Ring Perception and Aromaticity Assignment

The function rings identifies all possible rings in one or many molecules (here sdfset[1]) using the exhaustive ring perception algorithm from Hanser et al. (1996). In addition, the function can return all smallest possible rings as well as aromaticity information.

The following example returns all possible rings in a list. The argument upper allows to specify an upper length limit for rings. Choosing smaller length limits will reduce the search space resulting in shortened compute times. Note: each ring is represented by a character vector of atom symbols that are numbered by their position in the atom block of the corresponding SDF/SDFset object.

 ringatoms <- rings(sdfset[1], upper=Inf, type="all", arom=FALSE, inner=FALSE)

For visual inspection, the corresponding compound structure can be plotted with the ring bonds highlighted in color:

 atomindex <- as.numeric(gsub(".*_", "", unique(unlist(ringatoms))))
 plot(sdfset[1], print=FALSE, colbonds=atomindex) 

Alternatively, one can include the atom numbers in the plot:

 plot(sdfset[1], print=FALSE, atomnum=TRUE, no_print_atoms="H") 

Aromaticity information of the rings can be returned in a logical vector by setting arom=TRUE:

 rings(sdfset[1], upper=Inf, type="all", arom=TRUE, inner=FALSE) 

## $RINGS
## $RINGS$ring1
## [1] "N_10" "O_6"  "C_32" "C_31" "C_30"
## 
## $RINGS$ring2
## [1] "C_12" "C_14" "C_15" "C_13" "C_11"
## 
## $RINGS$ring3
## [1] "C_23" "O_2"  "C_27" "C_28" "O_3"  "C_25"
## 
## $RINGS$ring4
## [1] "C_23" "C_21" "C_18" "C_22" "C_26" "C_25"
## 
## $RINGS$ring5
##  [1] "O_3"  "C_28" "C_27" "O_2"  "C_23" "C_21" "C_18" "C_22" "C_26" "C_25"
## 
## 
## $AROMATIC
## ring1 ring2 ring3 ring4 ring5 
##  TRUE FALSE FALSE  TRUE FALSE

Return rings with no more than 6 atoms that are also aromatic:

 rings(sdfset[1], upper=6, type="arom", arom=TRUE, inner=FALSE) 

## $AROMATIC_RINGS
## $AROMATIC_RINGS$ring1
## [1] "N_10" "O_6"  "C_32" "C_31" "C_30"
## 
## $AROMATIC_RINGS$ring4
## [1] "C_23" "C_21" "C_18" "C_22" "C_26" "C_25"

Count shortest possible rings and their aromaticity assignments by setting type=count and inner=TRUE. The inner (smallest possible) rings are identified by first computing all possible rings and then selecting only the inner rings. For more details, consult the help documentation with ?rings.

 rings(sdfset[1:4], upper=Inf, type="count", arom=TRUE, inner=TRUE) 

##      RINGS AROMATIC
## CMP1     4        2
## CMP2     3        3
## CMP3     4        2
## CMP4     3        3