I also provide mod_python based services. See here for more details.
Currently, this site does not host the services. See Servers to get a list of servers that host these services. The documentation for each service is independent of the actual server hosting the service.
The documentation for the various resources is currently manually generated. As a result, there's no practical way to generate code to use these services. In the future I'll probably provide a WADL document for the services. Of course, it is reminiscent of WSDL, which was something I wanted to move away from. See here for an interesting discussion.
If you would like to modify the services you can download cdkrest-src-0.5.tgz, cdkrest-src-0.5.zip. The code is licensed under the LGPL.
ant restTo see other options do
ant infoThe JAR file contains the services as well as the Noelios restlet engine to host the services. This makes hosting the Java based services very easy since all you need to do is to run the JAR file. By default, it will start a server located at
http://localhost:8182. You will likely want to start it on a specific
host and port as shown below
java -jar cdkrest.jar -p 6666 -s my.own.host -l services.logNot that this will block a terminal so you will likely want to use nohup and run it in the background. You can then visit any of the services described above as
http://my.own.host:6666/cdk/fingerprint/CCOCCCOFor this example you should see a single line of 1's and 0's in your browser.
Note that the depiction service provided by cdkrest.jar employs Swing and hence requires the X11 windowing system. If you plan to run these on a headless server an easy fix is to run a virtual framebuffer (such as Xvfb). In this case, the start up would look like:
Xvfb :2 -screen 1 800x600x16 & export DISPLAY=:2.1 nohup java -jar cdkrest.jar -p 6666 -s my.own.host -l services.log &In addition, it appears that the code tries to bind an ipv6 socket to an ipv4 address (as reported by Ola Spjuth). In such a case, adding
-Djava.net.preferIPv4Stack=trueto the command line should let it work.
Installation instructions for Gentoo Linux have been provided by Anders Lovgren and Ola Spjuth.
/cdk
/cdk/depict
/cdk/depict/{smiles}
/cdk/depict/{width}/{height}/{smiles}
/cdk/descriptors
/cdk/descriptors/{smiles}
/cdk/descriptor/{klass}
/cdk/descriptor/{klass}/{smiles}
/cdk/descriptor/tpsa/{smiles}
/cdk/descriptor/xlogp/{smiles}
/cdk/mw/{smiles}
/cdk/mf/{smiles}
/cdk/fingerprint
/cdk/fingerprint/{smiles}
/cdk/fingerprint/{type}/{smiles}
/cdk/substruct/{target}/{query}
/cdk/substruct
The convention employed by the following descriptions is as follows
| Function | Return 2D depictions of SMILES input |
| Accept | * |
| Return type | image/jpeg |
| URL | [GET] /cdk/depict/{smiles} |
{smiles} should be a valid SMILES string or a Base64 encoded
SMILES string (appropriately quoted). The resultant image will have
a width and height of 200 pixels respectively. |
|
| URL | [GET] /cdk/depict/{width}/{height}/{smiles} |
{smiles} should be a valid SMILES string or a Base64 encoded
SMILES string (appropriately quoted). {width} and
{height} should be integer values defining the width and height
of the resultant image |
|
| URL | [POST] /cdk/depict |
POST requests to this URL should include at least one form variable called
molecule containing a SMILES or SDF string. No Base64 encoding is
required. If no other form variable is specified the resultant image is
200x200. To get other dimensions you can specify width and
height as form variables, containing the desired width and height
as integers.
|
| Function | List or calculate molecular descriptors |
| Accept | text/plain * |
| Return type | text/plain text/xml |
| URL | [GET] /cdk/descriptors |
If text/plain is specified
in the "Accept" header, the return is a plain text document with each descriptor
resource on a separate line. Otherwise an XML document with multiple specification-ref
elements, whose href attribute is a link to the individual descriptor specification
resource. See below for more details.
|
|
| URL | [GET] /cdk/descriptors/{smiles} |
{smiles} should be a valid SMILES string.
If text/plain is specified
in the "Accept" header, the return is a plain text document with each descriptor
value resource on a separate line. Otherwise an XML document with multiple descriptor-ref
elements, whose href attribute is a link to the individual descriptor value resource.
See below for more details.
|
|
| URL | [GET] /cdk/descriptor/{klass} |
{klass} should be a fully qualified CDK molecular descriptor class. A list of classes
can be found here or alternatively, obtained from the service URL shown above.
This service ignores the "Accept" header and the Content-type of the result is always text/xml.
The XML result is a "descriptor specification", that provides information regarding the descriptor
implementation.
|
|
| URL | [GET] /cdk/descriptor/{klass}/{smiles} |
{klass} should be a fully qualified CDK molecular descriptor class. A list of classes
can be found here or alternatively, obtained from the service URL shown above.
{smiles} should be a valid SMILES string.
This service ignores the "Accept" header and the Content-type of the result is always text/xml.
The result is a document listing the value(s) of the descriptor (with the names of each descriptor
calculated) for the specified molecule
|
| Function | Return fingerprints for one or more molecules |
| Accept | * |
| Return type | text/plain |
| URL | [GET] /cdk/fingerprint/{smiles} |
{smiles} should be a valid SMILES or Base64 encoded SMILES string (appropriately quoted).
Will return a binary string (1's & 0's)
representation of the CDK path based fingerprint. The length of the string indicates the size
of the fingerpint |
|
| URL | [GET] /cdk/fingerprint/{type}/{smiles} |
{smiles} should be a valid SMILES or Base64 encoded SMILES string (appropriately quoted).
{type} can be one of
std, maccs or estate. Will return a binary string (1's & 0's)
representation of the fingerprint. The length of the string indicates the size
of the fingerpint |
|
| URL | [POST] /cdk/fingerprint |
POST requests to this URL should include two form variables. The first should be called smiles
and will be a comma separated string of SMILES. There is no need to Base64 encode these strings.
The second should be called type and will be one of
std, maccs or estate. The returned document will consist of N lines, where
N is the number of SMILES specified. Each line will be a binary string (1's & 0's)
representation of the fingerprint. The length of the string indicates the size
of the fingerpint.
An example Python client would be
import urllib2
import urllib
url = 'http://localhost:8182/cdk/fingerprint'
slist = ','.join(['CCC(=O)CC','c1ccccc1','C(=O)CC(=O)COC'])
values = {'smiles' : slist, 'type' : 'maccs' }
data = urllib.urlencode(values)
req = urllib2.Request(url, data)
resp = urllib2.urlopen(req)
print resp.read()
|
| Function | Evaluate molecular weight of a SMILES input |
| Accept | * |
| Return type | text/plain |
| URL | [GET] /cdk/mw/{smiles} |
{smiles} should be a valid SMILES or Base64 encoded SMILES string
(appropriately quoted) |
| Function | Evaluate molecular formula of a SMILES input |
| Accept | text/plain text/html |
| Return type | text/plain text/html |
| URL | [GET] /cdk/mf/{smiles} |
{smiles} should be a valid SMILES or Base64 encoded SMILES string
(appropriately quoted). If text/html is requested via
an Accept header, the result will be an HTML form of the formula (so numbers show as
subscripts or superscripts) |
| Function | Determine whether a substructure is present in a target molecule(s) |
| Accept | * |
| Return type | text/plain |
| URL | [GET] /cdk/substruct/{target}/{query} |
{target} should be a valid SMILES or Base64 encoded SMILES string
(appropriately quoted) and {query} should
be a SMARTS pattern or a SMILES string. If the query is present in the target, the result
is the string "true", otherwise "false".If the SMILES could not be parsed, the error code is
400
(BAD REQUEST) and the result is "fail". If there was an error during parsing the SMARTS the response
code is 500
(INTERNAL SERVER ERROR) and there is no result. |
|
| URL | [POST] /cdk/substruct |
POST requests to this URL should include two form variables. The first should be called target
and will be a comma separated string of SMILES. The second should be called query and will be
a SMARTS pattern or a SMILES string.The result will be a plain text document with N lines, for N SMILES strings. For each line, if the query is present in the target, the line will equal "true", otherwise "false".If the SMILES could not be parsed, the line will be "fail". If there was an error during parsing the SMARTS the response code is 500 (INTERNAL SERVER ERROR) and there is no result. An example Python client would be
import urllib2
import urllib
url = 'http://localhost:8182/cdk/substruct'
slist = ','.join(['CCC(=O)CC','c1ccccc1','C(=O)CC(=O)COC'])
values = {'target' : slist, 'query' : '[#6]=O' }
data = urllib.urlencode(values)
req = urllib2.Request(url, data)
resp = urllib2.urlopen(req)
print resp.read()
|
| Function | Returns the TPSA of a molecule |
| Accept | * |
| Return type | text/plain |
| URL | [GET] /cdk/descriptor/tpsa/{smiles} |
{smiles} should be a valid SMILES or Base64 encoded SMILES string
(appropriately encoded) |
| Function | Returns version information for the services |
| Accept | * |
| Return type | text/plain |
| URL | [GET] /cdk |
| Note that this provides information for the whole application rather than any individual service. The result is plain text listing the version of the services, JRE version and operating system |
| Function | Returns the XLogP of a molecule |
| Accept | * |
| Return type | text/plain |
| URL | [GET] /cdk/descriptor/xlogp/{smiles} |
{smiles} should be a valid SMILES or Base64 encoded SMILES string
(appropriately quoted) |
http://rest.rguha.net/threed/d3.py/get3d?smiles=c1ccccc1Structures are returned as SD files. Please note that this is a wimpy server and if it gets too loaded, I will disable the service. Feel free to download the code and run it locally (you'll need to install smi23d and change the paths in the Python file)
| Hostname | Contact |
|---|---|
| http://toposome.chemistry.drexel.edu:6666 | Rajarshi Guha, rajarshi.guha@gmail.com |
| http://ws1.bmc.uu.se:8182 | Ola Spjuth, ola.spjuth@farmbio.uu.se |