MSTBxAnalysis

Version: 0.5.0-beta

Modular analysis tools for computational biophysics and biology. This project is a refactored and modernized version of the CompBiology-Biophysics script collection, designed for ease of use and extensibility.

Features

• Modular CLI: Use a single command mstbxanalysis to access all tools.
• Robust Loading: The CLI handles missing dependencies gracefully, loading only available modules.
• Easy Installation: Install via pip or set up a dedicated conda environment.
• Extensible Architecture: Adding a new analysis script is as simple as dropping a Python file into the modules/ directory.
• Cross-Platform: Compatible with Linux and macOS.

Installation

Using Pip (Recommended)

From the root of the repository:

pip install -e .

Note: Using -e (editable mode) installs the package as a symbolic link to your source code. This means any changes you make to the files in src/ will be immediately available in the mstbxanalysis command without needing to re-install. It also ensures all dependencies are correctly resolved.

Core Libraries and Recommendations

This project is primarily built using MDAnalysis and VMD's Tcl script interpreter. We strongly suggest that developers and contributors prioritize these libraries when adding new functionality. Please attempt to implement new analysis tools using these established methods before introducing additional dependencies.

Usage

The general syntax is:

mstbxanalysis [COMMAND] [OPTIONS]

Available Commands

Core MDAnalysis Tools

• rmsd: Calculate Root Mean Square Deviation (RMSD).
• mda-rgyr: Calculate Radius of Gyration (Rgyr).
• mda-rmsf: Calculate Root Mean Square Fluctuation (RMSF).
• mda-2dmatrix: Calculate and plot a 2D RMSD Distance Matrix.
• mda-convert-traj: Convert coordinates and trajectories between different formats.
• pbc-fix: Remove PBC effects and fit trajectories using MDAnalysis or VMD.

VMD-based Tools

• vmd-sasa: Calculate Surface Accessible Solvent Area (SASA).
• vmd-get-box: Calculate center and box size for docking (AutoDock/Vina).
• vmd-pbc-wrap: PBC wrapping and alignment using VMD/pbctools.
• vmd-rmsd-residue: Calculate average RMSD per residue and store in PDB beta column.
• vmd-segid-to-chain: Convert VMD segnames to chainIDs.
• vmd-merge-pdb: Merge multiple PDB files into a single system.
• vmd-reduce-traj: Reduce trajectory size by skipping frames.
• vmd-movie-render: Render movies from VMD scenes.
• vmd-molpack: Build biomolecular systems (orient, topology, solvate, ionize).
• vmd-molywood: Automate Molywood movie generation.
• vmd-make-segname: Set segment names for protein regions.
• vmd-jarzynski: Setup Jarzynski equality pulling scripts.
• vmd-make-tclforces: Mark PDB files for TclForces/TclBC.
• orient-z: Orient protein along the Z-axis using VMD.
• remove-rot-trans: Remove rotation and translation using VMD.

Simulation Prep & Building

• bigbabel: Process ligand databases (SDF split -> SMI -> PDB -> PDBQT).
• charmm-gui-prepare: Prepare PDB/MOL2 for CHARMM-GUI inputs.
• co-mol-md: Calculate ligand counts for concentration-based flooding.
• gmx-atom-index: Create or append to GROMACS index files (.ndx).
• make-flooding: Generate Packmol inputs for flooding MD.
• namd-to-charmm: Convert NAMD formats (PSF/PDB) to CHARMM.
• namd-to-gmx: Convert NAMD formats (PSF/PDB) to GROMACS.
• sdf-to-pdb: Batch convert SDF libraries to PDB with 3D coordinates.

Statistical & Thermodynamic Analysis

• dg-to-kd: Calculate dissociation constant (Kd) from ΔG.
• fel: Calculate Free Energy Landscapes (FEL).
• namd-stats: Extract thermodynamics and kinetics from NAMD logs.
• harm-potential: Calculate harmonic spring constants for umbrella sampling.

Sequence & Structure Analysis

• contact-map: Calculate contact frequencies between atom selections.
• get-seq: Retrieve sequences from PDB/NCBI and run BLASTp.
• prody-eda: Perform Essential Dynamics Analysis (PCA) using ProDy.
• r-msa: Run Multiple Sequence Alignment using R's msa package.

Workflows & Automation

• analysis-workflow: Run a full suite of MD analyses across project directories.
• vina-screening: Virtual screening workflow (SMI -> PDBQT -> Vina -> Sort).
• virtscreen: Simplified Vina screening loop for existing libraries.
• namd-hpc-segment: Manage segmented NAMD simulations on HPC (SLURM).
• easy-htmd: Basic setup for high-throughput MD.

Run mstbxanalysis [COMMAND] --help for specific options of each tool.

How to Add a New Analysis Script

MSTBxAnalysis is designed to be easily extensible. To add a new analysis tool, follow these steps:

1. Create a Module File: Navigate to src/mstbxanalysis/modules/ and create a new Python file. The filename should be descriptive (e.g., sasa_analysis.py). Note that underscores in the filename will be automatically converted to hyphens in the CLI command (e.g., mstbxanalysis sasa-analysis).

2. Define the CLI Command: In your new file, import click and define a function named command decorated with @click.command(). This function will be the entry point for your tool.

3. Add Options and Arguments: Use @click.option() to define the parameters your tool needs (input files, parameters, output names, etc.).

4. Implement the Logic: Write your analysis code inside the command function or call other functions from it.

Example Template (src/mstbxanalysis/modules/my_new_tool.py):

import click
import MDAnalysis as mda # If needed
# Import other libraries as necessary

@click.command()
@click.option('--input', '-i', required=True, help='Path to the input file')
@click.option('--param', default=1.0, help='A numerical parameter for analysis')
@click.option('--output', '-o', default='result.dat', help='Output file path')
def command(input, param, output):
    """
    Brief description of what this tool does.
    This description will appear in the 'mstbxanalysis --help' menu.
    """
    click.echo(f"Starting analysis on {input} with parameter {param}...")

    # 1. Load data
    # 2. Perform calculations
    # 3. Save results

    click.echo(f"Analysis complete! Results saved to {output}")

The system will automatically detect this new file and register it as a subcommand. You can immediately run it as:

mstbxanalysis my-new-tool --input data.pdb --param 2.5

Legacy Code

All original scripts from the CompBiology-Biophysics repository have been moved to the old.code/ directory for reference.

License

GPLv3