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MolVec

NCATS (chemical) ocr engine that can a way to vectorize chemical images into Chemical objects preserving the 2D layout as much as possible. The code is still very raw in terms of utility. Check out https://molvec.ncats.io for a demonstration of MolVec. Please forward questions and/or problems to [email protected].

#$ How To Build

You can build the whole project as a jar file with:

$ mvn clean pacakge

Or install the project into your maven repository using:

$ mvn install

Example Usage

    File image = ...
    String mol = Molvec.ocr(image);

Async Support

New in 0.8 MolVec supports asynchronous calls

   CompleteableFuture<String> future = Molvec.ocrAsync( image);
   String mol = future.get(5, TimeUnit.SECONDS);

Commandline interface

The Molvec jar has a runnable Main class with the following options

usage: molvec ([-gui],[[(-f <path> [-o <path>]) | (-dir <path> [-outDir <path>],[-parallel <count>])]],[-scale <value>],[-h])

Image to Chemical Structure Extractor Analyzes the given image and tries to find the chemical structure drawn and
convert it into a Mol format.

options:
     -dir <path>         path to a directory of image files to process. Supported formats include png, jpeg, tiff. Each
                         image file found will be attempted to be processed. If -out or -outDir is not specified then
                         each processed mol will be put in the same directory and named $filename.molThis option or -f
                         is required if not using -gui

     -f,--file <path>    path of image file to process. Supported formats include png, jpeg, tiff.  This option or -dir
                         is required if not using -gui

     -gui                Run Molvec in GUI mode. file and scale option may be set to preload file

     -h,--help           print helptext

     -o,--out <path>     path of output processed mol. Only valid when not using gui mode. If not specified output is
                         sent to STDOUT

     -outDir <path>      path to output directory to put processed mol files. If this path does not exist it will e
                         created

     -parallel <count>   Number of images to process simultaneously, if not specified defaults to 1

     -scale <value>      scale of image to show in viewer (only valid if gui mode AND file are specified)

Examples:

      $molvec -f /path/to/image.file

   parse the given image file and print out the structure mol to STDOUT

      $molvec -dir /path/to/directory

   serially parse all the image files inside the given directory and write out a new mol file for each image named
   $image.file.mol the new files will be put in the input directory

      $molvec -dir /path/to/directory -outDir /path/to/outputDir

   serially parse all the image files inside the given directory and write out a new mol file for each image named
   $image.file.mol the new files will be put in the directory specified by outDir

      $molvec -dir /path/to/directory -parallel 4

   parse in 4 concurrent parallel threads all the image files inside the given directory and write out a new mol file for
   each image named $image.file.mol the new files will be put in the directory specified by outDir

      $molvec -gui

   open the Molvec Graphical User interface without any image preloaded

      $molvec -gui -f /path/to/image.file

   open the Molvec Graphical User interface  with the given image file preloaded

      $molvec -gui -f /path/to/image.file -scale 2.0

   open the Molvec Graphical User interface  with the given image file preloaded zoomed in/out to the given scale

GUI

Molvec Comes with a Swing Viewer you can use to step through each step of the structure recognition process

Primitives