RDKit
Open-source cheminformatics and machine learning.
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

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. More...
 
void makeRingNeighborMap (const VECT_INT_VECT &brings, INT_INT_VECT_MAP &neighMap, unsigned int maxSize=0)
 For each ring in bring compute and strore the ring that are fused (share atleast one bond with it). More...
 
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 More...
 

Typedef Documentation

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

Definition at line 28 of file Rings.h.

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

Definition at line 26 of file Rings.h.

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

Definition at line 27 of file Rings.h.

Function Documentation

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
reslist of ring - each ring is a list of atom ids
bringsreference to a list of rings to the write the results to each ring here is list of bonds ids
molthe 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
void RingUtils::makeRingNeighborMap ( const VECT_INT_VECT brings,
INT_INT_VECT_MAP neighMap,
unsigned int  maxSize = 0 
)

For each ring in bring compute and strore the ring that are fused (share atleast one bond with it).

Useful both for the keulization stuff and aromaticity perception.

Parameters
bringslist of rings - each ring is specified as a list of bond IDs
neighMapan STL map into which the results are stored. Each entry in the map is indexed by the ring ID and the conents are the list rings (rather their IDs) that are fused with this ring
maxSizeif this is >0, rings that are larger than the threshold will not be considered as candidates to be neighbors
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
currthe ID for the irng that should be in the fused system
neighMapadjacency lists for for all rings in the molecule. See documentation for makeNeighMap
resused to return the results: a list of rings that are fused with curr in them
donea 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
depthused to track recursion depth