rcsb/qsa

Quick Structural Alignment

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Note this repository has been archived because it is not actively maintained anymore.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.

How to run

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).