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FastROCS server is setup to be running continuously in the background (maybe on a screen). The database is required to be in oeb format as one single file. For more information, click here
Preparing the database
For small databases
$ simple_omega.py <smiles_file> <output_name>.oeb //this script do not have option to limit how many conformers generate
Building FastROCS database for ZINC
- Converting smiles to oeb files
$ python ~khtang/code/smi2oeb.py /nfs/export/2D //this can be run in parallel ***This will take more than 2 weeks to buil for 1.5B+ molecules.
- Concatenate all oeb files
$ cat d.*/*.oeb > /some/dir/database.oeb
- Preparing the database will help with the loading time and reduce the numbers of conformers (if needed). Read more
$ ShapeDatabasePrep.py <database.oeb> <prepped_database.oeb> [max_confs]
In a screen
$ ShapeDatabaseServer.py prepped_database.oeb [portnumber]// this command would load database into the memory and client would listen to it in port 8080 by default.