This repository is an incubating area for new methods for the mmtf-spark project.
Install mmtf-spark, its prerequisites, and download MMTF-Hadoop Sequence files mmtf-spark installation guide.
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.
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