PROJECT_PY_MONTE_CARLO

This program is a implementation of a Replica Exchange Monte Carlo algorithm (REMC) described in the paper "A replica exchange Monte Carlo algorithm for protein folding in the HP model", by THACHUK C. and al.

Installation

Simply clone this repository by doing:

git clone [email protected]:FilouPlains/PROJECT_PY_MONTE_CARLO.git

Conda initialization

You need module that are not install into base python. To do so, and to simplify the process, an environment src/project_mc.yml have already been create.

To used it, simply type (if you are in PROJECT_PY_MONTE_CARLO/):

conda env create -n project_mc -f env/project_mc.yml
conda activate project_mc

You are now able to launch the program.

Simplest example

To launch the program, the minimap require argument are given next (if you are in PROJECT_PY_MONTE_CARLO/):

python3 src/main.py -i AA -s 1 -o file.csv

Obviously, there's a lot of parameters. simply type this to have the help:

python3 src/main.py -h

Or this:

python3 src/main.py --help

Now, let's describe one by one all possible arguments:

argument	description
-h, --help	Display the help.
-i, --input	Give the input sequence. You can type it or give a .fasta file.
-s, --step	The number of MC steps to perform. You have to give an integer.
-o, --output	Print a file (file.csv) with data in it from the MC algorithm.
-tmin, --minimal_temperature	The minimal temperature to start the replica (from tmin to tmax, both include, with a step of 1).
-tmax, --maximal_temperature	The maximal temperature to start the replica (from tmin to tmax, both include, with a step of 1).
-rp	Place the given sequence randomly on a grid. Note that if this parameters is not given, the sequence will be put linearly on the grid.
-mf, --mol_file	Give file.mol2 as output. You can, like this, visualize the trajectory. WARNINGS: Huge file and take time to be produce!
-remc	When given, do a replica exchange MC.
-co, --cut_off	Energy that serve as a cut-off. Only negative integer possible.
-ts, --total_step	Number of exchange to do. Note that the number of operation when this parameter is given is -s * -ts.

Note : Argument in bold HAVE TO BE GIVEN so the program could work well.

Note : Argument in italics HAVE TO BE GIVEN if the option -remc is input.

The most full example is given next:

python3 src/main.py
    -i sequence.fasta
    -s 10
    -o file.csv
    -tmin 20
    -tmax 30
    -mf file.mol2
    -rp
    -remc
    -co -5
    -ts 5

Note: Personalize error can been thrown. If you want a more detailed explanation, check doc/ERROR.md.

To take in consideration

The REMC algorithm take way more time to be done than the MC algorithm.