Note
Note this repository has been archived because it is not actively maintained anymore.
This repository contains the code for topology-independent structure similarity search and alignment.
The best way is to use Maven.
Where to download Maven
How to install Maven
Update code and compile:
git clone https://github.com/rcsb/qsa.git
cd qsa
mvn install
Specify memory (Linux, MacOS):
MAVEN_OPTS=-Xmx12g
Specify memory (Windows):
SET MAVEN_OPTS=-Xmx12g
Run:
mvn exec:java -Dexec.mainClass="analysis.Job" -Dexec.args="-h data"
Parameters are in the file data/parameters.txt. Results will be in data/jobs. Alignment scores are summarized in the file table.csv. The file alignments.py visualizes alignments in PyMOL (after association with the program, this can be done by double clicking the file).