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A program for extracting and aligning molecular pharmacophores
Clojure
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src/alijn
test/alijn
.gitignore
CMAEvolutionStrategy.properties
README.markdown
feature.parameters
feature.parameters.no-steric
log4j.properties
project.clj

README.markdown

alijn

A program for extracting and aligning molecular pharmacophores.

Usage

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.

Installation

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.

License

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