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mmtf-common

MMTF is a compressed, fast and useful format for serving macromolecular data.

License

License
GroupId

GroupId

org.rcsb
ArtifactId

ArtifactId

mmtf-common
Last Version

Last Version

0.0.1-alpha4
Release Date

Release Date
Type

Type

jar
Description

Description

mmtf-common
MMTF is a compressed, fast and useful format for serving macromolecular data.
Project URL

Project URL

http://maven.apache.org
Project Organization

Project Organization

RCSB PDB

Download mmtf-common

Filename Size
mmtf-common-0.0.1-alpha4.pom
mmtf-common-0.0.1-alpha4.jar 14 KB
mmtf-common-0.0.1-alpha4-sources.jar 13 KB
mmtf-common-0.0.1-alpha4-javadoc.jar 108 KB
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How to add to project

<!-- https://jarcasting.com/artifacts/org.rcsb/mmtf-common/ -->
<dependency>
    <groupId>org.rcsb</groupId>
    <artifactId>mmtf-common</artifactId>
    <version>0.0.1-alpha4</version>
</dependency>
// https://jarcasting.com/artifacts/org.rcsb/mmtf-common/
implementation 'org.rcsb:mmtf-common:0.0.1-alpha4'
// https://jarcasting.com/artifacts/org.rcsb/mmtf-common/
implementation ("org.rcsb:mmtf-common:0.0.1-alpha4")
'org.rcsb:mmtf-common:jar:0.0.1-alpha4'
<dependency org="org.rcsb" name="mmtf-common" rev="0.0.1-alpha4">
  <artifact name="mmtf-common" type="jar" />
</dependency>
@Grapes(
@Grab(group='org.rcsb', module='mmtf-common', version='0.0.1-alpha4')
)
libraryDependencies += "org.rcsb" % "mmtf-common" % "0.0.1-alpha4"
[org.rcsb/mmtf-common "0.0.1-alpha4"]

Dependencies

compile (1)

Group / Artifact Type Version
org.msgpack : jackson-dataformat-msgpack jar 0.7.1

test (4)

Group / Artifact Type Version
junit : junit jar 4.12
uk.co.jemos.podam : podam jar 2.3.5.RELEASE
org.unitils : unitils-core jar 3.4.2
commons-beanutils : commons-beanutils jar 1.9.2

Project Modules

There are no modules declared in this project.

Build Status Coverage Status Version Changelog

MMTF Java API and encoder/decoder

The macromolecular transmission format (MMTF) is a binary encoding of biological structures.

This repository holds the Java API, encoding and decoding libraries. Along with a description of the data in the MMTF using Java data types.

Releases are available on Maven central.

	<dependency>
	    <groupId>org.rcsb</groupId>
	    <artifactId>mmtf-codec</artifactId>
	    <version>1.0.9</version>
	</dependency>
        <dependency>
            <groupId>org.rcsb</groupId>
            <artifactId>mmtf-api</artifactId>
            <version>1.0.9</version>
        </dependency>

Quick getting started.

  1. Get the data for a PDB structure and print the number of chains:
StructureDataInterface dataInterface = new GenericDecoder(ReaderUtils.getDataFromUrl("4CUP"));
System.out.println("PDB Code: "+dataInterface.getStructureId()+" has "+dataInterface.getNumChains()+" chains");
  1. Show the charge information for the first group:
System.out.println("Group name: "+dataInterface.getGroupName(0)+" has the following atomic charges: "+dataInterface.getGroupAtomCharges(0));
  1. Show how many bioassemblies it has:
System.out.println("PDB Code: "+dataInterface.getStructureId()+" has "+dataInterface.getNumBioassemblies()+" bioassemblies");

For developers: release process

Prepare the release, setting new version numbers when prompted

mvn release:prepare

Perform the release, uploading artifacts to sonatype/maven central

mvn release:perform

To be able to upload to sonatype (to publish to maven central) you need to have an oss sonatype login, obtainable by signing up to their JIRA tracking system. Once you have a username and password add this to your ~/.m2/settings.xml maven file (<servers> section):

<server>
      <id>ossrh</id>
      <username>my_username</username>
      <password>my_password</password>
</server>

Finally edit the release tag in github and update the CHANGELOG.md file.

org.rcsb

RCSB PDB

Github repository of the RCSB Protein Data Bank

Versions

Version
0.0.1-alpha4
0.0.1-alpha3