Islandora Chemistry Solution Pack
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README.md

Chemistry Solution Pack Build Status

Introduction

Islandora Chemistry Solution Pack Module

Chemistry Solution Pack for Islandora Loads all required Fedora Objects, and creates an empty collection object to accept ingested files related to chemistry.

All bugs, feature requests and improvement suggestions are tracked at the DuraSpace JIRA.

Requirements

This module requires the following modules/libraries:

  • Islandora - Islandora core functionality.
  • OpenBabel - Required for basic functionality to work. OpenBabel converts the chemical structure files into a common format, creates images from them and extracts useful chemical data.
  • ChemDoodleWeb - Is used as a viewer for the object and allows a 3D representation of the molecule to be displayed. It is also used as a molecule editor so that structures can be used for searching.
  • Indigo Python API - Is required to be installed as a Drupal library as the directory indigo-python to create and search for molecular fingerprints. Indigo requires at least Python version 2.6.6 to run.
  • Checkmol - Required to identify functional groups in the molecule and allow searching based on that.
  • GeSHi - Required for syntax highlighting.
  • Jumboconverter installed as a library under jumbo-converter as retrievium-importer.jar.

Installation

For the module itself, install as usual, see this for further information.

For ChemDoodleWeb, download and unzip the library such that the ChemDoodleWeb.js is located in sites/all/libraries/ChemDoodleWeb/install/ChemDoodleWeb.js.

For GeSHi, download and unzip the library such that geshi.php is located in sites/all/libraries/geshi/geshi.php.

Configuration

Configure each module/library as outlined in their respective installation instructions.

FAQ

Q: What kind of limits exist for molecules?

A: Checkmol (used for identifying functional fragments inside molecules) has a limit of 1024 atoms. Additionally, some of the output formats for OpenBabel (generating InchiKeys in particular) handle at most 1000 atoms.

Troubleshooting/Issues

Having problems or solved a problem? Check out the Islandora google groups for a solution.

Maintainers/Sponsors

Current maintainers:

Past maintainers:

Development

If you would like to contribute to this module, please check out our helpful Documentation for Developers info, as well as our Developers section on the Islandora.ca site.

License

GPLv3