/chemical/structure Blog

Unfortunately, there was a problem with the Resolver the last few days. It reacted very slow to any kind of request. As a matter of fact, those things always seems to pop up when your are out of town and it got proven this time again. It is fixed by now, so we apologize for any inconveniences this might have created.

On an additional note: we have some scheduled database updates the next few days, so the service might react a little bit slower again – however – not even close to the extent it has been the previous days (which was a software bug combined with a network problem – and both worked “perfectly” together)

We run an update of the Chemical Identifier Resolver database tonight which grew the number of chemical structures known by the service quite a bit. The number of Standard InChIKeys indexed with their respective full structure representations is now approx. 93 million (92,939,226 to be exact). The service uses this index to work as an Standard InChIKey Resolver, e.g.

http://cactus.nci.nih.gov/chemical/structure/InChIKey=RZVAJINKPMORJF-UHFFFAOYSA-N/file?format=sdf
http://cactus.nci.nih.gov/chemical/structure/InChIKey=RZVAJINKPMORJF-UHFFFAOYSA-N/file?format=cdxml
http://cactus.nci.nih.gov/chemical/structure/InChIKey=RZVAJINKPMORJF-UHFFFAOYSA-N/smiles

Sorry, the Chemical Identifier Resolver currently might suffer hiccups from time to time, i.e. might react slow or with an error message – we are working on a larger update of the service.  I hope it will be finished tonight.

Markus

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:

http://cactus.nci.nih.gov/chemical/structure/InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N/image?footer=BSYNRYMUTXBXSQ-UHFFFAOYSA-N&width=500

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 which CACTVS has available for controlling the GIF/PNG generation try them – changes are good that they might work. Please visit also 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

We had the CCL and CHMINF-L announcement of our new service yesterday and the service “survived” ~100.000 requests during  its first day – admittedly, among all the ~100 visitors so far – it were a few power users who apparently fell in love with this service immediately.

Thanks to all of you for your interest,

Markus

The Chemical Identifier Resolver at http://cactus.nci.nih.gov/chemical/structure

This new service on http://cactus.nci.nih.gov is a resolver for different chemical structure representations and identifiers, including those that do not carry any information about the structure itself. For instance, it can work as a Standard InChIKey Resolver, an NCI/CADD Identifier Resolver or a Chemical Name Resolver. The service also allows one to convert a given structure identifier into another representation or structure identifier.

Representations/identifiers supported are: Standard InChI/InChIKey, NCI/CADD Identifiers (FICuS, FICTS, uuuuu), SMILES, SDF, names, and a few other types of IDs.  See the web page for more information.

For those identifiers that require lookup, the underlying database currently contains about 67 million unique structure records, from which the respective Standard InChIKeys and NCI/CADD Identifiers have been calculated. For lookup by chemical names, 68 million names associated with 16 million unique structure records are currently available in the database. The database continues to grow.

Closely related are the new capabilities of resolving/converting chemical structure identifiers by simply using a URL adhering to the following scheme:

http://cactus.nci.nih.gov/chemical/structure/"structure identifier"/"representation"[/xml]

We just list a few examples here that should give you an idea of what’s possible with this service.  For more detailed explanations, see the above web page.

Example: Standard InChI for chemical name string “aspirin“:

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

http://cactus.nci.nih.gov/chemical/structure/aspirin/stdinchi/xml

Example: Standard InChIKey of “ethanol” specified as SMILES string “CCO“:

http://cactus.nci.nih.gov/chemical/structure/CCO/stdinchikey

Example: Unique SMILES string of chemical name string “benzene“:

http://cactus.nci.nih.gov/chemical/structure/benzene/smiles

Example: SD File for chemical name string “morphine“:

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

Example: Chemical names for Standard InChIKey ”InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N” (Standard InChIKey of “ethanol“):

http://cactus.nci.nih.gov/chemical/structure/InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N/names

Example: Synonyms for chemical name string “aspirin“:

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

Hi, this is a new blog. We  will use it to present a series of new web services that we are currently working on.