/chemical/structure Blog

As you might already have found out, the Chemical Identifier Resolver allows to create a GIF image from a Standard InChIKey very easily:

http://cactus.nci.nih.gov/chemical/structure/InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N/image

The same  can be done for any chemical structure identifier accepted by the Resolver:

http://cactus.nci.nih.gov/chemical/structure/morphine/image

http://cactus.nci.nih.gov/chemical/structure/InChI=InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H/image

http://cactus.nci.nih.gov/chemical/structure/CC(=O)Oc1ccccc1C(O)=O/image

The images are all created by CACTVS. So far, the service returned always a 250×250 GIF image but for the generation of structure images you might of course ask for more control about how the structure image is to be created.  So we added a few (URL) options to the image method of the Resolver. For instance, the following image has just been created from the URL shown in the caption:

More options are:

Create a PNG image instead of GIF:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?format=png

Change width, height, linewidth and fontsize:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?width=500&height=500&linewidth=2&symbolfontsize=16

Add some background color:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?bgcolor=yellow

You can also use the html hex code color codes (the ‘#’ character has to be URL-escaped as ‘%23′ in this case):

ttp://cactus.nci.nih.gov/chemical/structure/aspirin/image?bgcolor=%23AADDEE

For an image with transparent background use ‘transparent’ as color name and switch off antialiasing:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?bgcolor=transparent&antialiasing=0

Show black atom labels instead of the default color scheme for the different atom element types:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?atomcolor=black

Control which hydrogen atoms are shown:

The default values is special, i.e. only hydrogen atoms in functional groups or defining stereochemistry are shown.

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?hsymbol=special

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?hsymbol=all

Control how carbon atoms are shown:
The default values is special, if all is used all carbon atoms are shown as atom symbol:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?csymbol=special

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?csymbol=all

Change the colors for hydrogen atoms:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?hcolor=gray

Use another color for bonds:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?bondcolor=red

Show R/S stereo labels:

http://cactus.nci.nih.gov/chemical/structure/taxol/image?showstereo=0

http://cactus.nci.nih.gov/chemical/structure/taxol/image?showstereo=1

Add some text to the image:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?header="Aspirin on the top"

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?footer="Aspirin on the bottom"

Add a frame:

http://cactus.nci.nih.gov/chemical/structure/aspirin/image?frame=1

There are more options and we will document them more exhaustively later. If you are familiar with all options CACTVS has available for controlling the GIF/PNG generation, try them – chances are good that they might work. Please also visit our GIF Generator at http://cactus.nci.nih.gov.

We’d like to present a new feature of the Chemical Identifier Resolver: in addition to the already available SD file format representation

http://cactus.nci.nih.gov/chemical/structure/aspirin/sdf

the service can now represent a structure (identifier) also in many different text-based structure (file) formats. The general URL format is:

http://cactus.nci.nih.gov/chemical/structure/"identifier"/file?format="format"

The different chemical structure representations are generated by the chemoinformatic toolkit CACTVS. Although CACTVS can offer a whole lot more formats (including binary ones) we make the following (few) available here:

alc (Alchemy format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=alc

cdxml (CambridgeSoft ChemDraw XML format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cdxml

cerius (MSI Cerius II format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cerius

charmm (Chemistry at HARvard Macromolecular Mechanics file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=charmm

cif (Crystallographic Information File)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cif

cml (Chemical Markup Language)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cml

ctx (Gasteiger Clear Text format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=ctx

gjf (Gaussian input data file)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=gjf

gromacs (GROMACS file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=gromacs

hyperchem (HyperChem file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=hyperchem

jme (Java Molecule Editor format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=jme

maestro (Schroedinger MacroModel structure file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=maestro

mol (Symyx molecule file)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=mol

mol2 (Tripos Sybyl MOL2 format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sybyl2
http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=mol2

mrv (ChemAxon MRV format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=mrv

pdb (Protein Data Bank)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=pdb

sdf (Symyx Structure Data Format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sdf

sdf3000 (Symyx Structure Data Format 3000)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sdf3000

sln (SYBYL Line Notation)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sln

smiles (SMILES)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=smile

xyz (xyz file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=xyz

All these workof course also with Standard InChIKey, SMILES or NCI/CADD Identifier as structure identifier:

http://cactus.nci.nih.gov/chemical/structure/InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N/file?format=pdb

http://cactus.nci.nih.gov/chemical/structure/CC(=O)Oc1ccccc1C(O)=O/file?format=mrv

http://cactus.nci.nih.gov/chemical/structure/045DA3288E1A0233-FICuS-01-39/file?format=cml