Query Chemical Identifier Resolver Images

A interface to the Chemical Identifier Resolver (CIR). (https://cactus.nci.nih.gov/chemical/structure_documentation).

Usage

cir_img(
  query,
  dir,
  format = c("png", "gif"),
  width = 500,
  height = 500,
  linewidth = 2,
  symbolfontsize = 16,
  bgcolor = NULL,
  antialiasing = TRUE,
  atomcolor = NULL,
  bondcolor = NULL,
  csymbol = c("special", "all"),
  hsymbol = c("special", "all"),
  hcolor = NULL,
  header = NULL,
  footer = NULL,
  frame = NULL,
  verbose = getOption("verbose"),
  ...
)

Arguments

query: character; Search term. Can be any common chemical identifier (e.g. CAS, INCHI(KEY), SMILES etc.)
dir: character; Directory to save the image.
format: character; Output format of the image. Can be one of "png", "gif".
width: integer; Width of the image.
height: integer; Height of the image.
linewidth: integer; Width of lines.
symbolfontsize: integer; Fontsize of atoms in the image.
bgcolor: character; E.g. transparent, white, %23AADDEE
antialiasing: logical; Should antialiasing be used?
atomcolor: character; Color of the atoms in the image.
bondcolor: character; Color of the atom bond lines.
csymbol: character; Can be one of "special" (default - i.e. only hydrogen atoms in functional groups or defining stereochemistry) or "all".
hsymbol: character; Can be one of "special" (default - i.e. none are shown) or "all" (all are printed).
hcolor: character; Color of the hydrogen atoms.
header: character; Should a header text be added to the image? Can be any string.
footer: character; Should a footer text be added to the image? Can be any string.
frame: integer; Should a frame be plotted? Can be on of NULL (default) or 1.
verbose: logical; Should a verbose output be printed on the console?
...: currently not used.

Value

image written to disk

Details

CIR can resolve can be of the following identifier: Chemical Names, IUPAC names, CAS Numbers, SMILES strings, IUPAC InChI/InChIKeys, NCI/CADD Identifiers, CACTVS HASHISY, NSC number, PubChem SID, ZINC Code, ChemSpider ID, ChemNavigator SID, eMolecule VID.

For an image with transparent background use ‘transparent’ as color name and switch off antialiasing (i.e. antialiasing = 0).

Note

You can only make 1 request per second (this is a hard-coded feature).

References

cir relies on the great CIR web service created by the CADD Group at NCI/NIH!
https://cactus.nci.nih.gov/chemical/structure_documentation,
https://cactus.nci.nih.gov/blog/?cat=10,
https://cactus.nci.nih.gov/blog/?p=1386,
https://cactus.nci.nih.gov/blog/?p=1456,

Examples

if (FALSE) { # \dontrun{
# might fail if API is not available
cir_img("CCO", dir = tempdir()) # SMILES

# multiple query strings and different formats
query = c("Glyphosate", "Isoproturon", "BSYNRYMUTXBXSQ-UHFFFAOYSA-N")
cir_img(query, dir = tempdir(), bgcolor = "transparent", antialising = 0)

# all parameters
query  = "Triclosan"
cir_img(query,
        dir = tempdir(),
        format = "png",
        width = 600,
        height = 600,
        linewidth = 5,
        symbolfontsize = 30,
        bgcolor = "red",
        antialiasing = FALSE,
        atomcolor = "green",
        bondcolor = "yellow",
        csymbol = "all",
        hsymbol = "all",
        hcolor = "purple",
        header = "My funky chemical structure..",
        footer = "..is just so awesome!",
        frame = 1,
        verbose = getOption("verbose"))
} # }