21_Analysis_Datastructure

This repository contains a collection of custom Python scripts developed for my thesis research. The primary focus is the analysis of molecular dynamics (MD) simulations.

Repository Content

This repository is a working collection of analysis scripts. While many scripts are located in the root directory, some system-specific data and analyses are grouped into sub-directories (e.g., 26_RbsB_only, 9_Martini3, PCA).

The scripts cover a wide range of custom MD analyses, including:

• Structural Analyses: RMSD, RMSF, Radius of Gyration (RoG), SASA, and secondary structure (DSSP).
• Conformational Dynamics: Principal Component Analysis (PCA), domain opening angles, and specific distance measurements.
• Interactions & Environment: Contact analysis, hydrogen bond analysis, water/ion residency, and diffusion calculations.
• System-Specific: Scripts tailored for specific proteins (RbsB, FkpA, SpeA) and simulation conditions (crowded, different force fields).
• Utilities: Trajectory processing (e.g., Rid_the_water.py), data aggregation, and plotting functions.
• etc etc

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🌿 Branching Strategy

This repository uses two primary branches:

• master: This branch may contain tested or stable versions of the code.
• VC_VM (Version Control Virtual Machine): This is the main development branch. Most analyses were conducted using the scripts from this branch, as the work was performed on virtual machines. In some cases, working scripts might be on VC_VM but not master yet.

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✍️ Note on Code Annotation

A quick note on the code comments:

You will find that most scripts in this repository are heavily annotated with function descriptions and inline comments. This was done using AI tools.

This approach was taken for two main reasons:

1. Ease of Reading: To make the code more legible and easier to understand when revisiting it.
2. Efficiency: ...because "I am lazy."

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⚠️ Disclaimer

This is a personal, academic repository. The code is provided "as-is" and was written specifically for the needs of a single research project. It is not intended as a polished, distributable software package. Expect some hard-coded paths (although I have tried avoiding those where possible), specific file-naming conventions, and scripts tailored to unique data structures.

🛠️ Core Technologies

The analysis scripts in this project leverage the following Python libraries (inclusive but BY FAR NOT complete list):

• MDAnalysis
• MDTraj
• NumPy
• Pandas
• Matplotlib
• SciPy
• etc etc