Index

Symbols

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

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

_

__bool__() (mod.protocols.Graph.Edge method) __getitem__() (mod.DGVertexMapper method) (mod.Graph.Aut method) (mod.Graph.VertexRange method) (mod.hyperflow.SolutionRange method) (mod.hyperflow.VarSumCustom method) (mod.hyperflow.VarSumEdge method) (mod.hyperflow.VarSumVertex method) (mod.protocols.VertexMap method) (mod.RCMatch method) (mod.Rule.VertexRange method) (mod.UnionGraph method) (mod.UnionGraph.VertexRange method) __init__() (mod.AtomData method) (mod.AtomId method) (mod.Charge method) (mod.CWDPath method) (mod.DG method) (mod.DG.HyperEdge method) (mod.DG.Vertex method) (mod.DGPrintData method) (mod.DGVertexMapper method) (mod.GraphPrinter method) (mod.hyperflow.Model method) (mod.hyperflow.ModelImplementationView method) (mod.hyperflow.VarCustom method) (mod.hyperflow.VarEdge method) (mod.hyperflow.VarSumCustom method) (mod.hyperflow.VarSumEdge method) (mod.hyperflow.VarSumVertex method) (mod.hyperflow.VarVertex method) (mod.hyperflow.VarVertexGraph method) (mod.Isotope method) (mod.LabelSettings method) (mod.protocols.Graph.Edge method) (mod.protocols.Graph.Vertex method) (mod.RCEvaluator method) (mod.RCMatch method) (mod.UnionGraph method)

__int__() (mod.AtomId method) (mod.Charge method) (mod.Isotope method) __iter__() (mod.DGVertexMapper method) (mod.hyperflow.SolutionRange method) (mod.UnionGraph method) __len__() (mod.DGVertexMapper method) (mod.hyperflow.SolutionRange method) (mod.UnionGraph method) __str__() (mod.BondType method)

A

absGap (mod.hyperflow.Model attribute) Action (C++ enum) (class in mod) Action::Error (C++ enumerator) Action::Ignore (C++ enumerator) Action::Warn (C++ enumerator) addAbstract() (mod.DG.Builder method) addBoolVariable() (mod.hyperflow.Model method) addConstraint() (mod.hyperflow.Model method) addDerivation() (mod.DG.Builder method) addEnumerationVar() (mod.hyperflow.Model method) addFloatVariable() (mod.hyperflow.Model method) addHyperEdge() (mod.DG.Builder method) addIntVariable() (mod.hyperflow.Model method) addSink() (mod.hyperflow.Model method) addSource() (mod.hyperflow.Model method) addSubset() (in module mod) addTransitEnumeration() (mod.hyperflow.Model method) addUniverse() (in module mod) allowHyperLoops (mod.hyperflow.Model attribute) allowIOReversal (mod.hyperflow.Model attribute) allowReversal (mod.hyperflow.Model attribute)

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

B

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

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

C

cacheEnergy() (mod.Graph method) Charge (C++ class) (class in mod) charge (mod.AtomData attribute) (mod.protocols.LabelledGraph.Vertex attribute) Charge::Charge (C++ function), [1] Charge::operator signed char (C++ function) Charge::operator<< (C++ function) Check (mod.IsomorphismPolicy attribute) clean mod command line option codomain (mod.protocols.VertexMap attribute) collapseHydrogens (mod.GraphPrinter attribute) comatch (mod.DGVertexMapper.Result attribute) command() (in module post) compose() (mod.RCMatch method) composeAll() (mod.RCMatch method)

Config (C++ class) (class in mod) config (in module mod) context (mod.Rule attribute) (mod.Rule.Edge attribute) (mod.Rule.Vertex attribute) core (mod.Rule.ContextGraph.Edge attribute) (mod.Rule.ContextGraph.Vertex attribute) (mod.Rule.LeftGraph.Edge attribute) (mod.Rule.LeftGraph.Vertex attribute) (mod.Rule.RightGraph.Edge attribute) (mod.Rule.RightGraph.Vertex attribute) createdGraphs (mod.DG attribute) createdRules (mod.RCEvaluator attribute) customBoolVariables (mod.hyperflow.Model attribute) customFloatVariables (mod.hyperflow.Model attribute) customIntVariables (mod.hyperflow.Model 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.DG.Builder attribute) (mod.DG.HyperEdge attribute) (mod.DG.Vertex attribute) (mod.DGPrintData attribute) (mod.hyperflow.Model attribute) DG.Builder (class in mod) DG.Builder.AddAbstractResult (class in mod) DG.Builder.ExecuteResult (class in mod) DG.HyperEdge (class in mod) DG.Vertex (class in mod) dg::AddAbstractResult (C++ class) dg::AddAbstractResult::getEdge (C++ function) dg::AddAbstractResult::getGraph (C++ function) dg::Builder (C++ class) dg::Builder::addAbstract (C++ function) dg::Builder::addDerivation (C++ function), [1] dg::Builder::addHyperEdge (C++ function), [1] dg::Builder::apply (C++ function), [1], [2] dg::Builder::execute (C++ function), [1], [2] dg::Builder::getDG (C++ function) dg::Builder::isActive (C++ function) dg::Builder::load (C++ function) dg::DG (C++ class) dg::DG::build (C++ function), [1] dg::DG::diff (C++ function) dg::DG::dump (C++ function), [1] dg::DG::EdgeIterator (C++ class) dg::DG::EdgeIterator::EdgeIterator (C++ function) dg::DG::EdgeRange (C++ class) dg::DG::edges (C++ function) dg::DG::findEdge (C++ function), [1] dg::DG::findVertex (C++ function) dg::DG::getCreatedGraphs (C++ function) dg::DG::getGraphDatabase (C++ function) dg::DG::getHyper (C++ function) dg::DG::getId (C++ function) dg::DG::getLabelSettings (C++ function) dg::DG::getNonHyper (C++ function) dg::DG::hasActiveBuilder (C++ function) dg::DG::HyperEdge (C++ class) dg::DG::HyperEdge::getDG (C++ function) dg::DG::HyperEdge::getId (C++ function) dg::DG::HyperEdge::getInverse (C++ function) dg::DG::HyperEdge::HyperEdge (C++ function) dg::DG::HyperEdge::isNull (C++ function) dg::DG::HyperEdge::numSources (C++ function) dg::DG::HyperEdge::numTargets (C++ function) dg::DG::HyperEdge::operator bool (C++ function) dg::DG::HyperEdge::print (C++ function) dg::DG::HyperEdge::rules (C++ function) dg::DG::HyperEdge::sources (C++ function) dg::DG::HyperEdge::targets (C++ function) dg::DG::InEdgeIterator (C++ class) dg::DG::InEdgeIterator::InEdgeIterator (C++ function) dg::DG::InEdgeRange (C++ class) dg::DG::isLocked (C++ function) dg::DG::listStats (C++ function) dg::DG::load (C++ function), [1] dg::DG::make (C++ function) dg::DG::numEdges (C++ function) dg::DG::numVertices (C++ function) dg::DG::operator<< (C++ function) dg::DG::OutEdgeIterator (C++ class) dg::DG::OutEdgeIterator::OutEdgeIterator (C++ function) dg::DG::OutEdgeRange (C++ class) dg::DG::print (C++ function) dg::DG::printNonHyper (C++ function) dg::DG::RuleIterator (C++ class) dg::DG::RuleIterator::RuleIterator (C++ function) dg::DG::RuleRange (C++ class) dg::DG::SourceIterator (C++ class) dg::DG::SourceIterator::SourceIterator (C++ function) dg::DG::SourceRange (C++ class) dg::DG::TargetIterator (C++ class) dg::DG::TargetIterator::TargetIterator (C++ function) dg::DG::TargetRange (C++ class) dg::DG::Vertex (C++ class) dg::DG::Vertex::getDG (C++ function) dg::DG::Vertex::getGraph (C++ function) dg::DG::Vertex::getId (C++ function) dg::DG::Vertex::getOutDegree (C++ function) dg::DG::Vertex::inDegree (C++ function) dg::DG::Vertex::inEdges (C++ function) dg::DG::Vertex::isNull (C++ function) dg::DG::Vertex::operator bool (C++ function) dg::DG::Vertex::outEdges (C++ function) dg::DG::Vertex::Vertex (C++ function) dg::DG::VertexIterator (C++ class)

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

E

edge (mod.DGVertexMapper attribute) (mod.hyperflow.VarEdge attribute) (mod.UnionGraph.Edge attribute) edgeFlow (in module mod) edgeLabelSep (mod.DGPrinter attribute) edges (mod.DG attribute) (mod.protocols.Graph attribute) edgesAsBonds (mod.GraphPrinter attribute) eLabelCount() (mod.Graph method) enable() (mod.hyperflow.Model.OverallAutocatalysis method) (mod.hyperflow.Model.OverallCatalysis method) enableAll() (mod.GraphPrinter method) enableCommands() (in module post) enableCompileSummary() (in module post) enableInvokeMake() (in module post) energy (mod.Graph attribute) enumerateIsomorphisms() (mod.Graph method) enumerateMonomorphisms() (mod.Graph method) enumerationVars (mod.hyperflow.Model attribute) environment variable MOD_DEBUGGER, [1], [2] MOD_ILP_SOLVER MOD_IPYTHON, [1], [2] MOD_NO_DEPRECATED, [1] MOD_NUM_POST_THREADS, [1] MOD_PLUGIN_PATH MOD_PYTHON, [1], [2], [3]

Error (mod.Action attribute) eval() (mod.hyperflow.Solution method) (mod.RCEvaluator method) exactMass (mod.Graph attribute) Exception (C++ class) Exception::append (C++ function) Exception::getName (C++ function) Exception::printStacktrace (C++ function) Exception::what (C++ function) exclude() (mod.hyperflow.Model method) excluded (mod.hyperflow.Model attribute) execute() (in module mod) (mod.DG.Builder method)

F

FatalError (C++ class) filterSubset() (in module mod) filterUniverse() (in module mod) findEdge() (mod.DG method) findSolutions() (mod.hyperflow.Model method) findVertex() (mod.DG method) first (mod.RCMatch attribute) flushCommands() (in module post) forceExistence (mod.hyperflow.Model.OverallAutocatalysis attribute) (mod.hyperflow.Model.OverallCatalysis attribute) fromDFS() (mod.Graph static method) (mod.Rule static method) fromDFSMulti() (mod.Graph static method) fromGMLFile() (mod.Graph static method) (mod.Rule static method) fromGMLFileMulti() (mod.Graph static method)

fromGMLString() (mod.Graph static method) (mod.Rule static method) fromGMLStringMulti() (mod.Graph static method) fromMOLFile() (mod.Graph static method) fromMOLFileMulti() (mod.Graph static method) fromMOLString() (mod.Graph static method) fromMOLStringMulti() (mod.Graph static method) fromSDFile() (mod.Graph static method) fromSDFileMulti() (mod.Graph static method) fromSDString() (mod.Graph static method) fromSDStringMulti() (mod.Graph static method) fromSMILES() (mod.Graph static method) fromSMILESMulti() (mod.Graph static method) Function (C++ class) Function<R(Args...)> (C++ class) Function<R(Args...)>::clone (C++ function) Function<R(Args...)>::operator() (C++ function) Function<R(Args...)>::print (C++ function)

G

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

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

H

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

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

I

id (mod.DG attribute) (mod.DG.HyperEdge attribute) (mod.DG.Vertex attribute) (mod.Graph attribute) (mod.hyperflow.Model attribute) (mod.hyperflow.Solution attribute) (mod.hyperflow.VarCustom attribute) (mod.hyperflow.VarEdge attribute) (mod.hyperflow.VarSumCustom attribute) (mod.hyperflow.VarSumEdge attribute) (mod.hyperflow.VarSumVertex attribute) (mod.hyperflow.VarVertex attribute) (mod.hyperflow.VarVertexGraph attribute) (mod.protocols.Graph.Vertex attribute) (mod.Rule attribute) Ignore (mod.Action attribute) image (mod.Graph attribute) imageCommand (mod.Graph attribute) implementationView (mod.hyperflow.Model attribute) incidentEdges (mod.protocols.Graph.Vertex attribute) include() (in module mod) inDegree (mod.DG.Vertex attribute) inEdges (mod.DG.Vertex attribute) inFlow (in module mod) InputError (C++ class) inputGraphs (in module mod) inputRules (in module mod) instantiateStereo() (mod.Graph method) Invalid (mod.AtomIds attribute) (mod.BondType attribute) inverse (mod.DG.HyperEdge attribute) inverse() (mod.protocols.VertexMap method)

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

L

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

labelType (mod.Rule attribute) LabelType::String (C++ enumerator) LabelType::Term (C++ enumerator) left (mod.Derivation attribute) (mod.Derivations attribute) (mod.DGVertexMapper attribute) (mod.Rule attribute) (mod.Rule.Edge attribute) (mod.Rule.Vertex attribute) leftPredicate (in module mod) linearEncoding (mod.Graph attribute) list() (mod.DG.Builder.ExecuteResult method) (mod.hyperflow.Solution method) (mod.hyperflow.SolutionRange method) listSpecification() (mod.hyperflow.Model method) listStats() (mod.DG method) load() (mod.DG static method) (mod.DG.Builder method) (mod.hyperflow.Model static method) loadingWarnings (mod.Graph attribute) loadString() (mod.hyperflow.Model 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) map (mod.DGVertexMapper.Result attribute) MapUnique (mod.SmilesClassPolicy attribute) match (mod.DGVertexMapper.Result attribute) Max (mod.AtomIds attribute) maxExternalId (mod.Graph attribute) (mod.Rule attribute) MDLOptions (C++ class) (class in mod) MDLOptions::addHydrogens (C++ member) MDLOptions::allowAbstract (C++ member) MDLOptions::applyV2000AtomAliases (C++ member) MDLOptions::fullyIgnoreV2000UnhandledKnownProperty (C++ member) MDLOptions::onImplicitValenceOnAbstract (C++ member) MDLOptions::onPatternCharge (C++ member) MDLOptions::onPatternIsotope (C++ member) MDLOptions::onPatternRadical (C++ member) MDLOptions::onRAD1 (C++ member) MDLOptions::onRAD3 (C++ member) MDLOptions::onRAD4 (C++ member) MDLOptions::onRAD5 (C++ member) MDLOptions::onRAD6 (C++ member) MDLOptions::onUnsupportedQueryBondType (C++ member) MDLOptions::onV2000AbstractISO (C++ member) MDLOptions::onV2000Charge4 (C++ member)

MDLOptions::onV2000UnhandledProperty (C++ member) MDLOptions::onV3000UnhandledAtomProperty (C++ member) minExternalId (mod.Graph attribute) (mod.Rule attribute) mirror (mod.GraphPrinter attribute) mod module mod command line option --debug --help --memcheck --nopost --profile --version --vgArgs -e -f -h -i -j -q -v clean MOD_DEBUGGER, [1] MOD_IPYTHON, [1] MOD_NO_DEPRECATED MOD_NUM_POST_THREADS mod_post command line option --help --install-format --install-format-sudo -h -j MOD_PYTHON, [1], [2] model (mod.hyperflow.Solution attribute) (mod.hyperflow.SolutionRange attribute) module mod post monomorphism() (mod.Graph method) (mod.Rule method)

N

name (mod.Graph attribute) (mod.hyperflow.VarCustom attribute) (mod.Rule attribute) NoneOnDuplicate (mod.SmilesClassPolicy attribute) numEdges (mod.DG attribute) (mod.protocols.Graph attribute) numLeftComponents (mod.Rule attribute)

numMILPConstraints (mod.hyperflow.ModelImplementationView attribute) numMILPVariables (mod.hyperflow.ModelImplementationView attribute) numRightComponents (mod.Rule attribute) numSources (mod.DG.HyperEdge attribute) numTargets (mod.DG.HyperEdge attribute) numVertices (mod.DG attribute) (mod.protocols.Graph attribute)

O

objectiveFunction (mod.hyperflow.Model attribute) objectiveValue (mod.hyperflow.Solution attribute) operator<< (C++ function) outDegree (mod.DG.Vertex attribute)

outEdges (mod.DG.Vertex attribute) outFlow (in module mod) overallAutocatalysis (mod.hyperflow.Model attribute) overallCatalysis (mod.hyperflow.Model attribute)

P

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

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

R

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

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

S

second (mod.RCMatch attribute) separatedIOInternalTransit (mod.hyperflow.Model attribute) separateIOInternalTransit() (mod.hyperflow.Model method) setImageOverwrite() (mod.DGPrinter method) setMirrorOverwrite() (mod.DGPrinter method) setMolDefault() (mod.GraphPrinter method) setReactionDefault() (mod.GraphPrinter method) setRotationOverwrite() (mod.DGPrinter method) simpleCarbons (mod.GraphPrinter attribute) Single (mod.BondType attribute) sinks (mod.hyperflow.Model attribute) size (mod.DGVertexMapper attribute) (mod.hyperflow.SolutionRange attribute) (mod.RCMatch attribute) smiles (mod.Graph attribute) smiles() (in module mod) SmilesClassPolicy (C++ enum) (class in mod) SmilesClassPolicy::MapUnique (C++ enumerator) SmilesClassPolicy::NoneOnDuplicate (C++ enumerator) SmilesClassPolicy::ThrowOnDuplicate (C++ enumerator) smilesWithIds (mod.Graph attribute) solutions (mod.hyperflow.Model attribute)

source (mod.protocols.Graph.Edge attribute) sources (mod.DG.HyperEdge attribute) (mod.hyperflow.Model attribute) Specialisation (mod.LabelRelation attribute) specificationLocked (mod.hyperflow.Model attribute) Stacktrace (C++ class) Stacktrace::print (C++ function) Stacktrace::Stacktrace (C++ function) StereoDeductionError (C++ class) stereoRelation (mod.LabelSettings attribute) strictTransit (mod.hyperflow.Model.OverallAutocatalysis attribute) (mod.hyperflow.Model.OverallCatalysis attribute) String (mod.LabelType attribute) stringLabel (mod.protocols.LabelledGraph.Edge attribute) (mod.protocols.LabelledGraph.Vertex attribute) subset (mod.DG.Builder.ExecuteResult attribute) (mod.DGStrat.GraphState attribute) summaryChapter() (in module post) summaryInput() (in module post) summaryRaw() (in module post) summarySection() (in module post) symbol (mod.AtomId attribute)

T

target (mod.protocols.Graph.Edge attribute) targets (mod.DG.HyperEdge attribute) Term (mod.LabelType attribute) TermParsingError (C++ class) thick (mod.GraphPrinter attribute)

ThrowOnDuplicate (mod.SmilesClassPolicy attribute) tikzpictureOption (mod.DGPrinter attribute) transitEnumeration (mod.hyperflow.Model attribute) transitInternalFlow (in module mod) Triple (mod.BondType attribute) TrustMe (mod.IsomorphismPolicy attribute) type (mod.LabelSettings attribute)

U

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

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

V

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

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

W

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

withPrettyStereo (mod.GraphPrinter attribute) withRawStereo (mod.GraphPrinter attribute) withRuleId (mod.DGPrinter attribute) withRuleName (mod.DGPrinter attribute) withShortcutEdges (mod.DGPrinter attribute) withShortcutEdgesAfterVisibility (mod.DGPrinter attribute) withStereo (mod.LabelSettings attribute) withTexttt (mod.GraphPrinter attribute) writeMILP() (mod.hyperflow.ModelImplementationView method)