Dissertation - Marvin V. Prakash

This the code i wrote for my MS Dissertation, It involves loading and processing of Protein-SSDna complexes, then analysing the various quantities in an coarse-grain manner.

Features

The process is comprised of multiple parts, which are:

• Preprocessing the pdb files by removing hydrogen molecules and HetAtoms, also broken chain atoms.
• Parsing of PDB files
• Identifying different unit types within a chain (protein, ssDNA, type_1, type_2)
• Calculating the center of mass for different unit types
• Validation of units based on the presence of necessary atoms
• Generation of Pandas DataFrames containing processed PDB data

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Installation

1. Clone the repository

   git clone https://github.com/M4Marvin/Dissertation-MS.git

2. Navigate to the project directory

   cd Dissertation-MS/

3. Create a new conda environment from the environment.yml file

   conda env create -f environment.yml

4. Activate the enviornment

    conda activate bio

Usage

For usage instruction take a look at the notebooks I provided.