instructions.txt

Instructions for using Fragment Hotspots in the context of the BioChemGraph project:

1 - clone the git repo at https://github.com/ccdc-opensource/hotspots
2 - move to the new local repo, and checkout the v107_EBI branch
	$ git checkout v107_EBI
3 - use the environment.yaml file to create a new environment that will be called csd_hotspots
	$ conda env create -f environment.yaml
4 - change to the new environment
	$ conda activate csd_hotspots
5 - go back to the parent directory, and install the hotspots package using pip
	$ cd ..
	$ pip install ./hotspots
6 - if not already available, download ghecom from https://pdbj.org/ghecom/download_src.html and put it in a directory where it can be unpacked. Using the current latest version the commands would be:
	$ cd <wherever the ghecom package is located>
	$ tar zxvf ghecom-src-20240220.tar.gz
	$ cd src
	$ make
7 - add an environment variable for ghecom:
	$ export GHECOM_EXE=<wherever the ghecom package is located>/ghecom
8 - run the "hotspots_json_out.py" script, with the directory containing the PDB or mmCIF files as an argument
	$ python hotspots/hotspots_json_out.py <path_to_files>

The results should be a nested folder containing information about the protein's hotspots as both a csv file and a json.
There will also be another csv file containing information about the timings for different parts of the process.
This second csv file also acts as a record of the files processed so far, so if the program crashes it will check automatically to avoid repeating files. 
If you want to run the same file again you can either edit or delete this csv file.

The ''--retain'' command line option allows intermediate files to be retained - current options are:

  * cavity - retain output of cavity detection step - currently only applies for Ghecom cavity detection.