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Extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files
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README.md

Introduction

The ChemScanner library attempts to extract and interpret reactions/molecules information from ChemDraw-related files format: CDX, CDXML, embedded CDX within DOC and DOCX, Perkin Elmer ELN.

Installation

Add this line to your application's Gemfile:

gem 'chem_scanner'

And then execute:

$ bundle

Or install it yourself as:

$ gem install chem_scanner

UI for ChemScanner

You can try the ChemScanner at https://eln.chemotion.net/ or https://eln.chemotion.net/chemscanner. The UI is more user-friendly which some additional features:

  • Export to Excel and CML.
  • Preview of the original scheme.
  • Import directly to Chemotion ELN
  • Add comment for each extracted scheme. These comments would also appear in the export and Chemotion ELN imported molecules/reactions.
  • ...

Usage

To scan/extract a single CDX file

require 'chem_scanner'

cdx = ChemScanner::Cdx.new
cdx.read('/path/to/cdx/file')
# Get array of scanned Canonical SMILES
cdx.molecules.map(&:get_cano_smiles)
# Get array of scanned Reactions in SMILES
cdx.reactions.map(&:reaction_smiles)

There are 5 classes correspond to 5 supported file formats: CDX, CDXML, DOC, DOCX, PerkinELN.

API

Molecule

  • Access "scanned" molecules
# Molecules - array of scanned molecules
cdx.molecules
# Get array of scanned Canonical SMILES
cdx.molecules.map(&:get_cano_smiles)
# Get one  molecule
molecule = cdx.molecules.first
# Number of scanned molecules
cdx.molecules.count
  • Molecule class:
# Canonical SMILES
molecule.get_cano_smiles
# Molfile
molecule.get_mdl
# RDKIT RWMol (https://www.rdkit.org/docs/cppapi/classRDKit_1_1RWMol.html)
molecule.rw_mol
# Molecule label (bold text near molecule)
molecule.label
# Molecule text (molecule description)
molecule.text
# Molecule details (additional information from Perkin Elmer ELN)
molecule.details

We are using a ruby-binding version of RDKit as a dependency of ChemScanner.

Reaction

Reaction consist of 3 groups of molecules: reactants, reagents and products. Each group is and array of molecules, which each element is an object of Molecule class. In addition, some abbreviations belong to the reaction are represented by SMILES. Those could be access via reagent_smiles

reaction = cdx.reactions.first
# Access extracted structure group
reactants = reaction.reactants
reagents = reaction.reagents
products = reaction.products
reagent_smiles = reaction.reagent_smiles

Further manipulation of each group would be similar to Molecule class.

  • Reaction properties

Reaction itself has description, yield, time, temperature and details properties. All these properties are extracted from the ChemDraw scheme, excep details field are additional information from PerkinELN.

  • Reaction step

Some multi-step reactions can also be recognized. If a reaction is a multi-step reaction, the "steps" could be accessed via:

# Get first scanned reaction
reaction = cdx.reactions.first
# Access first step
step = reaction.steps.first
step.number # Should be 1 
step.description
step.time
step.temperature
# List reagents SMILES
step.reagents

Each step has these following properties: description, time, temperature, and reagents

Supported File Formats

CDX, CDXML, PerkinELN usage and API are described above. Their outputs are simple molecules and reactions.

DOC and DOCX classes are little bit different. Since DOC and DOCX file can contain more than 1 embedded ChemDraw schemes, which each embedded scheme is 1 CDX scheme. ChemScanner attempts to extract all of them and put into one Hash map, called cdx_map.

require 'chem_scanner'

doc = ChemScanner::Doc.new
doc.read('/path/to/doc/file')
doc.cdx_map.each do |key, cdx|
  puts cdx.reactions.map(&:reaction_smiles)
end

# Access all molecules in all CDXs
doc.molecules.map(&:get_cano_smiles)
# Access all reactions in all CDXs
doc.reactions.map(&:get_cano_smiles)

DOCX is a bit different, ChemScanner can extract the CDX together with its preview image within the documents.

require 'chem_scanner'

docx = ChemScanner::Docx.new
docx.read('/path/to/docx/file')
docx.cdx_map.each do |key, cdx_info|
  # Get the CDX scheme
  cdx = cdx_info[:cdx]
  puts cdx.reactions.map(&:reaction_smiles)
  
  # Preview images, used for ChemScanner UI
  img_ext = cdx_info[:img_ext] # Could be '.png', '.emf'
  img_b64 = cdx_info[:img_b64] # Base64 encoded of image
end

# Access all molecules in all CDXs
docx.molecules.map(&:get_cano_smiles)
# Access all reactions in all CDXs
docx.reactions.map(&:get_cano_smiles)

Development

After checking out the repo, run bin/setup to install dependencies. Then, run rake spec to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/ComPlat/chem_scanner. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.

License

The gem is available as open source under the terms of the GNU AGPLv3 License.

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