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RDKit
Open-source cheminformatics and machine learning.
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functionality for finding subgraphs and paths in molecules More...
#include <vector>
#include <list>
#include <map>
Go to the source code of this file.
Namespaces | |
RDKit | |
Includes a bunch of functionality for handling Atom and Bond queries. | |
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 | |
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 More... | |
PATH_LIST | RDKit::findAllSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, int rootedAtAtom=-1) |
find all bond subgraphs of a particular size More... | |
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 More... | |
PATH_LIST | RDKit::findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1) |
find all paths of a particular size More... | |
INT_PATH_LIST_MAP | RDKit::findAllPathsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useBonds=true, bool useHs=false, int rootedAtAtom=-1) |
PATH_TYPE | RDKit::findAtomEnvironmentOfRadiusN (const ROMol &mol, unsigned int radius, unsigned int rootedAtAtom, bool useHs=false) |
find bond subgraphs of a particular radius around an atom More... | |
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.