webchem (version 1.1.1)

cir_img: Query Chemical Identifier Resolver Images

Description

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 = TRUE,
  ...
)

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 <U+2018>transparent<U+2019> as color name and switch off antialiasing (i.e. antialiasing = 0).

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

# NOT RUN {
# 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 = TRUE)
# }