Subgraphs.h File Reference

functionality for finding subgraphs and paths in molecules More...

#include <RDGeneral/export.h>
#include <vector>
#include <list>
#include <map>
#include <unordered_map>

Go to the source code of this file.

Namespaces
namespace	RDKit
	Std stuff.

Typedefs
typedef std::vector< int >	RDKit::PATH_TYPE
typedef std::list< PATH_TYPE >	RDKit::PATH_LIST
typedef PATH_LIST::const_iterator	RDKit::PATH_LIST_CI
typedef std::map< int, PATH_LIST >	RDKit::INT_PATH_LIST_MAP
typedef INT_PATH_LIST_MAP::const_iterator	RDKit::INT_PATH_LIST_MAP_CI
typedef INT_PATH_LIST_MAP::iterator	RDKit::INT_PATH_LIST_MAP_I

Functions
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP	RDKit::findAllSubgraphsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useHs=false, int rootedAtAtom=-1)
	find all bond subgraphs in a range of sizes
RDKIT_SUBGRAPHS_EXPORT PATH_LIST	RDKit::findAllSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, int rootedAtAtom=-1)
	find all bond subgraphs of a particular size
RDKIT_SUBGRAPHS_EXPORT PATH_LIST	RDKit::findUniqueSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, bool useBO=true, int rootedAtAtom=-1)
	find unique bond subgraphs of a particular size
RDKIT_SUBGRAPHS_EXPORT PATH_LIST	RDKit::findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1, bool onlyShortestPaths=false)
	find all paths of a particular size
RDKIT_SUBGRAPHS_EXPORT INT_PATH_LIST_MAP	RDKit::findAllPathsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1, bool onlyShortestPaths=false)
RDKIT_SUBGRAPHS_EXPORT PATH_TYPE	RDKit::findAtomEnvironmentOfRadiusN (const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom, bool useHs=false, bool enforceSize=true, std::unordered_map< unsigned int, unsigned int > *atomMap=nullptr)
	Find bond subgraphs of a particular radius around an atom. Return empty result if there is no bond at the requested radius.

Detailed Description

functionality for finding subgraphs and paths in molecules

Difference between subgraphs and paths : Subgraphs are potentially branched, whereas paths (in our terminology at least) cannot be. So, the following graph:

            C--0--C--1--C--3--C
                  |
                  2
                  |
                  C

has 3 subgraphs of length 3: (0,1,2),(0,1,3),(2,1,3) but only 2 paths of length 3: (0,1,3),(2,1,3)

Definition in file Subgraphs.h.