mm-dev

This repository is an incubating area for new methods for the mmtf-spark project.

Installation

Prerequisites

Install mmtf-spark, its prerequisites, and download MMTF-Hadoop Sequence files mmtf-spark installation guide.

Install mm-dev

Clone the mm-dev repository and build the project using Maven.

cd INSTALL_PATH
git clone https://github.com/sbl-sdsc/mm-dev.git
cd mm-dev
mvn install

The install goal will compile, test, and package the project’s code and then copy it into the local dependency repository, which Maven maintains on your local machine.

Run a Demo Application using spark-submit

This demo shows how calculate bridging water interactions between a ligand and a protein in the PDB.

Note: On Windows, use "" instead of "/" in the command below.

spark-submit --master local --class edu.sdsc.mm.dev.interactions.demos.WaterInteractions  INSTALL_PATH/mm-dev/target/mm-dev-0.0.1-SNAPSHOT.jar -r 2.0 -d 3.0 -b 1.645 -min 4 -max 4 -o water

The option --class specifies the class path and name of the main class (WaterInteractions)

The options after the .jar file are command line arguments for WaterInteractions:

     -r 2.0: maximum resolution of structure

     -d 3.0: maximum distance for interactions

     -b 1.645: maximum normalized b-factor (this z-score corresponds to the 90% confidence interval)

     -min 4: minimum number of interactions

     -max 4: maximum number of interactions

     -w: include other waters as interaction partners (not used in this example)

     -o: path to output directory