pyqmmm.md.rmsf_calculator

Calculate the RMSF across replicates using MDAnalysis

Module Contents

Functions

calculate_rmsf_per_trajectory(topology, trajectory, ...)

Calculate the RMSF per trajectory.

calculate_rmsf(topology, trajectories[, reference_file])

Calculate the RMSF with MDAnalysis.

Attributes

protein

pyqmmm.md.rmsf_calculator.calculate_rmsf_per_trajectory(topology, trajectory, reference, count)

Calculate the RMSF per trajectory.

Calculates the RMSF for each residue in a given trajectory. Aligns the trajectory to a reference, calculates the RMSF, and returns a DataFrame with the residue IDs, names, and RMSF values.

Parameters:

  • topology (str) – Path to the topology file.

  • trajectory (str) – Path to the trajectory file.

  • reference (MDAnalysis.core.universe.Universe) – The reference structure to which the trajectory is aligned.

  • count (int) – The index of the trajectory, used for naming in the resulting DataFrame.

Returns:

df – DataFrame containing resIDs, residue names, and RMSFs for a trajectory.

Return type:

pandas.DataFrame

pyqmmm.md.rmsf_calculator.calculate_rmsf(topology, trajectories, reference_file=None)

Calculate the RMSF with MDAnalysis.

The script works with analyzing the RMSF across multiple replicates. It expects the .crd extension from CCPTraj, which needs to be labeled as TRJ for MDAnalysis.

Parameters:

reference_file (str) – The path to a PDB file that you would like to use as a reference.

pyqmmm.md.rmsf_calculator.protein