Mda

Implementation of RMSD analysis using MDAnalysis.

mdaRMSD(target, reference)

Bases: RMSDBase

Calculate ligand RMSD using MDAnalysis.

calculate(selection='(not resname HOH) and (not name H*)', superimpose=False, save=False, output_filename=None)

Calculate RMSD between docked and reference ligand using MDAnalysis.

PARAMETER	DESCRIPTION
selection	MDAnalysis atom selection string. Default excludes waters and hydrogens. TYPE: str DEFAULT: '(not resname HOH) and (not name H*)'
superimpose	If True, optimally superimpose the ligand onto the reference before computing RMSD (minimized RMSD). If False, compute in-place RMSD using the docked coordinates as-is. Default is False. TYPE: bool DEFAULT: False
save	If True, write results to a text file. Default is False. TYPE: bool DEFAULT: False
output_filename	Output file path (without extension) if save is True. TYPE: str | None DEFAULT: None

RETURNS	DESCRIPTION
list[float]	List of RMSD values, one per frame in the trajectory.