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 <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

_

__bool__() (mod.protocols.Graph.Edge method) __call__() (mod.stochsim.DrawMassAction method) (mod.stochsim.DrawTimeExponential method) __eq__() (mod.DGPetriNetMarking method) (mod.EventTrace method) __getitem__() (mod.CausalityFlowQuery method) (mod.DGPetriNetMarking method) (mod.DGVertexMapper method) (mod.EventTrace method) (mod.FlowSolutionRange method) (mod.FlowVarSumCustom method) (mod.FlowVarSumEdge method) (mod.FlowVarSumVertex method) (mod.Graph.Aut method) (mod.Graph.VertexRange method) (mod.protocols.VertexMap method) (mod.RCMatch method) (mod.Rule.VertexRange method) (mod.UnionGraph method) (mod.UnionGraph.VertexRange method) __init__() (in module mod) (mod.AtomData method) (mod.AtomId method) (mod.CausalityEdgeAction method) (mod.CausalityFlowQuery method) (mod.CausalityInputAction method) (mod.CausalityOutputAction method) (mod.Charge method) (mod.CWDPath method) (mod.DG method) (mod.DGHyperEdge method) (mod.DGPetriNet method) (mod.DGPetriNetMarking method) (mod.DGPrintData method) (mod.DGVertex method) (mod.DGVertexMapper method) (mod.EventTrace method) (mod.Flow method) (mod.FlowVarSumCustom method) (mod.FlowVarSumEdge method) (mod.FlowVarSumVertex method) (mod.GraphPrinter method) (mod.Isotope method) (mod.LabelSettings method) (mod.protocols.Graph.Edge method) (mod.protocols.Graph.Vertex 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.UnionGraph method) __len__() (mod.DGVertexMapper method) (mod.EventTrace method) (mod.FlowSolutionRange method) (mod.UnionGraph method) __setitem__() (mod.CausalityFlowQuery method) __str__() (mod.BondType method) (mod.EventTrace method) (mod.FlowVarCustom method) (mod.FlowVarEdge method) (mod.FlowVarSumCustom method) (mod.FlowVarSumEdge method) (mod.FlowVarSumVertex method) (mod.FlowVarVertex method) (mod.FlowVarVertexGraph method) (mod.RCMatch method) (mod.UnionGraph method)

A

absGap (mod.Flow attribute) Action (C++ enum) (class in mod) action (mod.EventTrace.Event attribute) Action::Error (C++ enumerator) Action::Ignore (C++ enumerator) Action::Warn (C++ enumerator) add() (mod.DGPetriNetMarking method) (mod.EventTrace method) addAbstract() (mod.DGBuilder method) addConstraint() (mod.Flow method) addDerivation() (mod.DGBuilder method) addEnumerationVar() (mod.Flow method) addIntVariable() (mod.Flow method) addSink() (mod.Flow method) addSource() (mod.Flow method) addSubset() (in module mod) 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.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) 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::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::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::MassActionKinetics (C++ class) causality::MassActionKinetics::draw (C++ function) causality::MassActionKinetics::MassActionKinetics (C++ function) causality::MassActionKinetics::syncSize (C++ function) causality::OutputAction (C++ class) causality::OutputAction::applyTo (C++ function) causality::OutputAction::OutputAction (C++ function), [1] causality::OutputAction::vertex (C++ member) CausalityDAG (class in mod) CausalityEdgeAction (class in mod) CausalityFlowQuery (class in mod) CausalityInputAction (class in mod) CausalityOutputAction (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) compose() (mod.RCMatch method) composeAll() (mod.RCMatch method) 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.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) CWDPath (class in mod)

D

degree (mod.protocols.Graph.Vertex 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.DGPetriNet attribute) (mod.DGPrintData attribute) (mod.DGVertex attribute) (mod.Flow attribute) dg() (mod.stochsim.Simulator method) 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), [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::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::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::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::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::operator[] (C++ function) dg::VertexMapper::size (C++ function) dg::VertexMapper::value_type (C++ type) dg::VertexMapper::VertexMapper (C++ function) DGBuilder (class in mod) DGExecuteResult (class in mod) dgFlow (mod.FlowSolutionSet attribute) DGHyperEdge (class in mod) DGPetriNet (class in mod) DGPetriNetMarking (class in mod) DGPrintData (class in mod) DGPrinter (class in mod) dgPrinter (mod.FlowPrinter attribute) DGStrat (class in mod) DGStrat.GraphState (class in mod) DGVertex (class in mod) DGVertexMapper (class in mod) diffDGs() (in module mod) disableAll() (mod.GraphPrinter method) domain (mod.protocols.VertexMap attribute) Double (mod.BondType attribute) draw() (in module mod) (mod.stochsim.DrawFunction method) DrawFunction (class in mod.stochsim) DrawMassAction (class in mod.stochsim) DrawTimeExponential (class in mod.stochsim) dump() (mod.DG method) (mod.EventTrace method) (mod.Flow method)

E

edge (mod.CausalityEdgeAction attribute) (mod.DGVertexMapper attribute) (mod.FlowVarEdge attribute) (mod.UnionGraph.Edge attribute) 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) enableAll() (mod.GraphPrinter method) energy (mod.Graph attribute) enumerationVars (mod.Flow attribute) environment variable MOD_ILP_SOLVER MOD_IPYTHON, [1], [2] MOD_NO_DEPRECATED, [1] MOD_NUM_POST_THREADS, [1] MOD_PLUGIN_PATH MOD_PYTHON, [1], [2]

Error (mod.Action attribute) eval() (mod.FlowSolution method) (mod.FlowSolutionOld method) (mod.RCEvaluator method) EventTrace (class in mod) EventTrace.Event (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) ExpandByStrategy (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.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::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::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++ 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) forceExistence (mod.FlowOverallAutocatalysis attribute) (mod.FlowOverallCatalysis 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.DGPetriNetMarking method) getAvailableILPSolvers (C++ function) getAvailableILPSolvers() (in module mod) getConfig (C++ function) getConfig() (in module mod) getEmptyPostPlaces() (mod.DGPetriNetMarking method) getEnergyBounds() (mod.FlowThermodynamics method) getGMLString() (mod.Graph method) (mod.Rule method) getNonZeroPlaces() (mod.DGPetriNetMarking method) getPostPlaces() (mod.DGPetriNet method) getVertexFromExternalId() (mod.Graph method) (mod.Rule method) Graph (class in mod) (class in mod.protocols) graph (mod.DGVertex attribute) (mod.FlowVarVertexGraph 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::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::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::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::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) 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::IncidentEdgeRange (C++ class) graph::Union::IncidnetEdgeIterator (C++ class) graph::Union::IncidnetEdgeIterator::IncidentEdgeIterator (C++ function) 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::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)

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.protocols.Graph.Vertex attribute) (mod.Rule attribute) Ignore (mod.Action attribute) image (mod.Graph attribute) imageCommad (mod.Graph attribute) incidentEdges (mod.protocols.Graph.Vertex 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) inverse() (mod.protocols.VertexMap method) isEnabled() (mod.DGPetriNetMarking method) isMolecule (mod.Graph attribute) isNull() (mod.DGHyperEdge method) (mod.DGVertex 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)

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.DGExecuteResult method) (mod.FlowSolution method) (mod.FlowSolutionRange method) (mod.FlowSolutionSet method) listSpecification() (mod.Flow method) listStats() (mod.DG method) load() (mod.DG static method) (mod.DGBuilder method) (mod.EventTrace static method) (mod.Flow static method) loadingWarnings (mod.Graph attribute) 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() (in module mod) MapUnique (mod.SmilesClassPolicy attribute) MassActionKinetics (class in mod) Max (mod.AtomIds attribute) maxExternalId (mod.Graph attribute) (mod.Rule 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 <args> -e <code> -f <filename> -h -i -j <N> -q -v clean mod.stochsim module MOD_IPYTHON, [1] MOD_NO_DEPRECATED MOD_NUM_POST_THREADS mod_post command line option --help --install-format --install-format-sudo -h -j <N> MOD_PYTHON, [1] 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.DGPetriNetMarking attribute) numEdges (mod.DG attribute) (mod.protocols.Graph attribute)

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

pop() (mod.RCMatch method) popEdgeColour() (mod.DGPrinter method) popEdgeLabel() (mod.DGPrinter method) popEdgeVisible() (mod.DGPrinter method) popFilePrefix() (in module mod) popInEdgeLabel() (mod.FlowPrinter method) popOutEdgeLabel() (mod.FlowPrinter method) popVertexColour() (mod.DGPrinter method) popVertexLabel() (mod.DGPrinter method) popVertexVisible() (mod.DGPrinter method) post::makeUniqueFilePrefix (C++ function) 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) printNonHyper() (mod.DG method) printStereo() (mod.protocols.LabelledGraph.Vertex 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) pushInEdgeLabel() (mod.FlowPrinter method) pushOutEdgeLabel() (mod.FlowPrinter method) pushVertexColour() (mod.DGPrinter method) pushVertexLabel() (mod.DGPrinter method) pushVertexVisible() (mod.DGPrinter method)

R

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) RCMatch (class in mod) reconnectSource() (mod.DGPrintData method) reconnectTarget() (mod.DGPrintData method) relation (mod.LabelSettings attribute) relaxed (mod.Flow attribute) remove() (mod.DGPetriNetMarking method) removeDuplicate() (mod.DGPrintData method) repeat (in module mod) 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.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::create (C++ function) rule::Composer::eval (C++ function) rule::Composer::getProducts (C++ function) rule::Composer::getRuleDatabase (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::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::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::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::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::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::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::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::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::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::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.DGHyperEdge attribute)

S

second (mod.RCMatch attribute) separatedIOInternalTransit (mod.Flow attribute) separateIOInternalTransit() (mod.Flow method) setEnergyBounds() (mod.FlowThermodynamics 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.DGVertexMapper attribute) (mod.FlowSolutionRange attribute) (mod.FlowSolutionSet 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) solutionsOld (mod.Flow attribute) source (mod.protocols.Graph.Edge 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.protocols.LabelledGraph.Edge attribute) (mod.protocols.LabelledGraph.Vertex attribute) subset (mod.DGExecuteResult attribute) (mod.DGStrat.GraphState attribute) symbol (mod.AtomId attribute) syncSize() (in module mod) (mod.DGPetriNet method) (mod.DGPetriNetMarking method) (mod.stochsim.DrawFunction method)

T

target (mod.protocols.Graph.Edge attribute) targets (mod.DGHyperEdge attribute) temperature (mod.FlowThermodynamics attribute) Term (mod.LabelType attribute) TermParsingError (C++ class) thermodynamics (mod.Flow attribute)

thick (mod.GraphPrinter attribute) ThrowOnDuplicate (mod.SmilesClassPolicy attribute) tikzpictureOption (mod.DGPrinter attribute) time (mod.EventTrace attribute) (mod.EventTrace.Event attribute) Triple (mod.BondType attribute) TrustMe (mod.IsomorphismPolicy attribute) type (mod.LabelSettings attribute)

U

unfilteredFlowColour (mod.FlowPrinter 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.DGExecuteResult attribute) (mod.DGStrat.GraphState attribute)

V

version (C++ function) version() (in module mod) vertex (mod.CausalityInputAction attribute) (mod.CausalityOutputAction attribute) (mod.FlowVarVertex attribute) (mod.UnionGraph.Vertex attribute) 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) 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) 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)