Configuring OSR tools for Document to Structure

The following instructions must be used to make sure Document to Structure can convert images to structures, using one of the supported tools.

CLiDE

To use CLiDE with d2s, you need to obtain the CLiDE batch product and a license from Keymodule.

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 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 OSRA environment variable is set, it will be used to find OSRA. The OSRA variable 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 GGA'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 IMAGO environment variable is set, it will be used to find Imago. The IMAGO variable can either refer to the directory containing the imago_console command, or to the command itself.