CLI Enumeration

Step 1. Coding the Reactions

• Pick out the reactions that you want to enumerate. This can be done either through already-made reactions that are in commons.docking.org or you can use those reaction SMARTS and inclusion/exclusion SMARTS as examples/guidelines to make your own reaction/s. We recommend using the daylight SMARTS as a resource if you plan on doing this: https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html.
• Once you have your reaction we recommend testing the inclusion and exclusion SMARTS through our website which has many modules and tools called TLDR. We have a specific tool called BBfilter(https://tldr.docking.org/start/bbfilter) that outputs building blocks from a large database based on the inclusion and exclusion SMARTS that are provided. Based on the correctness of the molecules that are outputted, the in/exclusion SMARTS should be adjusted to fit your needs.
• Once all the SMARTS have been finalized you can either submit this reaction into our reaction database called ChemistryCommons at commons.docking.org and email us once you do or email the SMARTS directly to us("chemistry4biology at gmail dot com") so that we can set your reaction up on the cluster.

Step 2. Setting Up

• After you have made your reaction you are ready to get them ready on the cluster. If you don't have an account on the cluster already please email us at "chemistry4biology at gmail dot com" to help you get set up. Login into your cluster account and make sure you are in your home directory.
• Next, you will need to make a directory in your home directory that will store the enumeration results: "mkdir <name>".
• Then you will need to copy the necessary scripts over and this can be done by doing: "cp /nfs/exj/Fe/scripts ." .
• You will also need to copy an example reaction directory by doing: "cp /nfs/exj/Fe/Test ." . Use "mv Test <name>" to change the name into whatever you'd like.
• "cd <changed name>" into this directory to then change the parameters. To keep things simple you can just type "vim Reaction" press i and then change the id's to the ones of your reaction and in/exclusion rules. Then press esc and type :wq! to save.
• Next, ssh into a node such as n-1-18("ssh n-1-18") so that you're able to meet the requirements to run the scripts and then source the environment by doing "source /nfs/home/ak87/exa/UCSF/SynthI/BESPOKE/arthor-env/bin/activate" to get all the necessary packages for the scripts run.

Step 3. Running the Scripts and Building your library

Congratulations you have completed the setup and are ready to run enumeration. All you need to do now is go into your reaction directory by using the command cd <name> and the run the script with "bash ../scripts/Etest.bash .". After enumeration is completed cd into your results directly and your enumerated file should be located inside!