Configuring OSR tools for Document to Structure

Follow the instructions below in order to convert images to structures using Document to Structure, using one of the supported tools.

CLiDE

To use CLiDE with d2s, you need a specific license. Please contact [email protected] to obtain it.

On Windows, CLiDE will be used automatically after installation, without further configuration.

On Linux and Mac OS X, you can install CLiDE batch to any directory. To make it usable by d2s, you should only make sure that either clide-batch.sh is in your $PATH, or that you create a symbolic link from $HOME/.chemaxon/naming/clide-batch.sh to the installed copy of CLiDE, using this command: 

ln -s /<clide-directory>/clide-batch.sh $HOME/.chemaxon/naming/clide-batch.sh

Alternatively, on all platforms, if the chemaxon.naming.clide.path java system property or the CLIDE environment variable is set, it will be used to find the CLiDE installation directory.

Please note that you need to activate your license before CLiDE works from d2s. Please follow the instructions provided by Keymodule to do so.

OSRA

To use OSRA with d2s, you first need to download and install OSRA.

On Windows, OSRA will be used automatically after installation, without further configuration.

On Linux and Mac OS X, you can install OSRA to any directory. To make it usable by d2s, you should only make that the osra command is in your $PATH.

Alternatively, on all platforms, if the chemaxon.naming.osra.path java system property or the OSRA environment variable is set, it will be used to find OSRA. These can either refer to the directory containing the osra command, or to the command itself.

Imago

To use Imago, you need to download the command line utility from EPAM's website. You should then unzip the downloaded file either to a directory on the PATH, or inside the ChemAxon naming directory:

  • On Windows: C:\Users\<USER>\chemaxon\naming\imago_console.exe

  • On Linux and Mac OS X: $HOME/.chemaxon/naming/imago_console

Alternatively, on all platforms, if the chemaxon.naming.imago.path java system property or the IMAGO environment variable is set, it will be used to find Imago. These can either refer to the directory containing the imago_console command, or to the command itself.