Index

Symbols

--debug mod command line option --help mod command line option 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 <args> mod command line option

-e <code> mod command line option -f <filename> mod command line option -h mod command line option mod_post command line option -i mod command line option -j <N> mod command line option mod_post command line option -q mod command line option -v mod command line option

_

__call__() (mod.stochsim.DrawMassAction method) (mod.stochsim.ExponentialTransfer method) (mod.stochsim.LinearTransfer method) __getitem__() (mod.CausalityFlowQuery method) (mod.EventTrace method) (mod.GraphAut method) (mod.PetriNetMarking method) __init__() (in module mod) (mod.AtomData method) (mod.AtomId method) (mod.CausalityFlowQuery method) (mod.Charge method) (mod.DG method) (mod.DGPrintData method) (mod.EventTrace method) (mod.Flow method) (mod.GraphPrinter method) (mod.Isotope method) (mod.LabelSettings method) (mod.PetriNet method) (mod.PetriNetMarking method)

__int__() (mod.AtomId method) (mod.Charge method) (mod.Isotope method) __len__() (mod.EventTrace method) __setitem__() (mod.CausalityFlowQuery method) __str__() (mod.BondType method) (mod.EventTrace method) (mod.PetriNetMarking method)

A

absGap (mod.Flow attribute) add() (mod.PetriNetMarking method) addAbstract() (mod.DGBuilder method) addConstraint() (mod.Flow method) addDerivation() (mod.DGBuilder method) addEdge() (mod.EventTrace method) addEnumerationVar() (mod.Flow method) addIntVariable() (mod.Flow method) addSink() (mod.Flow method) addSource() (mod.Flow method) addSubset() (in module mod) addTransfer() (mod.EventTrace method) addUniverse() (in module mod) AllOrNone (mod.SmilesClassPolicy attribute) allowHyperLoops (mod.Flow attribute) allowIOReversal (mod.Flow attribute) allowReversal (mod.Flow attribute) apply() (mod.DGBuilder 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.GraphVertex attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphVertex 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)

B

bfsExclusive (mod.FlowOverallAutocatalysis attribute) BondType (C++ enum) (class in mod) bondType (mod.GraphEdge attribute) (mod.RuleLeftGraphEdge attribute) (mod.RuleRightGraphEdge 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 (C++ class) causality::DAG::getDG (C++ function) causality::DAG::getPrintData (C++ function) causality::EventTrace (C++ class) causality::EventTrace::addEdge (C++ function) causality::EventTrace::addTransfer (C++ function) causality::EventTrace::begin (C++ function) causality::EventTrace::const_iterator (C++ type) causality::EventTrace::EdgeEvent (C++ class) causality::EventTrace::EdgeEvent::edge (C++ member) causality::EventTrace::EdgeEvent::time (C++ member) causality::EventTrace::end (C++ function) causality::EventTrace::Event (C++ type) causality::EventTrace::EventTrace (C++ function) causality::EventTrace::getInitialState (C++ function) causality::EventTrace::iterator (C++ type) causality::EventTrace::operator<< (C++ function) causality::EventTrace::operator[] (C++ function) causality::EventTrace::print (C++ function) causality::EventTrace::size (C++ function) causality::EventTrace::TransferEvent (C++ class) causality::EventTrace::TransferEvent::count (C++ member) causality::EventTrace::TransferEvent::time (C++ member) causality::EventTrace::TransferEvent::vertex (C++ member) 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::MassActionKinetics (C++ class) causality::MassActionKinetics::draw (C++ function) causality::MassActionKinetics::MassActionKinetics (C++ function) causality::MassActionKinetics::syncSize (C++ function) causality::PetriNet (C++ class) causality::PetriNet::getDG (C++ function) causality::PetriNet::getPostPlaces (C++ function) causality::PetriNet::make (C++ function) causality::PetriNet::syncSize (C++ function) causality::PetriNetMarking (C++ class) causality::PetriNetMarking::add (C++ function)

causality::PetriNetMarking::fire (C++ function) causality::PetriNetMarking::getAllEnabled (C++ function) causality::PetriNetMarking::getEmptyPostPlaces (C++ function) causality::PetriNetMarking::getNet (C++ function) causality::PetriNetMarking::getNonZeroPlaces (C++ function) causality::PetriNetMarking::getNumTokens (C++ function) causality::PetriNetMarking::isEnabled (C++ function) causality::PetriNetMarking::operator<< (C++ function) causality::PetriNetMarking::operator[] (C++ function) causality::PetriNetMarking::PetriNetMarking (C++ function) causality::PetriNetMarking::remove (C++ function) causality::PetriNetMarking::syncSize (C++ function) CausalityDAG (class in mod) CausalityFlowQuery (class in mod) Charge (C++ class) (class in mod) charge (mod.AtomData attribute) (mod.GraphVertex attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphVertex 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 collapseHydrogens (mod.GraphPrinter attribute) Config (C++ class) (class in mod) config (in module mod) ConfigSetting (C++ class) ConfigSetting::get (C++ function) ConfigSetting::set (C++ function) constrainRouting (mod.CausalityFlowQuery attribute) context (mod.Rule attribute) (mod.RuleEdge attribute) (mod.RuleVertex attribute) core (mod.RuleContextGraphEdge attribute) (mod.RuleContextGraphVertex attribute) (mod.RuleLeftGraphEdge attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphEdge attribute) (mod.RuleRightGraphVertex attribute) count (mod.EventTrace.TransferEvent attribute) CWDPath (class in mod) CWDPath.__init__() (in module mod)

D

degree (mod.GraphVertex attribute) (mod.RuleContextGraphVertex attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphVertex attribute) (mod.RuleVertex attribute) 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.CausalityDAG attribute) (mod.CausalityFlowQuery attribute) (mod.DGHyperEdge attribute) (mod.DGPrintData attribute) (mod.DGVertex attribute) (mod.Flow attribute) (mod.PetriNet attribute) dg::Builder (C++ class) dg::Builder::addAbstract (C++ function) dg::Builder::addDerivation (C++ function), [1] dg::Builder::apply (C++ function), [1], [2] dg::Builder::execute (C++ function), [1], [2] dg::Builder::isActive (C++ function) dg::Builder::load (C++ function) dg::DG (C++ class) dg::DG::build (C++ function) dg::DG::diff (C++ function) dg::DG::dump (C++ function) 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::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::getProducts (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::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::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::setLabelsAsLatexMath (C++ function) dg::Printer::setMirrorOverwrite (C++ function) dg::Printer::setRotationOverwrite (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) DGBuilder (class in mod) DGExecuteResult (class in mod) dgFlow (mod.FlowSolutionSet attribute) DGHyperEdge (class in mod) DGHyperEdge.__init__() (in module mod) DGPrintData (class in mod) DGPrinter (class in mod) dgPrinter (mod.FlowPrinter attribute) DGStrat (class in mod) DGStratGraphState (class in mod) DGVertex (class in mod) DGVertex.__init__() (in module mod) diffDGs() (in module mod) disableAll() (mod.GraphPrinter method) Double (mod.BondType attribute) draw() (in module mod) DrawMassAction (class in mod.stochsim) dump() (mod.DG method) (mod.Flow method)

E

edge (mod.EventTrace.EdgeEvent attribute) (mod.FlowVarEdge attribute) edgeLabelSep (mod.DGPrinter attribute) edges (mod.DG attribute) (mod.Graph attribute) (mod.Rule attribute) (mod.RuleContextGraph attribute) (mod.RuleLeftGraph attribute) (mod.RuleRightGraph attribute) edgesAsBonds (mod.GraphPrinter attribute) eLabelCount() (mod.Graph method) enable() (mod.FlowOverallAutocatalysis method) (mod.FlowOverallCatalysis method) enableAll() (mod.GraphPrinter method) energy (mod.Graph attribute) enumerationVars (mod.Flow attribute) environment variable MOD_ILP_SOLVER MOD_NO_DEPRECATED, [1] MOD_NUM_POST_THREADS MOD_PLUGIN_PATH

eval() (mod.FlowSolution method) (mod.FlowSolutionOld method) (mod.RCEvaluator method) EventTrace (class in mod) EventTrace.EdgeEvent (class in mod) EventTrace.TransferEvent (class in mod) 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) excluded (mod.Flow attribute) execute() (in module mod) (mod.DGBuilder method) ExponentialTransfer (class in mod.stochsim)

F

FatalError (C++ class) filterSubset() (in module mod) filterUniverse() (in module mod) findEdge() (mod.DG method) findSolutions() (mod.Flow method) findVertex() (mod.DG method) fire() (mod.PetriNetMarking method) 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::dump (C++ function) 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::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::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++ member) flow::Flow::OverallAutocatalysisProxy (C++ class) flow::Flow::OverallAutocatalysisProxy::enable (C++ function) flow::Flow::OverallAutocatalysisProxy::getBFSExclusive (C++ function) flow::Flow::OverallAutocatalysisProxy::getForceExistence (C++ function) flow::Flow::OverallAutocatalysisProxy::getStrictTransit (C++ function) flow::Flow::OverallAutocatalysisProxy::setBFSExclusive (C++ function) flow::Flow::OverallAutocatalysisProxy::setForceExistence (C++ function) flow::Flow::OverallAutocatalysisProxy::setStrictTransit (C++ function) flow::Flow::overallCatalysis (C++ member) flow::Flow::OverallCatalysisProxy (C++ class) flow::Flow::OverallCatalysisProxy::enable (C++ function) flow::Flow::OverallCatalysisProxy::getForceExistence (C++ function) flow::Flow::OverallCatalysisProxy::getStrictTransit (C++ function) flow::Flow::OverallCatalysisProxy::setForceExistence (C++ function) flow::Flow::OverallCatalysisProxy::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::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::popInOutEdgeLabel (C++ function) flow::Printer::pushInOutEdgeLabel (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::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) FlowSolutionRange.__getitem__() (in module mod) FlowSolutionRange.__iter__() (in module mod) FlowSolutionRange.__len__() (in module mod) FlowSolutionRange.list() (in module mod) FlowSolutionSet (class in mod) FlowVar (class in mod) FlowVarCustom (class in mod) FlowVarCustom.__str__() (in module mod) FlowVarEdge (class in mod) FlowVarEdge.__str__() (in module mod) FlowVarSumCustom (class in mod) FlowVarSumCustom.__getitem__() (in module mod) FlowVarSumCustom.__init__() (in module mod) FlowVarSumCustom.__str__() (in module mod) FlowVarSumEdge (class in mod) FlowVarSumEdge.__getitem__() (in module mod) FlowVarSumEdge.__init__() (in module mod) FlowVarSumEdge.__str__() (in module mod) FlowVarSumVertex (class in mod) FlowVarSumVertex.__getitem__() (in module mod) FlowVarSumVertex.__init__() (in module mod) FlowVarSumVertex.__str__() (in module mod) FlowVarVertex (class in mod) FlowVarVertex.__str__() (in module mod) FlowVarVertexGraph (class in mod) FlowVarVertexGraph.__str__() (in module mod) forceExistence (mod.FlowOverallAutocatalysis attribute) (mod.FlowOverallCatalysis attribute) 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.GraphAutGroup attribute) get2DX() (mod.RuleVertex method) get2DY() (mod.RuleVertex method) getAllEnabled() (mod.PetriNetMarking method) getAvailableILPSolvers (C++ function) getAvailableILPSolvers() (in module mod) getConfig (C++ function) getConfig() (in module mod) getEmptyPostPlaces() (mod.PetriNetMarking method) getGMLString() (mod.Graph method) (mod.Rule method) getNonZeroPlaces() (mod.PetriNetMarking method) getPostPlaces() (mod.PetriNet method) getVertexFromExternalId() (mod.Graph method) (mod.Rule method) Graph (class in mod) graph (mod.DGVertex attribute) (mod.FlowVarVertexGraph attribute) (mod.GraphEdge attribute) (mod.GraphVertex attribute) (mod.RuleContextGraphEdge attribute) (mod.RuleLeftGraphEdge attribute) (mod.RuleRightGraphEdge attribute) Graph.aut() (in module mod) 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::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::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::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::graphDFS (C++ function) graph::Graph::graphGML (C++ function) graph::Graph::graphGMLString (C++ function) graph::Graph::IncidentEdgeRange (C++ class) graph::Graph::IncidnetEdgeIterator (C++ class) graph::Graph::IncidnetEdgeIterator::IncidentEdgeIterator (C++ function) graph::Graph::instantiateStereo (C++ function) graph::Graph::isomorphism (C++ function) graph::Graph::makeGraph (C++ function), [1] 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::printStereo (C++ function), [1] graph::Graph::printTermState (C++ function) graph::Graph::setImage (C++ function) graph::Graph::setImageCommand (C++ function) graph::Graph::setName (C++ function) graph::Graph::smiles (C++ function), [1] 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::getMirror (C++ function) graph::Printer::getRaiseCharges (C++ function) graph::Printer::getRotation (C++ function) graph::Printer::getSimpleCarbons (C++ function) graph::Printer::getThick (C++ function) graph::Printer::getWithColour (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::setMirror (C++ function) graph::Printer::setMolDefault (C++ function) graph::Printer::setRaiseCharges (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::setWithIndex (C++ function) graph::Printer::setWithPrettyStereo (C++ function) graph::Printer::setWithRawStereo (C++ function) graph::Printer::setWithTexttt (C++ function) GraphAut (class in mod) GraphAutGroup (class in mod) GraphAutGroupGensRange (class in mod) graphDatabase (mod.DG attribute) graphDFS (mod.Graph attribute) graphDFS() (in module mod) graphDFSWithIds (mod.Graph attribute) GraphEdge (class in mod) GraphEdge.__init__() (in module mod) graphGML() (in module mod) graphGMLString() (in module mod) GraphPrinter (class in mod) graphPrinter (mod.DGPrinter attribute) GraphVertex (class in mod) GraphVertex.__init__() (in module mod) graphvizPrefix (mod.DGPrinter attribute)

H

hasActiveBuilder (mod.DG attribute)

haxListDerivations() (mod.FlowSolutionOld method)

I

id (mod.DG attribute) (mod.DGHyperEdge attribute) (mod.DGVertex 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.GraphVertex attribute) (mod.Rule attribute) (mod.RuleContextGraphVertex attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphVertex attribute) (mod.RuleVertex attribute) image (mod.Graph attribute) imageCommad (mod.Graph attribute) incidentEdges (mod.GraphVertex attribute) (mod.RuleContextGraphVertex attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphVertex attribute) (mod.RuleVertex attribute) include() (in module mod) inDegree (mod.DGVertex attribute) inEdges (mod.DGVertex attribute) initialState (mod.EventTrace attribute) InputError (C++ class) inputGraphs (in module mod) inputRules (in module mod)

instantiateStereo() (mod.Graph method) Invalid (mod.AtomIds attribute) (mod.BondType attribute) inverse (mod.DGHyperEdge attribute) isEnabled() (mod.PetriNetMarking method) isMolecule (mod.Graph attribute) isNull() (mod.DGHyperEdge method) (mod.DGVertex method) (mod.GraphEdge method) (mod.GraphVertex method) (mod.RuleContextGraphEdge method) (mod.RuleContextGraphVertex method) (mod.RuleEdge method) (mod.RuleLeftGraphEdge method) (mod.RuleLeftGraphVertex method) (mod.RuleRightGraphEdge method) (mod.RuleRightGraphVertex method) (mod.RuleVertex 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.GraphVertex attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphVertex attribute) Isotope::Isotope (C++ function), [1] Isotope::operator int (C++ function) Isotope::operator<< (C++ function)

L

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) 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.Rule attribute) (mod.RuleEdge attribute) (mod.RuleVertex attribute) leftPredicate (in module mod) linearEncoding (mod.Graph attribute) LinearTransfer (class in mod.stochsim) list() (mod.DGExecuteResult method) (mod.FlowSolution method) (mod.FlowSolutionSet method) listSpecification() (mod.Flow method) listStats() (mod.DG method) load() (mod.DG method) (mod.DGBuilder method) (mod.Flow static method) loadString() (mod.Flow static method) locked (mod.DG attribute) LogicError (C++ class)

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 (C++ function) makeUniqueFilePrefix() (in module mod) MapUnique (mod.SmilesClassPolicy attribute) MassActionKinetics (class in mod) Max (mod.AtomIds attribute) maxExternalId (mod.Graph attribute) (mod.Rule attribute) minExternalId (mod.Graph attribute) (mod.Rule attribute) mirror (mod.GraphPrinter attribute) mod module mod command line option --debug --help --memcheck --nopost --profile --version --vgArgs <args> -e <code> -f <filename> -h -i -j <N> -q -v clean

mod.stochsim module MOD_NO_DEPRECATED mod_post command line option --help -h -j <N> module mod mod.stochsim monomorphism() (mod.Graph method) (mod.Rule method) multiplicity (mod.CausalityFlowQuery attribute)

N

name (mod.FlowVarCustom attribute) (mod.Graph attribute) (mod.Rule attribute) net (mod.PetriNetMarking attribute) numEdges (mod.DG attribute) (mod.Graph attribute) (mod.Rule attribute) (mod.RuleContextGraph attribute) (mod.RuleLeftGraph attribute) (mod.RuleRightGraph attribute)

numLeftComponents (mod.Rule attribute) numRightComponents (mod.Rule attribute) numSources (mod.DGHyperEdge attribute) numTargets (mod.DGHyperEdge attribute) numTokens (mod.PetriNetMarking attribute) numVertices (mod.DG attribute) (mod.Graph attribute) (mod.Rule attribute) (mod.RuleContextGraph attribute) (mod.RuleLeftGraph attribute) (mod.RuleRightGraph attribute)

O

objectiveFunction (mod.Flow attribute) operator<< (C++ function) outDegree (mod.DGVertex attribute)

outEdges (mod.DGVertex attribute) overallAutocatalysis (mod.Flow attribute) overallCatalysis (mod.Flow attribute)

P

PetriNet (class in mod) PetriNetMarking (class in mod) popEdgeColour() (mod.DGPrinter method) popEdgeLabel() (mod.DGPrinter method) popEdgeVisible() (mod.DGPrinter method) popFilePrefix() (in module mod) popInOutEdgeLabel() (mod.FlowPrinter method) popVertexColour() (mod.DGPrinter method) popVertexLabel() (mod.DGPrinter method) popVertexVisible() (mod.DGPrinter method) prefixFilename() (in module mod) print() (mod.DG method) (mod.DGHyperEdge method) (mod.EventTrace method) (mod.FlowSolution method) (mod.FlowSolutionOld method) (mod.FlowSolutionRange method) (mod.FlowSolutionSet method) (mod.Graph method) (mod.RCEvaluator method) (mod.Rule method)

printEnumerationTree() (mod.Flow method) printExpanded() (mod.Flow method) printExpandedVertex() (mod.Flow method) printFiltered (mod.FlowPrinter attribute) printGML() (mod.Graph method) (mod.Rule method) printStereo() (mod.GraphVertex method) (mod.RuleLeftGraphVertex method) (mod.RuleRightGraphVertex method) printTermState() (mod.Graph method) (mod.Rule method) printUnfiltered (mod.FlowPrinter attribute) products (mod.DG attribute) (mod.RCEvaluator attribute) pushEdgeColour() (mod.DGPrinter method) pushEdgeLabel() (mod.DGPrinter method) pushEdgeVisible() (mod.DGPrinter method) pushFilePrefix() (in module mod) pushInOutEdgeLabel() (mod.FlowPrinter method) pushVertexColour() (mod.DGPrinter method) pushVertexLabel() (mod.DGPrinter method) pushVertexVisible() (mod.DGPrinter method)

R

radical (mod.GraphVertex attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphVertex attribute) raiseCharges (mod.GraphPrinter attribute) RCEvaluator (class in mod) rcEvaluator() (in module 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) reconnectSource() (mod.DGPrintData method) reconnectTarget() (mod.DGPrintData method) relation (mod.LabelSettings attribute) relaxed (mod.Flow attribute) remove() (mod.PetriNetMarking method) removeDuplicate() (mod.DGPrintData method) repeat (in module mod) revive() (in module mod) right (mod.Derivation attribute) (mod.Derivations attribute) (mod.Rule attribute) (mod.RuleEdge attribute) (mod.RuleVertex 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.RuleContextGraph attribute) (mod.RuleContextGraphVertex attribute) (mod.RuleEdge attribute) (mod.RuleLeftGraph attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraph attribute) (mod.RuleRightGraphVertex attribute) (mod.RuleVertex attribute) rule::Composer (C++ class) rule::Composer::create (C++ function) rule::Composer::eval (C++ function) rule::Composer::getProducts (C++ function) rule::Composer::getRuleDatabase (C++ function) rule::Composer::print (C++ function) rule::RCExp::Bind (C++ class) rule::RCExp::ComposeBase (C++ class) rule::RCExp::ComposeCommon (C++ class) rule::RCExp::ComposeParallel (C++ class) rule::RCExp::ComposeSub (C++ class) rule::RCExp::ComposeSuper (C++ class) rule::RCExp::Expression (C++ class) rule::RCExp::Id (C++ class) rule::RCExp::Unbind (C++ class) rule::RCExp::Union (C++ class) 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::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::IncidentEdgeRange (C++ class) rule::Rule::ContextGraph::IncidnetEdgeIterator (C++ class) rule::Rule::ContextGraph::IncidnetEdgeIterator::IncidentEdgeIterator (C++ function) rule::Rule::ContextGraph::numEdges (C++ function) rule::Rule::ContextGraph::numVertices (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::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::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::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::IncidentEdgeRange (C++ class) rule::Rule::IncidnetEdgeIterator (C++ class) rule::Rule::IncidnetEdgeIterator::IncidentEdgeIterator (C++ function) 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::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::IncidentEdgeRange (C++ class) rule::Rule::LeftGraph::IncidnetEdgeIterator (C++ class) rule::Rule::LeftGraph::IncidnetEdgeIterator::IncidentEdgeIterator (C++ function) rule::Rule::LeftGraph::numEdges (C++ function) rule::Rule::LeftGraph::numVertices (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::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] 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::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::IncidentEdgeRange (C++ class) rule::Rule::RightGraph::IncidnetEdgeIterator (C++ class) rule::Rule::RightGraph::IncidnetEdgeIterator::IncidentEdgeIterator (C++ function) rule::Rule::RightGraph::numEdges (C++ function) rule::Rule::RightGraph::numVertices (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::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::ruleGML (C++ function) rule::Rule::ruleGMLString (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::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) RuleContextGraph (class in mod) RuleContextGraphEdge (class in mod) RuleContextGraphEdge.__init__() (in module mod) RuleContextGraphVertex (class in mod) RuleContextGraphVertex.__init__() (in module mod) ruleDatabase (mod.RCEvaluator attribute) RuleEdge (class in mod) RuleEdge.__init__() (in module mod) ruleGML() (in module mod) ruleGMLString() (in module mod) RuleLeftGraph (class in mod) RuleLeftGraphEdge (class in mod) RuleLeftGraphEdge.__init__() (in module mod) RuleLeftGraphVertex (class in mod) RuleLeftGraphVertex.__init__() (in module mod) RuleRightGraph (class in mod) RuleRightGraphEdge (class in mod) RuleRightGraphEdge.__init__() (in module mod) RuleRightGraphVertex (class in mod) RuleRightGraphVertex.__init__() (in module mod) rules (mod.Derivations attribute) (mod.DGHyperEdge attribute) RuleVertex (class in mod) RuleVertex.__init__() (in module mod)

S

separatedIOInternalTransit (mod.Flow attribute) separateIOInternalTransit() (mod.Flow method) setMirrorOverwrite() (mod.DGPrinter method) setMolDefault() (mod.GraphPrinter 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) size (mod.FlowSolutionRange attribute) (mod.FlowSolutionSet 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) solutionsOld (mod.Flow attribute) source (mod.GraphEdge attribute) (mod.RuleContextGraphEdge attribute) (mod.RuleEdge attribute) (mod.RuleLeftGraphEdge attribute) (mod.RuleRightGraphEdge attribute)

sources (mod.DGHyperEdge attribute) (mod.Flow attribute) Specialisation (mod.LabelRelation attribute) specificationLocked (mod.Flow attribute) Stacktrace (C++ class) Stacktrace::print (C++ function) Stacktrace::Stacktrace (C++ function) StereoDeductionError (C++ class) stereoRelation (mod.LabelSettings attribute) strictTransit (mod.FlowOverallAutocatalysis attribute) (mod.FlowOverallCatalysis attribute) String (mod.LabelType attribute) stringLabel (mod.GraphEdge attribute) (mod.GraphVertex attribute) (mod.RuleLeftGraphEdge attribute) (mod.RuleLeftGraphVertex attribute) (mod.RuleRightGraphEdge attribute) (mod.RuleRightGraphVertex attribute) subset (mod.DGExecuteResult attribute) (mod.DGStratGraphState attribute) symbol (mod.AtomId attribute) syncSize() (in module mod) (mod.PetriNet method) (mod.PetriNetMarking method)

T

target (mod.GraphEdge attribute) (mod.RuleContextGraphEdge attribute) (mod.RuleEdge attribute) (mod.RuleLeftGraphEdge attribute) (mod.RuleRightGraphEdge attribute) targets (mod.DGHyperEdge attribute) Term (mod.LabelType attribute) TermParsingError (C++ class)

thick (mod.GraphPrinter attribute) ThrowOnDuplicate (mod.SmilesClassPolicy attribute) time (mod.EventTrace.EdgeEvent attribute) (mod.EventTrace.TransferEvent attribute) Triple (mod.BondType attribute) TrustMe (mod.IsomorphismPolicy attribute) type (mod.LabelSettings attribute)

U

unfilteredFlowColour (mod.FlowPrinter attribute) Unification (mod.LabelRelation attribute)

universe (mod.DGExecuteResult attribute) (mod.DGStratGraphState attribute)

V

version (C++ function) version() (in module mod) vertex (mod.EventTrace.TransferEvent attribute) (mod.FlowVarVertex attribute) vertexLabelSep (mod.DGPrinter attribute) vertices (mod.DG attribute) (mod.Graph attribute) (mod.Rule attribute) (mod.RuleContextGraph attribute) (mod.RuleLeftGraph attribute) (mod.RuleRightGraph attribute)

vLabelCount() (mod.Graph method)

W

withColour (mod.GraphPrinter attribute) withFlowLabels (mod.FlowPrinter attribute) withGraphImages (mod.DGPrinter attribute) withGraphName (mod.DGPrinter 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)