plotStruc: Plot compound structures
In ChemmineR: Cheminformatics Toolkit for R
Description
Usage
Arguments
Details
Value
Note
Author(s)
References
See Also
Examples
Description
Plots compound structure(s) for molecules stored in SDF and SDFset containers.
Usage
1
2
3
4
5
6
7
Arguments
sdf
Object of class SDF
atomcex
Font size for atom labels
atomnum
If TRUE, then the atom numbers are included in the plot. They are the position numbers of each atom in the atom block of an SDF.
no_print_atoms
Excludes specified atoms from being plotted.
noHbonds
If TRUE, then the C-hydrogens and their bonds - explicitly defined in an SDF - are excluded from the plot.
bondspacer
Numeric value specifying the plotting distance for double/triple bonds.
colbonds
Highlighting of subgraphs in main structure by providing a numeric vector of atom numbers, here position index in atom block.
The bonds of connected atoms will be plotted in the color provided under bondcol.
bondcol
A character or numeric vector of length one to specify the color to use for substructure highlighting under colbonds.
regenCoords
If ChemmineOB is installed and this option is TRUE, then Open
Babel will be used to re-generate the 2D coords for each
compound before plotting it. This often results in a nicer
layout. If you want to save the results of the coord
re-generation, call the regenerateCoords function
first yourself and save the result.
...
Arguments to be passed to/from other methods.
Details
The function plotStruc depicts a single 2D compound structure based
on the XY-coordinates specified in the atom block of an SDF. The generic method
plot can be used as a convenient shorthand to plot one or many
structures at once. Both functions depend on the availability of the
XY-coordinates in the source SD file and only 2D (not 3D) representations are plotted
correctly.
Additional arguments that can only be passed on to the plot function when supplied with
an SDFset object:
griddim: numeric vector of length two to define the dimensions for arranging several structures in one plot.
print_cid: character vector for printing custom compound labels. Default is print_cid=cid(sdfset).
print: if print=TRUE, then a summary of the SDF content for each supplied compound is printed to the screen.
This behavior is turned off with print=TRUE.
Value
Prints summary of SDF/SDFset to screen and plots their structures to graphics device.
Note
The compound depictions created by this function are not as pretty as the structure representations generated with the sdf.visualize function. This will be improved in the future.
Author(s)
Thomas Girke
References
...
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
## Import SDFset sample set
data(sdfsample)
(sdfset <- sdfsample)
## Plot single compound structure
plotStruc(sdfset[[1]])
## Plot several compounds structures
plot(sdfset[1:4])
## Highlighting substructures (here all rings)
myrings <- as.numeric(gsub(".*_", "", unique(unlist(rings(sdfset[1])))))
plot(sdfset[1], colbonds=myrings)
## Customize plot
plot(sdfset[1:4], griddim=c(2,2), print_cid=letters[1:4], print=FALSE, noHbonds=FALSE)
Example output
An instance of "SDFset" with 100 molecules
$CMP1
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
O_1 7.0468 0.0839 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 12.2708 1.0492 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_60 1.8411 -1.5985 0 0 0 0 0 0 0 0 0 0 0 0 0
H_61 2.6597 -1.2843 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 16 2 0 0 0 0
2 2 23 1 0 0 0 0
... ... ... ... ... ... ... ...
63 33 60 1 0 0 0 0
64 33 61 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650001" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"700" "7"
"..."
$CMP2
An instance of "SDF"
<<header>>
Molecule_Name
"650002"
Source
" -OEChem-07071010512D"
Comment
""
Counts_Line
" 49 51 0 0 0 0 0 0 0999 V2000"
<<atomblock>>
C1 C2 C3 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16
O_1 3.732 0.997 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 2 -2.003 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_48 10.6863 2.6555 0 0 0 0 0 0 0 0 0 0 0 0 0
H_49 10.4379 -3.272 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 15 2 0 0 0 0
2 2 18 2 0 0 0 0
... ... ... ... ... ... ... ...
50 25 47 1 0 0 0 0
51 26 48 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650002" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"497" "5"
"..."
$CMP3
An instance of "SDF"
<<header>>
Molecule_Name
"650003"
Source
" -OEChem-07071010512D"
Comment
""
Counts_Line
" 44 47 0 0 0 0 0 0 0999 V2000"
<<atomblock>>
C1 C2 C3 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16
S_1 4.326 1.9917 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 2.5369 -1.0961 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_43 2.4361 3.5824 0 0 0 0 0 0 0 0 0 0 0 0 0
H_44 3.1175 3.0307 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 23 1 0 0 0 0
2 1 24 1 0 0 0 0
... ... ... ... ... ... ... ...
46 26 43 1 0 0 0 0
47 26 44 1 0 0 0 0
<<datablock>> (28 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650003" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"638" "6"
"..."
$CMP4
An instance of "SDF"
<<header>>
Molecule_Name
"650004"
Source
" -OEChem-07071010512D"
Comment
""
Counts_Line
" 59 61 0 0 0 0 0 0 0999 V2000"
<<atomblock>>
C1 C2 C3 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16
S_1 7.1279 1.5981 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 3.732 3.5981 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_58 15.4379 0.403 0 0 0 0 0 0 0 0 0 0 0 0 0
H_59 14.591 0.176 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 15 1 0 0 0 0
2 1 22 1 0 0 0 0
... ... ... ... ... ... ... ...
60 32 58 1 0 0 0 0
61 32 59 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650004" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"698" "6"
"..."
$CMP1
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
O_1 7.0468 0.0839 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 12.2708 1.0492 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_60 1.8411 -1.5985 0 0 0 0 0 0 0 0 0 0 0 0 0
H_61 2.6597 -1.2843 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 16 2 0 0 0 0
2 2 23 1 0 0 0 0
... ... ... ... ... ... ... ...
63 33 60 1 0 0 0 0
64 33 61 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650001" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"700" "7"
"..."
ChemmineR documentation built on Feb. 28, 2021, 2:02 a.m.
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Description Usage Arguments Details Value Note Author(s) References See Also Examples
Description
Plots compound structure(s) for molecules stored in SDF and SDFset containers.
Usage
1 2 3 4 5 6 7 |
Arguments
sdf |
Object of class |
atomcex |
Font size for atom labels |
atomnum |
If |
no_print_atoms |
Excludes specified atoms from being plotted. |
noHbonds |
If |
bondspacer |
Numeric value specifying the plotting distance for double/triple bonds. |
colbonds |
Highlighting of subgraphs in main structure by providing a numeric vector of atom numbers, here position index in atom block.
The bonds of connected atoms will be plotted in the color provided under |
bondcol |
A character or numeric vector of length one to specify the color to use for substructure highlighting under |
regenCoords |
If ChemmineOB is installed and this option is TRUE, then Open
Babel will be used to re-generate the 2D coords for each
compound before plotting it. This often results in a nicer
layout. If you want to save the results of the coord
re-generation, call the |
... |
Arguments to be passed to/from other methods. |
Details
The function plotStruc depicts a single 2D compound structure based
on the XY-coordinates specified in the atom block of an SDF. The generic method
plot can be used as a convenient shorthand to plot one or many
structures at once. Both functions depend on the availability of the
XY-coordinates in the source SD file and only 2D (not 3D) representations are plotted
correctly.
Additional arguments that can only be passed on to the plot function when supplied with
an SDFset object:
griddim: numeric vector of length two to define the dimensions for arranging several structures in one plot.
print_cid: character vector for printing custom compound labels. Default is print_cid=cid(sdfset).
print: if print=TRUE, then a summary of the SDF content for each supplied compound is printed to the screen.
This behavior is turned off with print=TRUE.
Value
Prints summary of SDF/SDFset to screen and plots their structures to graphics device.
Note
The compound depictions created by this function are not as pretty as the structure representations generated with the sdf.visualize function. This will be improved in the future.
Author(s)
Thomas Girke
References
...
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Import SDFset sample set
data(sdfsample)
(sdfset <- sdfsample)
## Plot single compound structure
plotStruc(sdfset[[1]])
## Plot several compounds structures
plot(sdfset[1:4])
## Highlighting substructures (here all rings)
myrings <- as.numeric(gsub(".*_", "", unique(unlist(rings(sdfset[1])))))
plot(sdfset[1], colbonds=myrings)
## Customize plot
plot(sdfset[1:4], griddim=c(2,2), print_cid=letters[1:4], print=FALSE, noHbonds=FALSE)
|
Example output
An instance of "SDFset" with 100 molecules
$CMP1
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
O_1 7.0468 0.0839 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 12.2708 1.0492 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_60 1.8411 -1.5985 0 0 0 0 0 0 0 0 0 0 0 0 0
H_61 2.6597 -1.2843 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 16 2 0 0 0 0
2 2 23 1 0 0 0 0
... ... ... ... ... ... ... ...
63 33 60 1 0 0 0 0
64 33 61 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650001" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"700" "7"
"..."
$CMP2
An instance of "SDF"
<<header>>
Molecule_Name
"650002"
Source
" -OEChem-07071010512D"
Comment
""
Counts_Line
" 49 51 0 0 0 0 0 0 0999 V2000"
<<atomblock>>
C1 C2 C3 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16
O_1 3.732 0.997 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 2 -2.003 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_48 10.6863 2.6555 0 0 0 0 0 0 0 0 0 0 0 0 0
H_49 10.4379 -3.272 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 15 2 0 0 0 0
2 2 18 2 0 0 0 0
... ... ... ... ... ... ... ...
50 25 47 1 0 0 0 0
51 26 48 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650002" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"497" "5"
"..."
$CMP3
An instance of "SDF"
<<header>>
Molecule_Name
"650003"
Source
" -OEChem-07071010512D"
Comment
""
Counts_Line
" 44 47 0 0 0 0 0 0 0999 V2000"
<<atomblock>>
C1 C2 C3 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16
S_1 4.326 1.9917 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 2.5369 -1.0961 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_43 2.4361 3.5824 0 0 0 0 0 0 0 0 0 0 0 0 0
H_44 3.1175 3.0307 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 23 1 0 0 0 0
2 1 24 1 0 0 0 0
... ... ... ... ... ... ... ...
46 26 43 1 0 0 0 0
47 26 44 1 0 0 0 0
<<datablock>> (28 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650003" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"638" "6"
"..."
$CMP4
An instance of "SDF"
<<header>>
Molecule_Name
"650004"
Source
" -OEChem-07071010512D"
Comment
""
Counts_Line
" 59 61 0 0 0 0 0 0 0999 V2000"
<<atomblock>>
C1 C2 C3 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16
S_1 7.1279 1.5981 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 3.732 3.5981 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_58 15.4379 0.403 0 0 0 0 0 0 0 0 0 0 0 0 0
H_59 14.591 0.176 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 15 1 0 0 0 0
2 1 22 1 0 0 0 0
... ... ... ... ... ... ... ...
60 32 58 1 0 0 0 0
61 32 59 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650004" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"698" "6"
"..."
$CMP1
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
O_1 7.0468 0.0839 0 0 0 0 0 0 0 0 0 0 0 0 0
O_2 12.2708 1.0492 0 0 0 0 0 0 0 0 0 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
H_60 1.8411 -1.5985 0 0 0 0 0 0 0 0 0 0 0 0 0
H_61 2.6597 -1.2843 0 0 0 0 0 0 0 0 0 0 0 0 0
<<bondblock>>
C1 C2 C3 C4 C5 C6 C7
1 1 16 2 0 0 0 0
2 2 23 1 0 0 0 0
... ... ... ... ... ... ... ...
63 33 60 1 0 0 0 0
64 33 61 1 0 0 0 0
<<datablock>> (33 data items)
PUBCHEM_COMPOUND_CID PUBCHEM_COMPOUND_CANONICALIZED
"650001" "1"
PUBCHEM_CACTVS_COMPLEXITY PUBCHEM_CACTVS_HBOND_ACCEPTOR
"700" "7"
"..."
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