bio.singa:singa-chemistry

The chemistry package of SiNGA handles aspects that range into chemoinformatics, such as parsing and manipulation of chemical entities as well as their annotation with features.

License	GNU GPL v3
GroupId	bio.singa
ArtifactId	singa-chemistry
Last Version	0.7.0
Release Date	Sep 23, 2020
Type	jar
Description	The chemistry package of SiNGA handles aspects that range into chemoinformatics, such as parsing and manipulation of chemical entities as well as their annotation with features.

Download singa-chemistry

Filename	Size
singa-chemistry-0.7.0.pom
singa-chemistry-0.7.0.jar	136 KB
singa-chemistry-0.7.0-sources.jar	73 KB
singa-chemistry-0.7.0-javadoc.jar	590 KB

How to add to project

Apache Maven

<!-- https://jarcasting.com/artifacts/bio.singa/singa-chemistry/ -->
<dependency>
    <groupId>bio.singa</groupId>
    <artifactId>singa-chemistry</artifactId>
    <version>0.7.0</version>
</dependency>

Gradle Groovy

// https://jarcasting.com/artifacts/bio.singa/singa-chemistry/
implementation 'bio.singa:singa-chemistry:0.7.0'

Gradle Kotlin

// https://jarcasting.com/artifacts/bio.singa/singa-chemistry/
implementation ("bio.singa:singa-chemistry:0.7.0")

Apache Buildr

'bio.singa:singa-chemistry:jar:0.7.0'

Apache Ivy

<dependency org="bio.singa" name="singa-chemistry" rev="0.7.0">
  <artifact name="singa-chemistry" type="jar" />
</dependency>

Groovy Grape

@Grapes(
@Grab(group='bio.singa', module='singa-chemistry', version='0.7.0')
)

Scala SBT

libraryDependencies += "bio.singa" % "singa-chemistry" % "0.7.0"

Leiningen

[bio.singa/singa-chemistry "0.7.0"]

Dependencies

compile (5)

Group / Artifact	Type	Version
bio.singa : singa-features	jar	0.7.0
bio.singa : singa-mathematics	jar	0.7.0
uk.ac.ebi.beam : beam-core	jar	1.2.1
uk.ac.ebi.beam : beam-func	jar	1.2.1
org.slf4j : slf4j-api	jar	1.7.21

test (3)

Group / Artifact	Type	Version
org.junit.jupiter : junit-jupiter-api	jar	5.3.1
org.junit.jupiter : junit-jupiter-engine	jar	5.3.1
org.slf4j : slf4j-log4j12	jar	1.7.21

Project Modules

There are no modules declared in this project.

SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.

Many aspects of the API are under development. API changes are frequent, never the less we try to keep them minimal.

Quick start

SiNGA is deployed to the Maven Central Repository. Simply add the desired modules to your pom.xml:

<dependencies>
    <dependency>
        <groupId>bio.singa</groupId>
        <artifactId>singa-[module]</artifactId>
        <version>0.7.0</version>
    </dependency>
    <!-- more dependencies -->
</dependencies>

Documentation

The full JavaDocs are available at singa-bio.github.io/singa-doc.

Requirements

Make sure you have the following tools and libraries installed:

• Java 8 or later

For p-value calculation for Fit3D:

• R installation 3.4.x or later
• local package installation privileges or the sfsmisc package pre-installed

Contributors

• Christoph Leberecht | christoph.leberecht(at)hs-mittweida.de | https://github.com/cleberecht
• Florian Kaiser | contact(at)fkaiser.bio | https://github.com/fkaiserbio

Projects using SiNGA

• Fit3D - template-based detection of small structural motifs | https://github.com/fkaiserbio/fit3d
• MMM - template-free detection of substructure conservation | https://github.com/fkaiserbio/mmm
• PNAtor - generation of PNA aptamer structures | https://github.com/eisold/PNAtor

SiNGA

Developing scientific software for structural and systems biology.

Versions

Version
0.7.0 Sep 23, 2020
0.6.0 Jul 17, 2019
0.5.0 Jun 26, 2019
0.4.2 Aug 7, 2018
0.4.0 Jul 24, 2018