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singa-all release 0.2.3

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@cleberecht cleberecht released this 25 Oct 15:26
· 648 commits to master since this release
0.2.3
56eea3c

Updates and features

Mathematics

JavaFx

  • added possibility to render before and after graph drawing in graph renderers

Chemistry

  • improved writing of structures or parts of structures to pdb files
  • improved match format for Fit3D search results
  • added PS-score to evaluate alignments (see: 10.1093/bioinformatics/btt024)
  • added Fofanov p-value estimation for matches found using Fit3D (see: 10.1109/BIBMW.2008.4686202)
  • Affinity Alignments can be used to find representative structural motifs for a set of similar motifs
  • added possibility to calculate gyration of any substructure (see: 10.1134/S0026893308040195)
  • added possibility to validate interactions from PLIP with structures
  • PLIP interactions may be used to generate interaction shells
  • modified ChEBI data retrival process (dropping ChEBI API)
  • UniProt parsing now also annotates EC Numbers when available

Simulation

  • revised module definition an implementation completely
  • modules are now defined using functions that define updates during epochs
  • added method to automatically estimate the time step size during simulation to minimize error
  • added new module to simulate mediated membrane transport (see: 10.1016/S0006-3495(04)74082-5)

Installation

You can add all SiNGA to your project by adding the following dependency to your pom.xml.

<dependency>
    <groupId>de.bioforscher.singa</groupId>
    <artifactId>'artifact'</artifactId>
    <version>0.2.3</version>
</dependency>
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