groups: Enumeration of Functional Groups and Atom Neighbors

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/AllClasses.R

Description

Returns frequency information of functional groups in molecules provided as SDF or SDFset objects. Alternatively, the function can return for each atom its atom/bond neighbor information.

Usage

1
groups(x, groups = "fctgroup", type = "countMA")

Arguments

x

SDF or SDFset containers

groups

if groups="fctgroup", frequencies of functional groups are returned; if groups="neighbors", atom/bond neighbor information is returned.

type

if type="all", then the complete neighbor information is generated for each atom in a molecule; if type="count", the neighbors are enumerated in a list and if type="countMA", then the counts of atom neighbors or functional groups are returned in a frequency matrix.

Details

At this point this function is in an experimental stage.

Value

...

Author(s)

Thomas Girke

References

...

See Also

...

Examples

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11
## Instances of SDFset class
data(sdfsample)
sdfset <- sdfsample

## Enumerate functional groups
groups(sdfset[1:20], groups="fctgroup", type="countMA") 

## Report atom/bond neighbors
groups(sdfset[1:4], groups="neighbors", type="countMA")
groups(sdfset[1:4], groups="neighbors", type="count")
groups(sdfset[1:4], groups="neighbors", type="all")

Example output

      RNH2 R2NH R3N ROPO3 ROH RCHO RCOR RCOOH RCOOR ROR RCCH RCN
CMP1     0    2   1     0   0    0    0     0     0   2    0   0
CMP2     0    2   2     0   1    0    0     0     0   0    0   0
CMP3     0    1   1     0   1    0    1     0     0   0    0   0
CMP4     0    1   3     0   0    0    0     0     0   2    0   0
CMP5     0    1   1     0   0    0    0     0     0   1    0   0
CMP6     0    0   1     0   1    0    0     0     0   0    0   0
CMP7     0    1   0     0   0    0    0     0     1   0    0   0
CMP8     0    0   1     0   0    0    0     0     0   0    0   0
CMP9     0    1   0     0   0    0    0     0     0   2    0   0
CMP10    0    1   1     0   0    0    0     0     0   0    0   0
CMP11    0    1   1     0   0    0    0     0     0   1    0   0
CMP12    0    1   1     0   0    0    0     0     0   1    0   0
CMP13    0    0   2     0   0    0    0     0     0   1    0   0
CMP14    0    1   1     0   0    0    0     0     0   0    0   0
CMP15    0    1   1     0   0    0    0     0     1   1    0   0
CMP16    0    0   1     0   0    0    0     0     0   1    0   1
CMP17    0    1   0     0   0    0    0     0     1   1    0   0
CMP18    0    1   1     0   0    0    0     0     0   1    0   0
CMP19    0    1   1     0   1    0    0     0     0   0    0   0
CMP20    0    2   0     0   0    0    0     0     1   1    0   0
     C:C_1_1_C_2_2_O_2_1 C:C_2_1_C_2_1 C:C_2_1_C_2_1_N_2_1 C:C_2_1_C_2_2_N_3_1
CMP1                   1             2                   1                   1
CMP2                   0             2                   0                   0
CMP3                   0             1                   0                   0
CMP4                   0             0                   0                   0
     C:C_2_1_C_3_1 C:C_2_1_C_3_2_O_2_1 C:C_2_1_N_2_1_N_2_2 C:C_2_1_N_2_1_O_1_2
CMP1             4                   2                   1                   2
CMP2             1                   0                   0                   0
CMP3             1                   0                   0                   0
CMP4             1                   2                   0                   1
     C:C_2_1_N_3_1_O_1_2 C:C_2_1_O_2_1 C:C_2_2_C_3_1 C:C_3_1 C:C_3_1_C_3_2
CMP1                   1             2             2       1             2
CMP2                   0             0             1       0             0
CMP3                   0             0             1       2             0
CMP4                   0             0             2       0             1
     C:C_3_1_N_3_1 N:C_2_1_C_3_1_C_3_1 N:C_3_1_C_3_1 N:C_3_2_O_2_1
CMP1             1                   1             2             1
CMP2             0                   1             1             0
CMP3             0                   1             1             0
CMP4             0                   1             0             0
     O:C_2_1_C_3_1 O:C_3_1_N_2_1 O:C_3_2 C:C_2_1_C_2_1_C_2_2 C:C_2_1_C_2_2
CMP1             2             1       3                   0             0
CMP2             0             0       2                   1             3
CMP3             0             0       2                   0             1
CMP4             0             0       3                   1             0
     C:C_2_1_C_3_2 C:C_2_1_N_2_1 C:C_2_1_N_3_1 C:C_2_1_O_1_1
CMP1             0             0             0             0
CMP2             1             1             1             1
CMP3             1             0             1             0
CMP4             0             1             0             0
     C:C_3_1_C_3_2_N_3_1 C:C_3_1_N_2_1_O_1_2 C:C_3_2_N_2_1_N_3_1
CMP1                   0                   0                   0
CMP2                   1                   1                   1
CMP3                   1                   1                   0
CMP4                   1                   0                   1
     C:N_2_1_N_2_2_N_3_1 C:N_2_1_N_3_1_O_1_2 C:N_3_1 N:C_1_1_C_3_1_C_3_1
CMP1                   0                   0       0                   0
CMP2                   1                   1       1                   1
CMP3                   0                   0       0                   0
CMP4                   0                   0       2                   2
     N:C_2_1_C_3_1 N:C_3_1_C_3_2 O:C_2_1 C:C_1_1_C_1_1_C_3_1
CMP1             0             0       0                   0
CMP2             1             1       1                   0
CMP3             0             0       0                   1
CMP4             1             1       0                   0
     C:C_2_1_C_2_1_C_3_2 C:C_2_2_C_3_1_C_3_1 C:C_3_1_C_3_1_C_3_2
CMP1                   0                   0                   0
CMP2                   0                   0                   0
CMP3                   1                   1                   1
CMP4                   0                   0                   0
     C:C_3_1_C_3_1_O_1_2 C:C_3_1_N_2_2_S_2_1 C:C_3_2_N_3_1_O_1_1
CMP1                   0                   0                   0
CMP2                   0                   0                   0
CMP3                   1                   1                   1
CMP4                   0                   0                   0
     C:N_2_1_N_2_2_S_2_1 N:C_3_2_N_2_1 O:C_3_1 S:C_3_1_C_3_1 C:C_1_1_N_3_1
CMP1                   0             0       0             0             0
CMP2                   0             0       0             0             0
CMP3                   1             2       1             1             0
CMP4                   0             0       0             0             1
     C:C_2_1 C:C_3_1_N_3_1_O_1_2 C:C_3_1_S_2_1 C:N_2_2_N_3_1_S_2_1
CMP1       0                   0             0                   0
CMP2       0                   0             0                   0
CMP3       0                   0             0                   0
CMP4       1                   1             1                   1
     C:N_3_1_N_3_1_O_1_2 C:O_2_1 O:C_1_1_C_3_1 S:C_2_1_C_3_1
CMP1                   0       0             0             0
CMP2                   0       0             0             0
CMP3                   0       0             0             0
CMP4                   1       2             2             1
$CMP1

C:C_1_1_C_2_2_O_2_1       C:C_2_1_C_2_1 C:C_2_1_C_2_1_N_2_1 C:C_2_1_C_2_2_N_3_1 
                  1                   2                   1                   1 
      C:C_2_1_C_3_1 C:C_2_1_C_3_2_O_2_1 C:C_2_1_N_2_1_N_2_2 C:C_2_1_N_2_1_O_1_2 
                  4                   2                   1                   2 
C:C_2_1_N_3_1_O_1_2       C:C_2_1_O_2_1       C:C_2_2_C_3_1             C:C_3_1 
                  1                   2                   2                   1 
      C:C_3_1_C_3_2       C:C_3_1_N_3_1 N:C_2_1_C_3_1_C_3_1       N:C_3_1_C_3_1 
                  2                   1                   1                   2 
      N:C_3_2_O_2_1       O:C_2_1_C_3_1       O:C_3_1_N_2_1             O:C_3_2 
                  1                   2                   1                   3 

$CMP2

      C:C_2_1_C_2_1 C:C_2_1_C_2_1_C_2_2       C:C_2_1_C_2_2       C:C_2_1_C_3_1 
                  2                   1                   3                   1 
      C:C_2_1_C_3_2       C:C_2_1_N_2_1       C:C_2_1_N_3_1       C:C_2_1_O_1_1 
                  1                   1                   1                   1 
      C:C_2_2_C_3_1 C:C_3_1_C_3_2_N_3_1 C:C_3_1_N_2_1_O_1_2 C:C_3_2_N_2_1_N_3_1 
                  1                   1                   1                   1 
C:N_2_1_N_2_2_N_3_1 C:N_2_1_N_3_1_O_1_2             C:N_3_1 N:C_1_1_C_3_1_C_3_1 
                  1                   1                   1                   1 
      N:C_2_1_C_3_1 N:C_2_1_C_3_1_C_3_1       N:C_3_1_C_3_1       N:C_3_1_C_3_2 
                  1                   1                   1                   1 
            O:C_2_1             O:C_3_2 
                  1                   2 

$CMP3

C:C_1_1_C_1_1_C_3_1       C:C_2_1_C_2_1 C:C_2_1_C_2_1_C_3_2       C:C_2_1_C_2_2 
                  1                   1                   1                   1 
      C:C_2_1_C_3_1       C:C_2_1_C_3_2       C:C_2_1_N_3_1       C:C_2_2_C_3_1 
                  1                   1                   1                   1 
C:C_2_2_C_3_1_C_3_1             C:C_3_1 C:C_3_1_C_3_1_C_3_2 C:C_3_1_C_3_1_O_1_2 
                  1                   2                   1                   1 
C:C_3_1_C_3_2_N_3_1 C:C_3_1_N_2_1_O_1_2 C:C_3_1_N_2_2_S_2_1 C:C_3_2_N_3_1_O_1_1 
                  1                   1                   1                   1 
C:N_2_1_N_2_2_S_2_1 N:C_2_1_C_3_1_C_3_1       N:C_3_1_C_3_1       N:C_3_2_N_2_1 
                  1                   1                   1                   2 
            O:C_3_1             O:C_3_2       S:C_3_1_C_3_1 
                  1                   2                   1 

$CMP4

      C:C_1_1_N_3_1             C:C_2_1 C:C_2_1_C_2_1_C_2_2       C:C_2_1_C_3_1 
                  1                   1                   1                   1 
C:C_2_1_C_3_2_O_2_1       C:C_2_1_N_2_1 C:C_2_1_N_2_1_O_1_2       C:C_2_2_C_3_1 
                  2                   1                   1                   2 
      C:C_3_1_C_3_2 C:C_3_1_C_3_2_N_3_1 C:C_3_1_N_3_1_O_1_2       C:C_3_1_S_2_1 
                  1                   1                   1                   1 
C:C_3_2_N_2_1_N_3_1 C:N_2_2_N_3_1_S_2_1             C:N_3_1 C:N_3_1_N_3_1_O_1_2 
                  1                   1                   2                   1 
            C:O_2_1 N:C_1_1_C_3_1_C_3_1       N:C_2_1_C_3_1 N:C_2_1_C_3_1_C_3_1 
                  2                   2                   1                   1 
      N:C_3_1_C_3_2       O:C_1_1_C_3_1             O:C_3_2       S:C_2_1_C_3_1 
                  1                   2                   3                   1 

$CMP1
                O_1                 O_2                 O_3                 O_4 
            "C_3_2"       "C_2_1_C_3_1"       "C_2_1_C_3_1"             "C_3_2" 
                O_5                 O_6                 N_7                 N_8 
            "C_3_2"       "C_3_1_N_2_1"       "C_3_1_C_3_1" "C_2_1_C_3_1_C_3_1" 
                N_9                N_10                C_11                C_12 
      "C_3_1_C_3_1"       "C_3_2_O_2_1" "C_2_1_C_2_1_N_2_1"       "C_2_1_C_3_1" 
               C_13                C_14                C_15                C_16 
      "C_2_1_C_3_1"       "C_2_1_C_2_1"       "C_2_1_C_2_1" "C_2_1_N_2_1_O_1_2" 
               C_17                C_18                C_19                C_20 
      "C_3_1_N_3_1" "C_2_1_C_2_2_N_3_1" "C_2_1_N_3_1_O_1_2"       "C_2_1_C_3_1" 
               C_21                C_22                C_23                C_24 
      "C_3_1_C_3_2"       "C_2_2_C_3_1" "C_2_1_C_3_2_O_2_1"       "C_2_1_C_3_1" 
               C_25                C_26                C_27                C_28 
"C_2_1_C_3_2_O_2_1"       "C_2_2_C_3_1"       "C_2_1_O_2_1"       "C_2_1_O_2_1" 
               C_29                C_30                C_31                C_32 
"C_2_1_N_2_1_O_1_2" "C_2_1_N_2_1_N_2_2"       "C_3_1_C_3_2" "C_1_1_C_2_2_O_2_1" 
               C_33 
            "C_3_1" 

$CMP2
                O_1                 O_2                 O_3                 N_4 
            "C_3_2"             "C_3_2"             "C_2_1" "C_2_1_C_3_1_C_3_1" 
                N_5                 N_6                 N_7                 N_8 
"C_1_1_C_3_1_C_3_1"       "C_3_1_C_3_2"       "C_2_1_C_3_1"       "C_3_1_C_3_1" 
                C_9                C_10                C_11                C_12 
      "C_2_1_N_3_1" "C_3_1_C_3_2_N_3_1"       "C_2_1_C_2_1" "N_2_1_N_2_2_N_3_1" 
               C_13                C_14                C_15                C_16 
"C_3_2_N_2_1_N_3_1"       "C_2_1_C_3_1" "C_3_1_N_2_1_O_1_2"       "C_2_1_N_2_1" 
               C_17                C_18                C_19                C_20 
"C_2_1_C_2_1_C_2_2" "N_2_1_N_3_1_O_1_2"       "C_2_1_C_2_1"             "N_3_1" 
               C_21                C_22                C_23                C_24 
      "C_2_1_C_3_2"       "C_2_2_C_3_1"       "C_2_1_O_1_1"       "C_2_1_C_2_2" 
               C_25                C_26 
      "C_2_1_C_2_2"       "C_2_1_C_2_2" 

$CMP3
                S_1                 O_2                 O_3                 O_4 
      "C_3_1_C_3_1"             "C_3_1"             "C_3_2"             "C_3_2" 
                N_5                 N_6                 N_7                 N_8 
"C_2_1_C_3_1_C_3_1"       "C_3_1_C_3_1"       "C_3_2_N_2_1"       "C_3_2_N_2_1" 
                C_9                C_10                C_11                C_12 
"C_3_1_C_3_2_N_3_1"       "C_2_1_N_3_1"       "C_2_1_C_2_1"       "C_2_1_C_3_1" 
               C_13                C_14                C_15                C_16 
"C_2_1_C_2_1_C_3_2" "C_2_2_C_3_1_C_3_1" "C_3_2_N_3_1_O_1_1"       "C_2_2_C_3_1" 
               C_17                C_18                C_19                C_20 
"C_3_1_C_3_1_C_3_2" "C_3_1_C_3_1_O_1_2"       "C_2_1_C_3_2"       "C_2_1_C_2_2" 
               C_21                C_22                C_23                C_24 
"C_3_1_N_2_1_O_1_2" "C_1_1_C_1_1_C_3_1" "C_3_1_N_2_2_S_2_1" "N_2_1_N_2_2_S_2_1" 
               C_25                C_26 
            "C_3_1"             "C_3_1" 

$CMP4
                S_1                 O_2                 O_3                 O_4 
      "C_2_1_C_3_1"             "C_3_2"             "C_3_2"             "C_3_2" 
                O_5                 O_6                 N_7                 N_8 
      "C_1_1_C_3_1"       "C_1_1_C_3_1" "C_2_1_C_3_1_C_3_1" "C_1_1_C_3_1_C_3_1" 
                N_9                N_10                N_11                C_12 
"C_1_1_C_3_1_C_3_1"       "C_3_1_C_3_2"       "C_2_1_C_3_1" "C_3_1_C_3_2_N_3_1" 
               C_13                C_14                C_15                C_16 
"C_3_2_N_2_1_N_3_1"       "C_1_1_N_3_1" "N_2_2_N_3_1_S_2_1" "C_3_1_N_3_1_O_1_2" 
               C_17                C_18                C_19                C_20 
"N_3_1_N_3_1_O_1_2"             "N_3_1"             "C_2_1"             "N_3_1" 
               C_21                C_22                C_23                C_24 
      "C_2_1_C_3_1"       "C_3_1_S_2_1"       "C_2_1_N_2_1" "C_2_1_C_2_1_C_2_2" 
               C_25                C_26                C_27                C_28 
"C_2_1_N_2_1_O_1_2"       "C_3_1_C_3_2"       "C_2_2_C_3_1" "C_2_1_C_3_2_O_2_1" 
               C_29                C_30                C_31                C_32 
"C_2_1_C_3_2_O_2_1"       "C_2_2_C_3_1"             "O_2_1"             "O_2_1" 

ChemmineR documentation built on May 2, 2018, 2:32 a.m.