Ultrafast Shape Recognition with CREDO Atom Types (USRCAT)
USRCAT is an extension of the Ultrafast Shape Recognition
(USR) algorithm that includes pharmacophoric information.
There are several ways to install USRCAT. The recommended method is to run
$ python setup.py install
Another option is to simply add the usrcat subfolder source to your
After successful installation functions from the package can be easily be imported
with something like
# use RDKit as backend for USRCAT from usrcat.toolkits.rd import generate_moments
USRCAT is written in the Python programming language
and tested with version 2.7 but should also work with 2.6. The following Python
modules are required: NumPy and SciPy.
Also required are the Python bindings for at least one of the supported cheminformatics
toolkits. Currently supported are OEChem and RDKit.
The following code shows an example of how to generate the USRCAT moments with
RDKit as cheminformatics backend:
from rdkit import Chem from rdkit.Chem import AllChem from usrcat.toolkits.rd import generate_moments # Imatinib molecule = Chem.MolFromSmiles('Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)C[NH+]5CC[NH+](CC5)C') # generate 10 conformers AllChem.EmbedMultipleConfs(molecule) # generates the USRCAT moments for all conformers moments = generate_moments(molecule)
Code contributions to implement USRCAT with other chemical toolkits (or to
improve the existing code) are much appreciated. Please see the existing function
based on OpenEye's OEChem toolkit as an example of how to implement the USRCAT
USRCAT is released under the MIT License.