A program for extracting and aligning molecular pharmacophores.
Included with the program is an example defintion of features (data/example/features.smarts) and a set of 11 known binders to comt (data/example/comt_subset.sdf).
The feature definitions are extraced from the Daylight online manual and the comt binders are taken from the Directory of Usefull Decoys.
To see a command line usage instruction use lein run --help.
To try the enclosed example type
lein run align -s 1 -f data/example/features.smarts data/example/comt_subset.sdf
Be aware that the program is still quite buggy.
Requires leiningen. Requires CDK 1.3.5.git which I have not been able to find a maven repository with. To install in local repository first fork cdk from github and issue the commands
ant dist-large
mvn install:install-file -DgroupId=org.openscience -DartifactId=cdk -Dversion=1.3.5.git -Dpackaging=jar -Dfile=dist/jar/cdk-1.3.5.git.jar
Requires jama-1.0.1.jar (google for it) which can be installed by issuing
mvn install:install-file -DgroupId=jama -DartifactId=jama -Dversion=1.0.1 -Dpackaging=jar -Dfile=jama-1.0.1.jar
After having installed leiningen and cloned the project, issue the following:
lein deps
lein native-deps
The program is now ready to run.
Not added yet.