Structure Comparison

Protein_alignment

Calculate RMSD between two protein structures by comparing Cα atoms. Compare specific chains or create a chain-to-chain heatmap.

Note: The aligned chains can also be visualized directly using the plot_structure_3d and plot_structure_3d_interactive functions by passing two structures. See Visualization for full details on these visualization functions.

Parameters:

• df1, df2: DataFrames from read_pdb().

• chains: List of two chain IDs or ‘Combo_matrix’ for full heatmap.

Examples:

# Compare specific chains
df1 = protplot.read_pdb('7lyn')
df2 = protplot.read_pdb('7lym')
protplot.Protein_alignment(df1, df2, chains=['A', 'A'])

# Compare all chains (matrix)
protplot.Protein_alignment(df1, df2, chains='Combo_matrix')

extract_phi_psi

Extract φ and ψ backbone torsion angles from atomic coordinates stored in a DataFrame.

Parameters:

• df: DataFrame from read_pdb() with N, CA, and C atoms.

Returns:

• Array of (phi, psi) angle pairs.

Examples:

df = protplot.read_pdb('7v7n')
angles = protplot.extract_phi_psi(df)