namanpujari / res_energies

Processes pdb files to generate individual residue energies of an entire protein structure. Can be used in theory to calculate the energy of an unfolded protein.

res_energies

Python programs that process pdb files to generate individual residue energies of an entire protein structure. Can be used in theory to calculate the energy of an unfolded protein.

PLEASE NOTE

Added an elementary way of efficiently running the code. When first running, set the mcce_result_present status to False. A bunch of statements indicating that the residues have been sent to the cluster will appear. Check qstat multiple times and wait till all jobs are complete. Then change mcce_result_present to True and run the the thing again with the same command in terminal. Check the output folder. It should have everything.

Usage

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Typing python main.py --help in the command line gives the following:

usage: main.py [-h] -pdb PDB_LOCATION -e MCCE_DIRECTORY -out OUTPUT_DIRECTORY
               [-s SUBMIT_JOB]

Run MCCE on multiple PDB files

optional arguments:
  -h, --help            show this help message and exit

Required arguments (please write absolute
                                                paths for all locations:
  -pdb PDB_LOCATION, --pdb_location PDB_LOCATION
                        Location where pdb (to be analysed is stored
  -e MCCE_DIRECTORY, --mcce_directory MCCE_DIRECTORY
                        Path to the directory where MCCE is installed.
  -out OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
                        Location where analysis will be stored

Optional arguments:
  -s SUBMIT_JOB, --submit_job SUBMIT_JOB
                        Flag whether to submit calculation for processing
                        through the server. Default is False, meaning the
                        machine will run it locally

Please note that SUBMIT_JOB is not implemented as of yet.

What it does

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1. Grabs the targeted pdb, and strips it of comments (basically any line not classified) as ATOM or HETATM.
2. Using a splitting algorithm defined in individual_res_energies.py it produces all the residues as their own pdb files
3. Using automated_mcce.py, it runs MCCE on each, individual residue.
4. Analyses all the fort.36 (wherever present) for all residue and finds average at each pH. Sums the values for all residues and provides a neat .csv for the final result. Csv files are also produced for each individual residues average energie for reference.

Example

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An example, and how the out_gfp46 folder was created in this repository.

1. Set mcce_results_present (in main.py) to False, then...

python main.py -pdb /home/naman/res_energies/gfp46.pdb -e /home/mcce/mcce3.5/ -out /home/naman/res_energies/out_gfp46

2. Wait till qstat returns nothing
3. Set mcce_results_present (in main.py) to True, then the same command as in step 1...

python main.py -pdb /home/naman/res_energies/gfp46.pdb -e /home/mcce/mcce3.5/ -out /home/naman/res_energies/out_gfp46