cir_img: Query Chemical Identifier Resolver Images

In ropensci/webchem: Chemical Information from the Web

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 = 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.

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).

Value

image written to disk

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

## 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 = getOption("verbose"))

## End(Not run)

ropensci/webchem documentation built on Feb. 23, 2024, 6:28 p.m.