https://github.com/biojava/biojava-spark

:collision: Algorithms that are built around BioJava and run on Apache Spark
https://github.com/biojava/biojava-spark

Last synced: about 1 month ago
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:collision: Algorithms that are built around BioJava and run on Apache Spark

• Host: GitHub
• URL: https://github.com/biojava/biojava-spark
• Owner: biojava
• License: lgpl-2.1
• Created: 2016-04-29T18:06:39.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2022-01-10T21:08:11.000Z (about 4 years ago)
• Last Synced: 2025-09-09T16:34:49.590Z (6 months ago)
• Language: Java
• Homepage:
• Size: 64.7 MB
• Stars: 8
• Watchers: 10
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# BioJava-Spark

Algorithms that are built around BioJava and are running on Apache Spark

[![Build Status](https://travis-ci.org/biojava/biojava-spark.svg?branch=master)](https://travis-ci.org/biojava/biojava-spark)

[![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE)

[![Status](http://img.shields.io/badge/status-experimental-red.svg?style=flat)](https://github.com/biojava/biojava-spark)

[![Version](http://img.shields.io/badge/version-0.2.1-blue.svg?style=flat)](https://github.com/biojava/biojava-spark/)

## Starting up

### Some initial instructions can be found on the mmtf-spark project

https://github.com/sbl-sdsc/mmtf-spark

## First download and untar a Hadoop sequence file of the PDB (~7 GB download) 

```bash

wget http://mmtf.rcsb.org/v1.0/hadoopfiles/full.tar

tar -xvf full.tar

```

Or you can get a C-alpha, phosphate, ligand only version (~800 Mb download)

```bash

wget http://mmtf.rcsb.org/v1.0/hadoopfiles/reduced.tar

tar -xvf reduced.tar

```

### Second add the biojava-spark dependecy to your pom

```xml

	org.biojava

	biojava-spark

	0.2.1

```

## Extra Biojava examples

### Do some simple quality filtering

```java

float maxResolution = 3.0f;

float maxRfree = 0.3f;

StructureDataRDD structureData = new StructureDataRDD("/path/to/file")

			.filterResolution(maxResolution)

			.filterRfree(maxRfree);

```

### Summarsing the elements in the PDB

```java

Map elementCountMap = BiojavaSparkUtils.findAtoms(structureData).countByElement();

```

### Finding inter-atomic contacts from the PDB

```java

Double mean = BiojavaSparkUtils.findContacts(structureData,

		new AtomSelectObject()

				.groupNameList(new String[] {"PRO","LYS"})

				.elementNameList(new String[] {"C"})

				.atomNameList(new String[] {"CA"}),

				cutoff)

		.getDistanceDistOfAtomInts("CA", "CA")

		.mean();

System.out.println("\nMean PRO-LYS CA-CA distance: " + mean);

```