UNM_BIOCOMP_HSCAF

Implements the HierS hierarchical scaffold algorithm (Wilkens, 2005). Designed for HierS scaffold analysis, for single molecules, datasets, or common-scaffold comparisons between pairs or groups of molecules.

Dependencies

• Java 8
• Maven 3.5+
• unm_biocomp_depict
• unm_biocomp_util
• ChemAxon JChem (19.3.0 ok)
• Access to ChemAxon Maven repository (see documentation).
  • Requires ChemAxon-Hub Artifactory credentials.

Compiling

mvn clean install

Deploying HSCAF

mvn --projects hscaf_war tomcat7:deploy

or

mvn --projects hscaf_war tomcat7:redeploy

Usage

java -classpath unm_biocomp_hscaf-0.0.1-SNAPSHOT-jar-with-dependencies.jar edu.unm.health.biocomp.hscaf.hier_scaffolds -i hscaf_testset.smi -inc_mol -inc_scaf -o hscaf_testset_out.smi -out_scaf hscaf_testset_scaf.smi -vvv

java -classpath unm_biocomp_hscaf-0.0.1-SNAPSHOT-jar-with-dependencies.jar edu.unm.health.biocomp.hscaf.bm_scaffolds -i hscaf_testset.smi

Developed at the UNM Translational Informatics Division.

• Public web app
• HierS: hierarchical scaffold clustering using topological chemical graphs. Wilkens SJ(1), Janes J, Su AI. J Med Chem. 2005 May 5;48(9):3182-93.