ClusterAnalysis Version 1.0

This program performs cluster analysis based on atomic coordinates from a PDB trajectory. It computes cluster sizes, adjacency lists, and neighbor statistics for selected atoms across frames in the trajectory.

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📦 Requirements

• A multi-frame PDB file with END statements between frames.
• Fortran compiler (e.g., gfortran)
• Coordinates must include CRYST1 lines to define box dimensions.

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🔧 Compilation

gfortran -o clusterAnalysis clusterAnalysis.f90

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▶️ Usage

./clusterAnalysis -pdb <pdb_file> -radius <cutoff> -selection <residue_name> [options]

Required Flags:

Flag	Description
-pdb	Path to the PDB file
-radius	Cutoff radius for neighbor search
-selection	Atom name to select (e.g., P, CA)

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Optional Flags:

Flag	Description	Default
-n	Max number of neighbors to consider	15
-sizes	Output file for main cluster sizes	size.xvg
-counts	Output file for total clusters per frame	cluster_counts.xvg
-hist	Output file for cluster size histogram	cluster_hist.xvg
-neighbors	Output file for adjacency lists	neighbors.dat
-npd	Output file for neighbors probability	neighbors_prob.xvg
-help / -h	Show usage information and exit

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📤 Output Files

• neighbors.dat: Adjacency list per atom per frame
• cluster_counts.xvg: Number of clusters in each frame
• cluster_hist.xvg: Cluster size distribution (probability)
• size.xvg: Main (largest) cluster size per frame
• neighbors_prob.xvg: Histogram of number of neighbors

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📈 Visualization

Output files are .xvg format, compatible with XMGrace for plotting:

xmgrace cluster_counts.xvg

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📌 Notes

• Only atoms matching the given -selection will be included in the analysis.
• Box periodicity is accounted for using CRYST1 dimensions in the PDB file.
• Ensure the PDB file has proper frame separation using END.
• Cluster Analysis 2.0 Will be able to read Gromacs Format Trajectories (.xtc format)

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That's it. Run, analyze, and plot.

Let me know if you want a sample PDB to test.