mcs2sdfset: Return MCS object as SDFset

In fmcsR: Mismatch Tolerant Maximum Common Substructure Searching

Description

Helper function to run atomsubset from ChemmineR library on MCS objects in order to obtain their results in SDFset format.

Usage

mcs2sdfset(x, ...)

Arguments

x	Object of class MCS
...	Arguments to be passed to/from other methods.

Details

Returns MCS data in form of a list containing two SDFset objects, one for the query and one for the target structure.

Value

List with two SDFset objects.

Note

...

Author(s)

Thomas Girke

References

...

See Also

fmcs

Examples

library(fmcsR)
data(sdfsample)
sdfset <- sdfsample
mcs <- fmcs(sdfset[[1]], sdfset[[2]], au=2, bu=1, matching.mode="aromatic")
mcs2sdfset(x=mcs, type="new")
mcs2sdfset(x=mcs, type="old")[[1]][[1]] 
plot(mcs2sdfset(x=mcs, type="new")[[1]][1]) 

Example output

Loading required package: ChemmineR
$query
An instance of "SDFset" with 4 molecules

$target
An instance of "SDFset" with 4 molecules

An instance of "SDF"

<<header>>
                            Molecule_Name 
                                 "650001" 
                                   Source 
                 "  -OEChem-07071010512D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 61 64  0     0  0  0  0  0  0999 V2000" 

<<atomblock>>
          C1      C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13 C14 C15 C16
N_7   7.9128 -1.4161   0   0   0   0   0   0   0   0   0   0   0   0   0
C_11  7.0468 -1.9161   0   0   0   0   0   0   0   0   0   0   0   0   0
...      ...     ... ... ... ... ... ... ... ... ... ... ... ... ... ...
C_15  5.9641 -3.1186   0   0   0   0   0   0   0   0   0   0   0   0   0
C_23 11.3769  1.5839   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
10    1   2   1   0   0   0   0
11    1   4   1   0   0   0   0
... ... ... ... ... ... ... ...
47   14  12   2   0   0   0   0
51   12  11   1   0   0   0   0

<<datablock>> (0 data items)
character(0)
$CMP1_fmcs_1
An instance of "SDF"

<<header>>
                            Molecule_Name 
                                 "650001" 
                                   Source 
                 "  -OEChem-07071010512D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 14 14  0     0  0  0  0  0  0999 V2000" 

<<atomblock>>
          C1      C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13 C14 C15 C16
N_1   7.9128 -1.4161   0   0   0   0   0   0   0   0   0   0   0   0   0
C_2   7.0468 -1.9161   0   0   0   0   0   0   0   0   0   0   0   0   0
...      ...     ... ... ... ... ... ... ... ... ... ... ... ... ... ...
C_13  5.9641 -3.1186   0   0   0   0   0   0   0   0   0   0   0   0   0
C_14 11.3769  1.5839   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1   2   1   0   0   0   0
2     1   4   1   0   0   0   0
... ... ... ... ... ... ... ...
13   14  12   2   0   0   0   0
14   12  11   1   0   0   0   0

<<datablock>> (0 data items)
character(0)

fmcsR documentation built on Nov. 8, 2020, 6:57 p.m.