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.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.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.UnionGraph method) __len__() (mod.DGVertexMapper method) (mod.UnionGraph method) __str__() (mod.BondType method) (mod.RCMatch method) (mod.UnionGraph method)

A

Action (C++ enum) (class in mod) Action::Error (C++ enumerator) Action::Ignore (C++ enumerator) Action::Warn (C++ enumerator) addAbstract() (mod.DG.Builder method) addDerivation() (mod.DG.Builder method) addHyperEdge() (mod.DG.Builder method) addSubset() (in module mod) addUniverse() (in module mod) AllOrNone (mod.SmilesClassPolicy 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

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) 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) 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) DG.Builder (class in mod) DG.Builder.ExecuteResult (class in mod) DG.HyperEdge (class in mod) DG.Vertex (class in mod) 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::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::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::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::Result (C++ class) dg::VertexMapper::Result::map (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) 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)

E

edge (mod.DGVertexMapper 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) 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) environment variable MOD_DEBUGGER, [1], [2] 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.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) execute() (in module mod) (mod.DG.Builder method)

F

FatalError (C++ class) filterSubset() (in module mod) filterUniverse() (in module mod) findEdge() (mod.DG method) findVertex() (mod.DG method) first (mod.RCMatch attribute) flushCommands() (in module post) 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) getConfig (C++ function) getConfig() (in module mod) getGMLString() (mod.Graph method) (mod.Rule method) getVertexFromExternalId() (mod.Graph method) (mod.Rule method) Graph (class in mod) (class in mod.protocols) graph (mod.DG.Vertex 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)

I

id (mod.DG attribute) (mod.DG.HyperEdge attribute) (mod.DG.Vertex attribute) (mod.Graph attribute) (mod.protocols.Graph.Vertex attribute) (mod.Rule attribute) Ignore (mod.Action attribute) image (mod.Graph attribute) imageCommand (mod.Graph attribute) incidentEdges (mod.protocols.Graph.Vertex attribute) include() (in module mod) inDegree (mod.DG.Vertex attribute) inEdges (mod.DG.Vertex attribute) 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) 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)

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) listStats() (mod.DG method) load() (mod.DG static method) (mod.DG.Builder method) loadingWarnings (mod.Graph attribute) 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) 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] module mod post monomorphism() (mod.Graph method) (mod.Rule method)

N

name (mod.Graph attribute) (mod.Rule attribute) numEdges (mod.DG attribute) (mod.protocols.Graph attribute) numLeftComponents (mod.Rule attribute)

numRightComponents (mod.Rule attribute) numSources (mod.DG.HyperEdge attribute) numTargets (mod.DG.HyperEdge attribute) numVertices (mod.DG attribute) (mod.protocols.Graph attribute)

O

operator<< (C++ function)

outDegree (mod.DG.Vertex attribute) outEdges (mod.DG.Vertex attribute)

P

pop() (mod.RCMatch method) popEdgeColour() (mod.DGPrinter method) popEdgeLabel() (mod.DGPrinter method) popEdgeVisible() (mod.DGPrinter method) popFilePrefix() (in module mod) 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.RCEvaluator method) (mod.Rule method) 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) products (mod.DG attribute) (mod.RCEvaluator attribute) pushEdgeColour() (mod.DGPrinter method) pushEdgeLabel() (mod.DGPrinter method) pushEdgeVisible() (mod.DGPrinter method) pushFilePrefix() (in module mod) 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) 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) 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::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::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) 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) size (mod.DGVertexMapper 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)

source (mod.protocols.Graph.Edge attribute) sources (mod.DG.HyperEdge attribute) Specialisation (mod.LabelRelation attribute) Stacktrace (C++ class) Stacktrace::print (C++ function) Stacktrace::Stacktrace (C++ function) StereoDeductionError (C++ class) stereoRelation (mod.LabelSettings 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) Triple (mod.BondType attribute) TrustMe (mod.IsomorphismPolicy attribute) type (mod.LabelSettings attribute)

U

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.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) 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)