RingUtils Namespace Reference

Typedefs
typedef std::vector< int >	INT_VECT
typedef std::vector< std::vector< int > >	VECT_INT_VECT
typedef std::map< int, std::vector< int > >	INT_INT_VECT_MAP

Functions
RDKIT_GRAPHMOL_EXPORT void	pickFusedRings (int curr, const INT_INT_VECT_MAP &neighMap, INT_VECT &res, boost::dynamic_bitset<> &done, int depth=0)
	Pick a set of rings that are fused together and contain a specified ring.
RDKIT_GRAPHMOL_EXPORT void	makeRingNeighborMap (const VECT_INT_VECT &brings, INT_INT_VECT_MAP &neighMap, unsigned int maxSize=0, unsigned int maxOverlapSize=0)
	For each ring in bring compute and store the ring that are fused (share at least one bond with it).
RDKIT_GRAPHMOL_EXPORT void	convertToBonds (const VECT_INT_VECT &res, VECT_INT_VECT &brings, const RDKit::ROMol &mol)
	converts a list of atom indices into a list of bond indices

Typedef Documentation

INT_INT_VECT_MAP

typedef std::map<int, std::vector<int> > RingUtils::INT_INT_VECT_MAP

Definition at line 29 of file Rings.h.

INT_VECT

typedef std::vector<int> RingUtils::INT_VECT

Definition at line 27 of file Rings.h.

VECT_INT_VECT

typedef std::vector<std::vector<int> > RingUtils::VECT_INT_VECT

Definition at line 28 of file Rings.h.

Function Documentation

convertToBonds()

RDKIT_GRAPHMOL_EXPORT void RingUtils::convertToBonds	(	const VECT_INT_VECT &	res,
		VECT_INT_VECT &	brings,
		const RDKit::ROMol &	mol
	)

converts a list of atom indices into a list of bond indices

Parameters

res	list of ring - each ring is a list of atom ids
brings	reference to a list of rings to the write the results to each ring here is list of bonds ids
mol	the molecule of interest

Assumptions:

• each list of atom ids in "res" form a legitimate ring
• each of these list of ordered such that a ring can be traversed

makeRingNeighborMap()

RDKIT_GRAPHMOL_EXPORT void RingUtils::makeRingNeighborMap	(	const VECT_INT_VECT &	brings,
		INT_INT_VECT_MAP &	neighMap,
		unsigned int	maxSize = 0,
		unsigned int	maxOverlapSize = 0
	)

For each ring in bring compute and store the ring that are fused (share at least one bond with it).

Useful both for the keulization stuff and aromaticity perception.

Parameters

brings	list of rings - each ring is specified as a list of bond IDs
neighMap	an STL map into which the results are stored. Each entry in the map is indexed by the ring ID and the contents are the list rings (rather their IDs) that are fused with this ring
maxSize	if this is >0, rings that are larger than the threshold will not be considered as candidates to be neighbors
maxOverlapSize	if this is >0, rings that overlap by more bonds than this will not be considered to be neighbors

pickFusedRings()

RDKIT_GRAPHMOL_EXPORT void RingUtils::pickFusedRings	(	int	curr,
		const INT_INT_VECT_MAP &	neighMap,
		INT_VECT &	res,
		boost::dynamic_bitset<> &	done,
		int	depth = 0
	)

Pick a set of rings that are fused together and contain a specified ring.

Parameters

curr	the ID for the irng that should be in the fused system
neighMap	adjacency lists for for all rings in the molecule. See documentation for makeNeighMap
res	used to return the results: a list of rings that are fused with curr in them
done	a bit vector recording the rings that are already dealt with this also can be used to avoid any rings that should not be included in the fused system
depth	used to track recursion depth