This code will generate db2 files from smiles/mol2.
- CORINA
- Openeye OMEGA (code is setup to use the openeye python toolkit, could be reworked to use command line version)
- Chemaxon JCHEM (cxcalc and molconvert)
- Openbabel
- Anaconda (Miniconda 3)
- Fork this repository
- Clone directory, cd into created directory
- Run install.sh
- Install conda to either a shared nfs path or the '/soft' directory
- Create the conda environment using 'conda env create -f environment.yml -n envname'
- Move required software to '/soft' directory. Software must be .tar.gz format
- Move required licenses to '/licenses' directory (Jchem/Omega). Software looks for jchem-license.cxl and oe-license.txt by default. These can be changed in the env.sh files
- Change paths in env.sh file (required changes are lines that are commented out)
- Modify the 'submit/build-3d.bash' file, source the conda environment on the first line
- Source the conda environment
- Set optional/required environment variables (see here)
- Run 'bash submit/submit-all.bash' to start job