.VarVertex attribute) (mod.hyperflow.VarVertexGraph attribute) (mod.protocols.Graph.Vertex attribute) (mod.Rule attribute) Ignore (mod.Action attribute) image (mod.Graph attribute) imageCommand (mod.Graph attribute) incidentEdges (mod.protocols.Graph.Vertex attribute) include() (in module mod) inDegree (mod.DG.Vertex attribute) inEdges (mod.DG.Vertex attribute) inFlow (in module mod) initialState (mod.causality.EventTrace attribute) InputError (C++ class) inputGraphs (in module mod) inputRate (mod.stochsim.DrawMassAction attribute) inputRules (in module mod) instantiateStereo() (mod.Graph method)

Invalid (mod.AtomIds attribute) (mod.BondType attribute) inverse (mod.DG.HyperEdge attribute) inverse() (mod.protocols.VertexMap method) isActive (mod.DG.Builder attribute) isBothReverseUsed (in module mod) isEdgeUsed (in module mod) isEnabled (mod.hyperflow.Model.OverallAutocatalysis attribute) (mod.hyperflow.Model.OverallCatalysis attribute) (mod.hyperflow.Model.Thermodynamics attribute) isEnabled() (mod.causality.Marking method) (mod.DGPetriNetMarking method) isInGreaterOut (in module mod) isInLessOut (in module mod) isInOutZero (in module mod) isInUsed (in module mod) isMolecule (mod.Graph attribute) isNull() (mod.DG.HyperEdge method) (mod.DG.Vertex method) (mod.protocols.Graph.Edge method) (mod.protocols.Graph.Vertex method) isomorphicLeftRight() (mod.Rule method) Isomorphism (mod.LabelRelation attribute) isomorphism() (mod.Graph method) (mod.Rule method) IsomorphismPolicy (C++ enum) (class in mod) IsomorphismPolicy::Check (C++ enumerator) IsomorphismPolicy::TrustMe (C++ enumerator) Isotope (C++ class) (class in mod) isotope (mod.AtomData attribute) (mod.protocols.LabelledGraph.Vertex attribute) Isotope::Isotope (C++ function), [1] Isotope::operator int (C++ function) Isotope::operator<< (C++ function) isOutUsed (in module mod) isOverallAutocata (in module mod) isOverallCata (in module mod) isVertexUsed (in module mod) iterations (mod.stochsim.Simulator property)

L

LabelledGraph (class in mod.protocols) LabelledGraph.Edge (class in mod.protocols) LabelledGraph.Vertex (class in mod.protocols) LabelRelation (C++ enum) (class in mod) LabelRelation::Isomorphism (C++ enumerator) LabelRelation::Specialisation (C++ enumerator) LabelRelation::Unification (C++ enumerator) labelsAsLatexMath (mod.DGPrinter attribute) LabelSettings (C++ class) (class in mod) labelSettings (mod.DG attribute) (mod.RCMatch attribute) LabelSettings::LabelSettings (C++ function), [1], [2] LabelSettings::operator!= (C++ function) LabelSettings::operator<< (C++ function) LabelSettings::operator== (C++ function) LabelSettings::relation (C++ member) LabelSettings::stereoRelation (C++ member) LabelSettings::type (C++ member) LabelSettings::withStereo (C++ member) LabelType (C++ enum) (class in mod) labelType (mod.Rule attribute) LabelType::String (C++ enumerator) LabelType::Term (C++ enumerator) left (mod.Derivation attribute) (mod.Derivations attribute) (mod.DGVertexMapper attribute) (mod.Rule attribute) (mod.Rule.Edge attribute) (mod.Rule.Vertex attribute)

leftPredicate (in module mod) linearEncoding (mod.Graph attribute) list() (mod.DG.Builder.ExecuteResult method) (mod.FlowSolution method) (mod.FlowSolutionRange method) (mod.FlowSolutionSet method) (mod.hyperflow.Solution method) (mod.hyperflow.SolutionRange method) listSpecification() (mod.Flow method) (mod.hyperflow.Model method) listStats() (mod.DG method) load() (mod.causality.EventTrace static method) (mod.DG static method) (mod.DG.Builder method) (mod.Flow static method) (mod.hyperflow.Model static method) loadingWarnings (mod.Graph attribute) loadString() (mod.Flow static method) (mod.hyperflow.Model static method) locked (mod.DG attribute) logConcentration (in module mod) logCount (mod.causality.EventTracePrinter attribute) LogicError (C++ class) logTime (mod.causality.EventTracePrinter attribute)

M

magicLibraryValue() (in module mod) makeAddDynamic() (mod.DGStrat static method) makeAddStatic() (mod.DGStrat static method) makeDuplicate() (mod.DGPrintData method) makeExecute() (mod.DGStrat static method) makeFilter() (mod.DGStrat static method) makeInverse() (mod.Rule method) makeLeftPredicate() (mod.DGStrat static method) makeParallel() (mod.DGStrat static method) makePermutation() (mod.Graph method) makeRepeat() (mod.DGStrat static method) makeRevive() (mod.DGStrat static method) makeRightPredicate() (mod.DGStrat static method) makeRule() (mod.DGStrat static method) makeSequence() (mod.DGStrat static method) makeUniqueFilePrefix() (in module mod) map (mod.DGVertexMapper.Result attribute) MapUnique (mod.SmilesClassPolicy attribute) match (mod.DGVertexMapper.Result attribute) Max (mod.AtomIds attribute) maxExternalId (mod.Graph attribute) (mod.Rule attribute) maxPointsPerVertex (mod.causality.EventTracePrinter attribute) MDLOptions (C++ class) (class in mod) MDLOptions::addHydrogens (C++ member) MDLOptions::allowAbstract (C++ member) MDLOptions::applyV2000AtomAliases (C++ member) MDLOptions::fullyIgnoreV2000UnhandledKnownProperty (C++ member) MDLOptions::onImplicitValenceOnAbstract (C++ member) MDLOptions::onPatternCharge (C++ member) MDLOptions::onPatternIsotope (C++ member) MDLOptions::onPatternRadical (C++ member) MDLOptions::onRAD1 (C++ member) MDLOptions::onRAD3 (C++ member) MDLOptions::onRAD4 (C++ member) MDLOptions::onRAD5 (C++ member) MDLOptions::onRAD6 (C++ member) MDLOptions::onUnsupportedQueryBondType (C++ member) MDLOptions::onV2000AbstractISO (C++ member) MDLOptions::onV2000Charge4 (C++ member) MDLOptions::onV2000UnhandledProperty (C++ member) MDLOptions::onV3000UnhandledAtomProperty (C++ member)

minExternalId (mod.Graph attribute) (mod.Rule attribute) mirror (mod.GraphPrinter attribute) mod module mod command line option --debug --help --memcheck --nopost --profile --version --vgArgs -e -f -h -i -j -q -v clean mod.stochsim module MOD_DEBUGGER, [1] MOD_IPYTHON, [1] MOD_NO_DEPRECATED MOD_NUM_POST_THREADS mod_post command line option --help --install-format --install-format-sudo -h -j MOD_PYTHON, [1], [2] model (mod.hyperflow.Solution attribute) (mod.hyperflow.SolutionRange attribute) module mod mod.stochsim post monomorphism() (mod.Graph method) (mod.Rule method) multiplicity (mod.causality.RealisabilityQuery attribute) (mod.CausalityFlowQuery attribute)

N

name (mod.FlowVarCustom attribute) (mod.Graph attribute) (mod.hyperflow.VarCustom attribute) (mod.Rule attribute) net (mod.causality.Marking attribute) (mod.DGPetriNetMarking attribute) NoneOnDuplicate (mod.SmilesClassPolicy attribute) numEdges (mod.DG attribute) (mod.protocols.Graph attribute)

numLeftComponents (mod.Rule attribute) numRightComponents (mod.Rule attribute) numSources (mod.DG.HyperEdge attribute) numTargets (mod.DG.HyperEdge attribute) numTokens (mod.causality.Marking attribute) (mod.DGPetriNetMarking attribute) numVertices (mod.DG attribute) (mod.protocols.Graph attribute)

O

objectiveFunction (mod.Flow attribute) (mod.hyperflow.Model attribute) objectiveValue (mod.hyperflow.Solution attribute) onDeadlock (mod.stochsim.Simulator attribute) onIterationBegin (mod.stochsim.Simulator attribute) onNewState (mod.stochsim.Simulator attribute) onRecompute (mod.stochsim.Simulator attribute) onRecomputeAvoided (mod.stochsim.Simulator attribute)

operator<< (C++ function) outDegree (mod.DG.Vertex attribute) outEdges (mod.DG.Vertex attribute) outFlow (in module mod) outputRate (mod.stochsim.DrawMassAction attribute) overallAutocatalysis (mod.Flow attribute) (mod.hyperflow.Model attribute) overallCatalysis (mod.Flow attribute) (mod.hyperflow.Model attribute)

P

pop() (mod.RCMatch method) popEdgeColour() (mod.DGPrinter method) popEdgeLabel() (mod.DGPrinter method) popEdgeVisible() (mod.DGPrinter method) popFilePrefix() (in module mod) popInEdgeLabel() (mod.FlowPrinter method) (mod.hyperflow.Printer method) popOptions() (mod.causality.EventTracePrinter method) popOutEdgeLabel() (mod.FlowPrinter method) (mod.hyperflow.Printer method) popVertexColour() (mod.DGPrinter method) popVertexLabel() (mod.DGPrinter method) popVertexOptions() (mod.causality.EventTracePrinter method) popVertexVisible() (mod.causality.EventTracePrinter method) (mod.DGPrinter method) post module post::command (C++ function) post::disableCommands (C++ function) post::disableCompileSummary (C++ function) post::disableInvokeMake (C++ function) post::enableCommands (C++ function) post::enableCompileSummary (C++ function) post::enableInvokeMake (C++ function) post::flushCommands (C++ function) post::makeUniqueFilePrefix (C++ function) post::reopenCommandFile (C++ function) post::summaryChapter (C++ function) post::summaryInput (C++ function) post::summaryRaw (C++ function), [1] post::summarySection (C++ function) prefixFilename() (in module mod) print() (mod.causality.EventTrace method) (mod.DG method) (mod.DG.HyperEdge method) (mod.FlowSolution method) (mod.FlowSolutionOld method) (mod.FlowSolutionRange method) (mod.FlowSolutionSet method) (mod.Graph method) (mod.hyperflow.Solution method) (mod.hyperflow.SolutionRange method) (mod.RCEvaluator method) (mod.Rule method)

printEnumerationTree() (mod.Flow method) (mod.hyperflow.Model method) printExpanded() (mod.Flow method) (mod.hyperflow.Model method) printExpandedVertex() (mod.Flow method) (mod.hyperflow.Model method) printFiltered (mod.FlowPrinter attribute) (mod.hyperflow.Printer attribute) printGML() (mod.Graph method) (mod.Rule method) printNonHyper() (mod.DG method) printStereo() (mod.protocols.LabelledGraph.Vertex method) printTermState() (mod.Graph method) (mod.Rule method) (mod.UnionGraph method) printUnfiltered (mod.FlowPrinter attribute) (mod.hyperflow.Printer attribute) push() (mod.RCMatch method) pushEdgeColour() (mod.DGPrinter method) pushEdgeLabel() (mod.DGPrinter method) pushEdgeVisible() (mod.DGPrinter method) pushFilePrefix() (in module mod) pushInEdgeLabel() (mod.FlowPrinter method) (mod.hyperflow.Printer method) pushOptions() (mod.causality.EventTracePrinter method) pushOutEdgeLabel() (mod.FlowPrinter method) (mod.hyperflow.Printer method) pushVertexColour() (mod.DGPrinter method) pushVertexLabel() (mod.DGPrinter method) pushVertexOptions() (mod.causality.EventTracePrinter method) pushVertexVisible() (mod.causality.EventTracePrinter method) (mod.DGPrinter method)

R

raiseCharges (mod.GraphPrinter attribute) raiseIsotopes (mod.GraphPrinter attribute) RCEvaluator (class in mod) RCExpBind (class in mod) RCExpComposeCommon (class in mod) RCExpComposeParallel (class in mod) RCExpComposeSub (class in mod) RCExpComposeSuper (class in mod) RCExpExp (class in mod) RCExpId (class in mod) RCExpUnbind (class in mod) RCExpUnion (class in mod) RCMatch (class in mod) reactionRate (mod.stochsim.DrawMassAction attribute) reconnectSource() (mod.DGPrintData method) reconnectTarget() (mod.DGPrintData method) relation (mod.LabelSettings attribute) relaxed (mod.Flow attribute) (mod.hyperflow.Model attribute) remove() (mod.causality.Marking method) (mod.DGPetriNetMarking method) removeDuplicate() (mod.DGPrintData method) reopenCommandFile() (in module post) repeat (in module mod) respectTransit (mod.causality.RealisabilityQuery attribute) revive() (in module mod) right (mod.Derivation attribute) (mod.Derivations attribute) (mod.DGVertexMapper attribute) (mod.Rule attribute) (mod.Rule.Edge attribute) (mod.Rule.Vertex attribute) rightPredicate (in module mod) rngReseed (C++ function) rngReseed() (in module mod) rngUniformReal (C++ function) rngUniformReal() (in module mod) rotation (mod.GraphPrinter attribute) Rule (class in mod) rule (mod.Derivation attribute) (mod.DGVertexMapper.Result attribute) (mod.Rule.ContextGraph attribute) (mod.Rule.ContextGraph.Vertex attribute) (mod.Rule.Edge attribute) (mod.Rule.LeftGraph attribute) (mod.Rule.LeftGraph.Edge attribute) (mod.Rule.LeftGraph.Vertex attribute) (mod.Rule.RightGraph attribute) (mod.Rule.RightGraph.Edge attribute) (mod.Rule.RightGraph.Vertex attribute) (mod.Rule.Vertex attribute) Rule.ContextGraph (class in mod) Rule.ContextGraph.Edge (class in mod) Rule.ContextGraph.EdgeRange (class in mod) Rule.ContextGraph.IncidentEdgeRange (class in mod) Rule.ContextGraph.Vertex (class in mod) Rule.ContextGraph.VertexRange (class in mod) Rule.Edge (class in mod) Rule.EdgeRange (class in mod) Rule.IncidentEdgeRange (class in mod) Rule.LeftGraph (class in mod) Rule.LeftGraph.Edge (class in mod) Rule.LeftGraph.EdgeRange (class in mod) Rule.LeftGraph.IncidentEdgeRange (class in mod) Rule.LeftGraph.Vertex (class in mod) Rule.LeftGraph.VertexRange (class in mod) Rule.RightGraph (class in mod) Rule.RightGraph.Edge (class in mod) Rule.RightGraph.EdgeRange (class in mod) Rule.RightGraph.IncidentEdgeRange (class in mod) Rule.RightGraph.Vertex (class in mod) Rule.RightGraph.VertexRange (class in mod) Rule.Vertex (class in mod) Rule.VertexRange (class in mod) rule::Composer (C++ class) rule::Composer::Composer (C++ function), [1] rule::Composer::eval (C++ function) rule::Composer::getCreatedRules (C++ function) rule::Composer::getRuleDatabase (C++ function) rule::Composer::operator= (C++ function) rule::Composer::print (C++ function) rule::CompositionMatch (C++ class) rule::CompositionMatch::compose (C++ function) rule::CompositionMatch::composeAll (C++ function) rule::CompositionMatch::CompositionMatch (C++ function), [1] rule::CompositionMatch::getFirst (C++ function) rule::CompositionMatch::getLabelSettings (C++ function) rule::CompositionMatch::getSecond (C++ function) rule::CompositionMatch::operator<< (C++ function) rule::CompositionMatch::operator= (C++ function) rule::CompositionMatch::operator[] (C++ function), [1] rule::CompositionMatch::pop (C++ function) rule::CompositionMatch::push (C++ function) rule::CompositionMatch::size (C++ function) rule::RCExp::Bind (C++ class) rule::RCExp::Bind::Bind (C++ function) rule::RCExp::Bind::getGraph (C++ function) rule::RCExp::Bind::operator<< (C++ function) rule::RCExp::ComposeCommon (C++ class) rule::RCExp::ComposeCommon::ComposeCommon (C++ function) rule::RCExp::ComposeCommon::connected (C++ member) rule::RCExp::ComposeCommon::first (C++ member) rule::RCExp::ComposeCommon::includeEmpty (C++ member) rule::RCExp::ComposeCommon::maximum (C++ member) rule::RCExp::ComposeCommon::operator<< (C++ function) rule::RCExp::ComposeCommon::second (C++ member) rule::RCExp::ComposeParallel (C++ class) rule::RCExp::ComposeParallel::ComposeParallel (C++ function) rule::RCExp::ComposeParallel::first (C++ member) rule::RCExp::ComposeParallel::operator<< (C++ function) rule::RCExp::ComposeParallel::second (C++ member) rule::RCExp::ComposeSub (C++ class) rule::RCExp::ComposeSub::allowPartial (C++ member) rule::RCExp::ComposeSub::ComposeSub (C++ function) rule::RCExp::ComposeSub::first (C++ member) rule::RCExp::ComposeSub::operator<< (C++ function) rule::RCExp::ComposeSub::second (C++ member) rule::RCExp::ComposeSuper (C++ class) rule::RCExp::ComposeSuper::allowPartial (C++ member) rule::RCExp::ComposeSuper::ComposeSuper (C++ function) rule::RCExp::ComposeSuper::enforceConstraints (C++ member) rule::RCExp::ComposeSuper::first (C++ member) rule::RCExp::ComposeSuper::operator<< (C++ function) rule::RCExp::ComposeSuper::second (C++ member) rule::RCExp::Expression (C++ class) rule::RCExp::Expression::Expression (C++ function), [1], [2], [3], [4], [5], [6], [7], [8] rule::RCExp::Expression::operator<< (C++ function) rule::RCExp::Id (C++ class) rule::RCExp::Id::getGraph (C++ function) rule::RCExp::Id::Id (C++ function) rule::RCExp::Id::operator<< (C++ function) rule::RCExp::Unbind (C++ class) rule::RCExp::Unbind::getGraph (C++ function) rule::RCExp::Unbind::operator<< (C++ function) rule::RCExp::Unbind::Unbind (C++ function) rule::RCExp::Union (C++ class) rule::RCExp::Union::getExpressions (C++ function) rule::RCExp::Union::operator<< (C++ function) rule::RCExp::Union::Union (C++ function) rule::Rule (C++ class) rule::Rule::ContextGraph (C++ class) rule::Rule::ContextGraph::Edge (C++ class) rule::Rule::ContextGraph::Edge::Edge (C++ function) rule::Rule::ContextGraph::Edge::getCore (C++ function) rule::Rule::ContextGraph::Edge::getGraph (C++ function) rule::Rule::ContextGraph::Edge::getRule (C++ function) rule::Rule::ContextGraph::Edge::isNull (C++ function) rule::Rule::ContextGraph::Edge::operator bool (C++ function) rule::Rule::ContextGraph::Edge::source (C++ function) rule::Rule::ContextGraph::Edge::target (C++ function) rule::Rule::ContextGraph::EdgeIterator (C++ class) rule::Rule::ContextGraph::EdgeIterator::EdgeIterator (C++ function) rule::Rule::ContextGraph::EdgeRange (C++ class) rule::Rule::ContextGraph::edges (C++ function) rule::Rule::ContextGraph::getRule (C++ function) rule::Rule::ContextGraph::IncidentEdgeIterator (C++ class) rule::Rule::ContextGraph::IncidentEdgeIterator::IncidentEdgeIterator (C++ function) rule::Rule::ContextGraph::IncidentEdgeRange (C++ class) rule::Rule::ContextGraph::numEdges (C++ function) rule::Rule::ContextGraph::numVertices (C++ function) rule::Rule::ContextGraph::operator== (C++ function) rule::Rule::ContextGraph::Vertex (C++ class) rule::Rule::ContextGraph::Vertex::getCore (C++ function) rule::Rule::ContextGraph::Vertex::getDegree (C++ function) rule::Rule::ContextGraph::Vertex::getGraph (C++ function) rule::Rule::ContextGraph::Vertex::getId (C++ function) rule::Rule::ContextGraph::Vertex::getRule (C++ function)

rule::Rule::ContextGraph::Vertex::incidentEdges (C++ function) rule::Rule::ContextGraph::Vertex::isNull (C++ function) rule::Rule::ContextGraph::Vertex::operator bool (C++ function) rule::Rule::ContextGraph::Vertex::Vertex (C++ function) rule::Rule::ContextGraph::VertexIterator (C++ class) rule::Rule::ContextGraph::VertexIterator::VertexIterator (C++ function) rule::Rule::ContextGraph::VertexRange (C++ class) rule::Rule::ContextGraph::vertices (C++ function) rule::Rule::Edge (C++ class) rule::Rule::Edge::Edge (C++ function) rule::Rule::Edge::getContext (C++ function) rule::Rule::Edge::getGraph (C++ function) rule::Rule::Edge::getLeft (C++ function) rule::Rule::Edge::getRight (C++ function) rule::Rule::Edge::getRule (C++ function) rule::Rule::Edge::isNull (C++ function) rule::Rule::Edge::operator bool (C++ function) rule::Rule::Edge::source (C++ function) rule::Rule::Edge::target (C++ function) rule::Rule::EdgeIterator (C++ class) rule::Rule::EdgeIterator::EdgeIterator (C++ function) rule::Rule::EdgeRange (C++ class) rule::Rule::edges (C++ function) rule::Rule::fromDFS (C++ function) rule::Rule::fromGMLFile (C++ function) rule::Rule::fromGMLString (C++ function) rule::Rule::getContext (C++ function) rule::Rule::getGMLString (C++ function) rule::Rule::getId (C++ function) rule::Rule::getLabelType (C++ function) rule::Rule::getLeft (C++ function) rule::Rule::getMaxExternalId (C++ function) rule::Rule::getMinExternalId (C++ function) rule::Rule::getName (C++ function) rule::Rule::getNumLeftComponents (C++ function) rule::Rule::getNumRightComponents (C++ function) rule::Rule::getRight (C++ function) rule::Rule::getVertexFromExternalId (C++ function) rule::Rule::IncidentEdgeIterator (C++ class) rule::Rule::IncidentEdgeIterator::IncidentEdgeIterator (C++ function) rule::Rule::IncidentEdgeRange (C++ class) rule::Rule::isomorphicLeftRight (C++ function) rule::Rule::isomorphism (C++ function) rule::Rule::LeftGraph (C++ class) rule::Rule::LeftGraph::Edge (C++ class) rule::Rule::LeftGraph::Edge::Edge (C++ function) rule::Rule::LeftGraph::Edge::getBondType (C++ function) rule::Rule::LeftGraph::Edge::getCore (C++ function) rule::Rule::LeftGraph::Edge::getGraph (C++ function) rule::Rule::LeftGraph::Edge::getRule (C++ function) rule::Rule::LeftGraph::Edge::getStringLabel (C++ function) rule::Rule::LeftGraph::Edge::isNull (C++ function) rule::Rule::LeftGraph::Edge::operator bool (C++ function) rule::Rule::LeftGraph::Edge::source (C++ function) rule::Rule::LeftGraph::Edge::target (C++ function) rule::Rule::LeftGraph::EdgeIterator (C++ class) rule::Rule::LeftGraph::EdgeIterator::EdgeIterator (C++ function) rule::Rule::LeftGraph::EdgeRange (C++ class) rule::Rule::LeftGraph::edges (C++ function) rule::Rule::LeftGraph::getRule (C++ function) rule::Rule::LeftGraph::IncidentEdgeIterator (C++ class) rule::Rule::LeftGraph::IncidentEdgeIterator::IncidentEdgeIterator (C++ function) rule::Rule::LeftGraph::IncidentEdgeRange (C++ class) rule::Rule::LeftGraph::numEdges (C++ function) rule::Rule::LeftGraph::numVertices (C++ function) rule::Rule::LeftGraph::operator!= (C++ function) rule::Rule::LeftGraph::operator< (C++ function) rule::Rule::LeftGraph::operator<< (C++ function) rule::Rule::LeftGraph::operator== (C++ function) rule::Rule::LeftGraph::Vertex (C++ class) rule::Rule::LeftGraph::Vertex::getAtomId (C++ function) rule::Rule::LeftGraph::Vertex::getCharge (C++ function) rule::Rule::LeftGraph::Vertex::getCore (C++ function) rule::Rule::LeftGraph::Vertex::getDegree (C++ function) rule::Rule::LeftGraph::Vertex::getGraph (C++ function) rule::Rule::LeftGraph::Vertex::getId (C++ function) rule::Rule::LeftGraph::Vertex::getIsotope (C++ function) rule::Rule::LeftGraph::Vertex::getRadical (C++ function) rule::Rule::LeftGraph::Vertex::getRule (C++ function) rule::Rule::LeftGraph::Vertex::getStringLabel (C++ function) rule::Rule::LeftGraph::Vertex::incidentEdges (C++ function) rule::Rule::LeftGraph::Vertex::isNull (C++ function) rule::Rule::LeftGraph::Vertex::operator bool (C++ function) rule::Rule::LeftGraph::Vertex::printStereo (C++ function), [1] rule::Rule::LeftGraph::Vertex::Vertex (C++ function) rule::Rule::LeftGraph::VertexIterator (C++ class) rule::Rule::LeftGraph::VertexIterator::VertexIterator (C++ function) rule::Rule::LeftGraph::VertexRange (C++ class) rule::Rule::LeftGraph::vertices (C++ function) rule::Rule::makeInverse (C++ function) rule::Rule::makeRule (C++ function), [1] rule::Rule::monomorphism (C++ function) rule::Rule::numEdges (C++ function) rule::Rule::numVertices (C++ function) rule::Rule::print (C++ function), [1], [2], [3] rule::Rule::printGML (C++ function) rule::Rule::printTermState (C++ function) rule::Rule::RightGraph (C++ class) rule::Rule::RightGraph::Edge (C++ class) rule::Rule::RightGraph::Edge::Edge (C++ function) rule::Rule::RightGraph::Edge::getBondType (C++ function) rule::Rule::RightGraph::Edge::getCore (C++ function) rule::Rule::RightGraph::Edge::getGraph (C++ function) rule::Rule::RightGraph::Edge::getRule (C++ function) rule::Rule::RightGraph::Edge::getStringLabel (C++ function) rule::Rule::RightGraph::Edge::isNull (C++ function) rule::Rule::RightGraph::Edge::operator bool (C++ function) rule::Rule::RightGraph::Edge::source (C++ function) rule::Rule::RightGraph::Edge::target (C++ function) rule::Rule::RightGraph::EdgeIterator (C++ class) rule::Rule::RightGraph::EdgeIterator::EdgeIterator (C++ function) rule::Rule::RightGraph::EdgeRange (C++ class) rule::Rule::RightGraph::edges (C++ function) rule::Rule::RightGraph::getRule (C++ function) rule::Rule::RightGraph::IncidentEdgeIterator (C++ class) rule::Rule::RightGraph::IncidentEdgeIterator::IncidentEdgeIterator (C++ function) rule::Rule::RightGraph::IncidentEdgeRange (C++ class) rule::Rule::RightGraph::numEdges (C++ function) rule::Rule::RightGraph::numVertices (C++ function) rule::Rule::RightGraph::operator!= (C++ function) rule::Rule::RightGraph::operator< (C++ function) rule::Rule::RightGraph::operator<< (C++ function) rule::Rule::RightGraph::operator== (C++ function) rule::Rule::RightGraph::Vertex (C++ class) rule::Rule::RightGraph::Vertex::getAtomId (C++ function) rule::Rule::RightGraph::Vertex::getCharge (C++ function) rule::Rule::RightGraph::Vertex::getCore (C++ function) rule::Rule::RightGraph::Vertex::getDegree (C++ function) rule::Rule::RightGraph::Vertex::getGraph (C++ function) rule::Rule::RightGraph::Vertex::getId (C++ function) rule::Rule::RightGraph::Vertex::getIsotope (C++ function) rule::Rule::RightGraph::Vertex::getRadical (C++ function) rule::Rule::RightGraph::Vertex::getRule (C++ function) rule::Rule::RightGraph::Vertex::getStringLabel (C++ function) rule::Rule::RightGraph::Vertex::incidentEdges (C++ function) rule::Rule::RightGraph::Vertex::isNull (C++ function) rule::Rule::RightGraph::Vertex::operator bool (C++ function) rule::Rule::RightGraph::Vertex::printStereo (C++ function), [1] rule::Rule::RightGraph::Vertex::Vertex (C++ function) rule::Rule::RightGraph::VertexIterator (C++ class) rule::Rule::RightGraph::VertexIterator::VertexIterator (C++ function) rule::Rule::RightGraph::VertexRange (C++ class) rule::Rule::RightGraph::vertices (C++ function) rule::Rule::setName (C++ function) rule::Rule::Vertex (C++ class) rule::Rule::Vertex::get2DX (C++ function) rule::Rule::Vertex::get2DY (C++ function) rule::Rule::Vertex::getContext (C++ function) rule::Rule::Vertex::getDegree (C++ function) rule::Rule::Vertex::getGraph (C++ function) rule::Rule::Vertex::getId (C++ function) rule::Rule::Vertex::getLeft (C++ function) rule::Rule::Vertex::getRight (C++ function) rule::Rule::Vertex::getRule (C++ function) rule::Rule::Vertex::incidentEdges (C++ function) rule::Rule::Vertex::isNull (C++ function) rule::Rule::Vertex::operator bool (C++ function) rule::Rule::Vertex::Vertex (C++ function) rule::Rule::VertexIterator (C++ class) rule::Rule::VertexIterator::VertexIterator (C++ function) rule::Rule::VertexRange (C++ class) rule::Rule::vertices (C++ function) ruleDatabase (mod.RCEvaluator attribute) ruleGML() (in module mod) ruleGMLString() (in module mod) rules (mod.Derivations attribute) (mod.DG.HyperEdge attribute)

S

second (mod.RCMatch attribute) separatedIOInternalTransit (mod.Flow attribute) (mod.hyperflow.Model attribute) separateIOInternalTransit() (mod.Flow method) (mod.hyperflow.Model method) setEnergyBounds() (mod.FlowThermodynamics method) (mod.hyperflow.Model.Thermodynamics method) setImageOverwrite() (mod.DGPrinter method) setMirrorOverwrite() (mod.DGPrinter method) setMolDefault() (mod.GraphPrinter method) setPostContent() (mod.causality.EventTracePrinter method) setPreContent() (mod.causality.EventTracePrinter method) setReactionDefault() (mod.GraphPrinter method) setRotationOverwrite() (mod.DGPrinter method) simpleCarbons (mod.GraphPrinter attribute) simulate() (mod.stochsim.Simulator method) Simulator (class in mod.stochsim) Single (mod.BondType attribute) sinks (mod.Flow attribute) (mod.hyperflow.Model attribute) size (mod.DGVertexMapper attribute) (mod.FlowSolutionRange attribute) (mod.FlowSolutionSet attribute) (mod.hyperflow.SolutionRange attribute) (mod.RCMatch attribute) smiles (mod.Graph attribute) smiles() (in module mod) SmilesClassPolicy (C++ enum) (class in mod) SmilesClassPolicy::MapUnique (C++ enumerator) SmilesClassPolicy::NoneOnDuplicate (C++ enumerator) SmilesClassPolicy::ThrowOnDuplicate (C++ enumerator) smilesWithIds (mod.Graph attribute) solutions (mod.Flow attribute) (mod.hyperflow.Model attribute)

solutionsOld (mod.Flow attribute) source (mod.protocols.Graph.Edge attribute) sources (mod.DG.HyperEdge attribute) (mod.Flow attribute) (mod.hyperflow.Model attribute) Specialisation (mod.LabelRelation attribute) specificationLocked (mod.Flow attribute) (mod.hyperflow.Model attribute) Stacktrace (C++ class) Stacktrace::print (C++ function) Stacktrace::Stacktrace (C++ function) StereoDeductionError (C++ class) stereoRelation (mod.LabelSettings attribute) strat (mod.stochsim.ExpandByStrategy attribute) strictTransit (mod.FlowOverallAutocatalysis attribute) (mod.FlowOverallCatalysis attribute) (mod.hyperflow.Model.OverallAutocatalysis attribute) (mod.hyperflow.Model.OverallCatalysis attribute) String (mod.LabelType attribute) stringLabel (mod.protocols.LabelledGraph.Edge attribute) (mod.protocols.LabelledGraph.Vertex attribute) subset (mod.DG.Builder.ExecuteResult attribute) (mod.DGStrat.GraphState attribute) summaryChapter() (in module post) summaryInput() (in module post) summaryRaw() (in module post) summarySection() (in module post) symbol (mod.AtomId attribute) syncSize() (mod.causality.Marking method) (mod.causality.MassActionKinetics method) (mod.causality.Net method) (mod.DGPetriNet method) (mod.DGPetriNetMarking method) (mod.stochsim.DrawFunction method)

T

target (mod.protocols.Graph.Edge attribute) targets (mod.DG.HyperEdge attribute) temperature (mod.FlowThermodynamics attribute) (mod.hyperflow.Model.Thermodynamics attribute) Term (mod.LabelType attribute) TermParsingError (C++ class) thermodynamics (mod.Flow attribute) (mod.hyperflow.Model attribute) thick (mod.GraphPrinter attribute)

ThrowOnDuplicate (mod.SmilesClassPolicy attribute) tikzpictureOption (mod.DGPrinter attribute) time (mod.causality.EventTrace attribute) (mod.causality.EventTrace.Event attribute) (mod.stochsim.Simulator property) transitEnumeration (mod.Flow attribute) (mod.hyperflow.Model attribute) transitInternalFlow (in module mod) Triple (mod.BondType attribute) TrustMe (mod.IsomorphismPolicy attribute) type (mod.LabelSettings attribute)

U

unfilteredFlowColour (mod.FlowPrinter attribute) (mod.hyperflow.Printer attribute) Unification (mod.LabelRelation attribute) UnionGraph (class in mod) UnionGraph.Edge (class in mod)

UnionGraph.EdgeRange (class in mod) UnionGraph.IncidentEdgeRange (class in mod) UnionGraph.Vertex (class in mod) UnionGraph.VertexRange (class in mod) universe (mod.DG.Builder.ExecuteResult attribute) (mod.DGStrat.GraphState attribute)

V

version (C++ function) version() (in module mod) vertex (mod.causality.InputAction attribute) (mod.causality.OutputAction attribute) (mod.FlowVarVertex attribute) (mod.hyperflow.VarVertex attribute) (mod.UnionGraph.Vertex attribute) vertexFlow (in module mod) vertexLabelSep (mod.DGPrinter attribute) VertexMap (C++ class) (class in mod.protocols) VertexMap::CodomainHandle (C++ type) VertexMap::CodomVertex (C++ type)

VertexMap::DomainHandle (C++ type) VertexMap::DomVertex (C++ type) VertexMap::getCodomain (C++ function) VertexMap::getDomain (C++ function) VertexMap::getInverse (C++ function) VertexMap::operator<< (C++ function) VertexMap::operator[] (C++ function) VertexMapRuleLeftGraphUnionGraph (class in mod) VertexMapRuleRightGraphUnionGraph (class in mod) VertexMapUnionGraphUnionGraph (class in mod) vertices (mod.DG attribute) (mod.protocols.Graph attribute) vLabelCount() (mod.Graph method)

W

Warn (mod.Action attribute) withColour (mod.GraphPrinter attribute) withFlowLabels (mod.FlowPrinter attribute) (mod.hyperflow.Printer attribute) withGraphImages (mod.DGPrinter attribute) withGraphName (mod.DGPrinter attribute) withGraphvizCoords (mod.GraphPrinter attribute) withIndex (mod.GraphPrinter attribute)

withInlineGraphs (mod.DGPrinter attribute) withPrettyStereo (mod.GraphPrinter attribute) withRawStereo (mod.GraphPrinter attribute) withRuleId (mod.DGPrinter attribute) withRuleName (mod.DGPrinter attribute) withShortcutEdges (mod.DGPrinter attribute) withShortcutEdgesAfterVisibility (mod.DGPrinter attribute) withStereo (mod.LabelSettings attribute) withTexttt (mod.GraphPrinter attribute)