Macrocycle Ligand Preparation (Building)
=============================

These instructions are specifically for building macrocycles on wynton. The scripts use RDKit ETKDGv3 to generate 10 main ring conformations and 20 "side chain" expansions. The rigid fragment is the main macrocyclic ring. Each db2 file therefore has 10 hierarchies. No changes have been made to generation of protonation states and tautomers, and calculation of partial charges, atomic desolvation, and strain.

Macrocycle Building Job Setup on Wynton
--------------------------------------------------------------

Source the environment

.. code-block:: bash

    source /wynton/group/bks/soft/DOCK-3.8.5/env.sh

Create the building jobs

.. code-block:: bash

    python /wynton/group/bks/soft/MACROCYCLES/final_submit_building_docker.py --output_folder [output folder name] --bundle_size [bundle size] --skip_name_check --scheduler sge --container_software apptainer [input smi file]

Submit the building jobs

.. code-block:: bash

    qsub building_array_job.sh

Macrocycle Building Job Setup on Cluster7
--------------------------------------------------------------
Source the environment:

.. code-block:: bash

    source /nfs/home/dkranthi/MACROCYCLE_BUILDING/082526_CHEMSTEP_BUILDING/building_env/bin/activate

Create the building jobs

.. code-block:: bash

    python /nfs/home/dkranthi/MACROCYCLE_BUILDING/submit/final_submit_building_docker.py --output_folder [output_dir] --bundle_size 100 --skip_name_check --scheduler slurm --container_software apptainer [input.smi]

Submit the building jobs

.. code-block:: bash

    sbatch building_array_job.sh