ResidueGraphTypes.hh File Reference

Graph structure for ResidueType. More...

#include <core/chemical/Atom.hh>
#include <core/chemical/Bond.hh>
#include <boost/graph/undirected_graph.hpp>
#include <boost/graph/filtered_graph.hpp>
#include <core/chemical/AtomTypeSet.fwd.hh>
#include <boost/graph/adjacency_list.hpp>

Classes
class	core::chemical::RealFilter
	A filtered graph that doesn't contain fake/virtual atoms and fake/virtual bonds. More...
class	core::chemical::HeavyAtomFilter
	The filter responsible for obtaining all heavy atoms. More...
class	core::chemical::AcceptorAtomFilter
	The filter responsible for obtaining all acceptor atoms. More...
class	core::chemical::HeavyAtomWithPolarHydrogensFilter
	The filter responsible for obtaining all heavy atoms with polar hydrogens attached to them. More...
class	core::chemical::HeavyAtomWithHydrogensFilter
	The filter responsible for finding heavy atoms with hydrogens. More...
class	core::chemical::HydrogenAtomFilter
	The filter responsible for all hydrogens. More...
class	core::chemical::AromaticAtomFilter
	The filter responsible for all aromatic atoms. More...
class	core::chemical::PolarHydrogenFilter
	The filter responsible for all polar hydrogens. More...
class	core::chemical::APolarHydrogenFilter
	The filter responsible for all apolar hydrogens. More...

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::chemical

Typedefs
typedef boost::undirected_graph< Atom, Bond >	core::chemical::ResidueGraph
typedef ResidueGraph::vertex_descriptor	core::chemical::VD
typedef ResidueGraph::edge_descriptor	core::chemical::ED
typedef utility::vector1< VD >	core::chemical::VDs
typedef boost::graph_traits < ResidueGraph > ::vertex_iterator	core::chemical::VIter
typedef std::pair< VIter, VIter >	core::chemical::VIterPair
typedef boost::graph_traits < ResidueGraph > ::edge_iterator	core::chemical::EIter
typedef std::pair< EIter, EIter >	core::chemical::EIterPair
typedef boost::graph_traits < ResidueGraph > ::out_edge_iterator	core::chemical::OutEdgeIter
typedef std::pair< OutEdgeIter, OutEdgeIter >	core::chemical::OutEdgeIterPair
typedef boost::graph_traits < ResidueGraph > ::adjacency_iterator	core::chemical::AdjacentIter
typedef std::pair < AdjacentIter, AdjacentIter >	core::chemical::AdjacentIterPair
typedef std::map< std::string, VD >	core::chemical::NameVDMap
typedef std::pair< std::string, VD >	core::chemical::NameVDPair
typedef std::pair < NameVDMap::iterator, bool >	core::chemical::NameVDInserted
typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS, boost::property < boost::vertex_name_t, core::chemical::VD > , boost::property < boost::edge_name_t, core::chemical::ED > >	core::chemical::LightWeightResidueGraph
typedef boost::graph_traits < LightWeightResidueGraph > ::vertex_descriptor	core::chemical::lwrg_VD
typedef boost::graph_traits < LightWeightResidueGraph > ::edge_descriptor	core::chemical::lwrg_ED
typedef boost::graph_traits < LightWeightResidueGraph > ::vertex_iterator	core::chemical::lwrg_vd_iter
typedef std::pair < lwrg_vd_iter, lwrg_vd_iter >	core::chemical::lwrg_vd_pair_iter
typedef boost::graph_traits < LightWeightResidueGraph > ::edge_iterator	core::chemical::lwrg_edge_iter
typedef boost::graph_traits < LightWeightResidueGraph > ::out_edge_iterator	core::chemical::lwrg_out_edge_iter
typedef std::pair < lwrg_out_edge_iter, lwrg_out_edge_iter >	core::chemical::lwrg_out_edge_iter_pair
typedef boost::filtered_graph < ResidueGraph, RealFilter, RealFilter >	core::chemical::RealResidueGraph
typedef RealResidueGraph::vertex_descriptor	core::chemical::RealResidueVD
typedef RealResidueGraph::edge_descriptor	core::chemical::RealResidueED
typedef boost::graph_traits < RealResidueGraph > ::vertex_iterator	core::chemical::RealResidueVIter
typedef boost::graph_traits < RealResidueGraph > ::edge_iterator	core::chemical::RealResidueEIter
typedef boost::graph_traits < RealResidueGraph > ::out_edge_iterator	core::chemical::RealResidueOutEdgeIter
typedef std::pair < RealResidueOutEdgeIter, RealResidueOutEdgeIter >	core::chemical::RealResidueOutEdgeIterPair
typedef std::pair < RealResidueVIter, RealResidueVIter >	core::chemical::RealResidueVIterPair
typedef boost::graph_traits < RealResidueGraph > ::adjacency_iterator	core::chemical::RealResidueAdjacentIter
typedef std::pair < RealResidueAdjacentIter, RealResidueAdjacentIter >	core::chemical::RealResidueAdjacentIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HeavyAtomFilter >	core::chemical::HeavyAtomGraph
typedef HeavyAtomGraph::vertex_descriptor	core::chemical::HeavyAtomVD
typedef HeavyAtomGraph::edge_descriptor	core::chemical::HeavyAtomED
typedef boost::graph_traits < HeavyAtomGraph > ::vertex_iterator	core::chemical::HeavyAtomVIter
typedef boost::graph_traits < HeavyAtomGraph > ::edge_iterator	core::chemical::HeavyAtomEIter
typedef boost::graph_traits < HeavyAtomGraph > ::out_edge_iterator	core::chemical::HeavyAtomOutEdgeIter
typedef std::pair < HeavyAtomOutEdgeIter, HeavyAtomOutEdgeIter >	core::chemical::HeavyAtomOutEdgeIterPair
typedef std::pair < HeavyAtomVIter, HeavyAtomVIter >	core::chemical::HeavyAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, AcceptorAtomFilter >	core::chemical::AcceptorAtomGraph
typedef boost::graph_traits < AcceptorAtomGraph > ::vertex_iterator	core::chemical::AcceptorAtomVIter
typedef boost::graph_traits < AcceptorAtomGraph > ::edge_iterator	core::chemical::AcceptorAtomEIter
typedef std::pair < AcceptorAtomVIter, AcceptorAtomVIter >	core::chemical::AcceptorAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HeavyAtomWithPolarHydrogensFilter >	core::chemical::HeavyAtomWithPolarHydrogensGraph
typedef boost::graph_traits < HeavyAtomWithPolarHydrogensGraph > ::vertex_iterator	core::chemical::HeavyAtomWithPolarHydrogensVIter
typedef boost::graph_traits < HeavyAtomWithPolarHydrogensGraph > ::edge_iterator	core::chemical::HeavyAtomWithPolarHydrogensEIter
typedef std::pair < HeavyAtomWithPolarHydrogensVIter, HeavyAtomWithPolarHydrogensVIter >	core::chemical::HeavyAtomWithPolarHydrogensVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HeavyAtomWithHydrogensFilter >	core::chemical::HeavyAtomWithHydrogensGraph
typedef boost::graph_traits < HeavyAtomWithHydrogensGraph > ::vertex_iterator	core::chemical::HeavyAtomWithHydrogensVIter
typedef boost::graph_traits < HeavyAtomWithHydrogensGraph > ::edge_iterator	core::chemical::HeavyAtomWithHydrogensEIter
typedef std::pair < HeavyAtomWithHydrogensVIter, HeavyAtomWithHydrogensVIter >	core::chemical::HeavyAtomWithHydrogensVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HydrogenAtomFilter >	core::chemical::HydrogenAtomGraph
typedef HydrogenAtomGraph::vertex_descriptor	core::chemical::HydrogenAtomVD
typedef HydrogenAtomGraph::edge_descriptor	core::chemical::HydrogenAtomED
typedef boost::graph_traits < HydrogenAtomGraph > ::vertex_iterator	core::chemical::HydrogenAtomVIter
typedef boost::graph_traits < HydrogenAtomGraph > ::edge_iterator	core::chemical::HHydrogenAtomEIter
typedef boost::graph_traits < HydrogenAtomGraph > ::out_edge_iterator	core::chemical::HydrogenAtomOutEdgeIter
typedef std::pair < HydrogenAtomOutEdgeIter, HydrogenAtomOutEdgeIter >	core::chemical::HydrogenAtomOutEdgeIterPair
typedef std::pair < HydrogenAtomVIter, HydrogenAtomVIter >	core::chemical::HydrogenAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, AromaticAtomFilter >	core::chemical::AromaticAtomGraph
typedef boost::graph_traits < AromaticAtomGraph > ::vertex_iterator	core::chemical::AromaticAtomVIter
typedef boost::graph_traits < AromaticAtomGraph > ::edge_iterator	core::chemical::AromaticAtomEIter
typedef std::pair < AromaticAtomVIter, AromaticAtomVIter >	core::chemical::AromaticAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, PolarHydrogenFilter >	core::chemical::PolarHydrogenGraph
typedef boost::graph_traits < PolarHydrogenGraph > ::vertex_iterator	core::chemical::PolarHydrogenVIter
typedef boost::graph_traits < PolarHydrogenGraph > ::edge_iterator	core::chemical::PolarHydrogenEIter
typedef std::pair < PolarHydrogenVIter, PolarHydrogenVIter >	core::chemical::PolarHydrogenVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, APolarHydrogenFilter >	core::chemical::APolarHydrogenGraph
typedef boost::graph_traits < APolarHydrogenGraph > ::vertex_iterator	core::chemical::APolarHydrogenVIter
typedef boost::graph_traits < APolarHydrogenGraph > ::edge_iterator	core::chemical::APolarHydrogenEIter
typedef std::pair < APolarHydrogenVIter, APolarHydrogenVIter >	core::chemical::APolarHydrogenVIterPair

Detailed Description

Graph structure for ResidueType.

This is the typedefs and filtered graphs for the graph implementation of ResidueType based on boost graphs. Filtered graphs are graph structures that have been filtered based on a certain criteria. For example, the Acceptor atom graph has been filtered so that every node and edge in the graph is associated with an acceptor atom. The properties of the filtered graphs can be determined by any criteria. Currently, atom types are used as the metric to filter the graphs. This does not have to be the case. Graphs can be filtered based on the atoms, orbitals, etc etc. It is up to your immagination. The unit tests for these show examples of how to use the filtered graphs.

Each filter graph has an operator that is used to determine if a node should be in the graph. An iterator through each node and edge of the graph is available. Specifically, if you want to iterate through the graph nodes, you would use this method: for(HeavyAtomVIterPair vp = boost::vertices(heavy_atom_graph); vp.first != vp.second; ++vp.first){}

Author

Steven Combs

This is the typedefs and filtered graphs for the graph implementation of ResidueType based on boost graphs. Filtered graphs are graph structures that have been filtered based on a certain criteria. For example, the Acceptor atom graph has been filtered so that every node and edge in the graph is associated with an acceptor atom. The properties of the filtered graphs can be determined by any criteria. Currently, atom types are used as the metric to filter the graphs. This does not have to be the case. Graphs can be filtered based on the atoms, orbitals, etc etc. It is up to your imagination. The unit tests for these show examples of how to use the filtered graphs.

Each filter graph has an operator that is used to determine if a node should be in the graph. An iterator through each node and edge of the graph is available. Specifically, if you want to iterate through the graph nodes, you would use this method: for(HeavyAtomVIterPair vp = boost::vertices(heavy_atom_graph); vp.first != vp.second; ++vp.first){}

Author

Steven Combs