CLiDE Batch

Chemical structure extraction in batch processing mode

CLiDE Batch is recommended for those who wish to extract structures in a fully automated manner

Key
Highlights

  • Ideal for automated bulk extraction
  • Major chemistry database providers have found it easy to integrate into workflows
  • The review of results is facilitated with
    • a confidence score for each specific which structure extracted, and
    • a fault flag which marks those structures which CLiDE detects as having possible interpretation errors

What’s in the box?

  • An easy-to-use command-line tool
  • Opens PDF and Word documents
  • Opens images of several types, including BMP, GIF, JPEG, PBM, PGM, PNG, PNM, PPM, TIFF, XBM and XPM
  • Extracts structures from structure diagrams
  • Attempts to interpret generic structures
  • Clears up atom positions within interpreted structures so that all rings and chains are formed as they were in their original document or image
  • Detects interpretation errors
  • Indicates structures that have any abnormalities (including recognition errors and valence violations)
  • Provides a confidence score between 0 and 1, indicating CLiDE’s confidence in the accuracy of the structure extraction
  • Supports the export of super atoms in expanded and contracted form
  • Provides a set of options to control the recognition process and the information should be saved into the exported files
  • Saves structures in the following formats:
    • MDL Molfile
    • MDL SDfile
    • MDL RGfile
    • CDX (ChemDraw)
    • CML (Chemical Markup Language)
    • MRV (ChemAxon Marvin Document)
    • XML (Extensible Markup Language)
  • Exported XML files can be opened in CLiDE Professional for reviewing the extracted structures alongside the input document or image
  • Clears up atom positions within interpreted structures so that all rings and chains are formed as they were in their original document or image

CLiDE batch examples

CLiDE Batch is ideal for high throughput. Below are a selected set of pages of a 71-page WIPO patent which CLiDE Batch processes in 1 minute and 10 seconds on a machine with an Intel Core i7-12700H CPU and 64GB RAM, or in 2 minutes and 36 seconds on a weaker machine with an Intel Core i7-3630-QM CPU and 8GB RAM. Note that the display of these pages were produced by CLiDE Professional which can open the XML output produced by CLiDE Batch.

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You need a high-performing, reliable and easy-to-use software solution to speed up your next big scientific breakthrough. Getting the right solution is integral to advance your research and workflow.