pyqmmm.md.rmsf_calculator

Calculate the RMSF across replicates using MDAnalysis.

INPUT-FILE FORMAT (first non-comment line is now optional CPU count)

# How many cores to use cpus = 48

# Topology and static reference /abs/path/to/system.prmtop /abs/path/to/reference.pdb

# Trajectories (nickname full/path/to/trajectory.crd) rep1 /abs/path/to/rep1/constP_prod.crd rep2 /abs/path/to/rep2/constP_prod.crd …

Module Contents

Functions

die(→ None)

calculate_rmsf_per_trajectory(→ pandas.DataFrame)

Compute per-residue RMSF for a single trajectory.

parse_rmsf_input_file(file_path)

returns:

  • n_cpus (int | None)

print_example_input(→ None)

main(→ None)

Attributes

RESET

RED

GRN

BLU

YLW

pyqmmm.md.rmsf_calculator.RESET = '\x1b[0m'
pyqmmm.md.rmsf_calculator.RED = '\x1b[1;31m'
pyqmmm.md.rmsf_calculator.GRN = '\x1b[1;32m'
pyqmmm.md.rmsf_calculator.BLU = '\x1b[1;34m'
pyqmmm.md.rmsf_calculator.YLW = '\x1b[1;33m'
pyqmmm.md.rmsf_calculator.die(msg: str, code: int = 1) → None
pyqmmm.md.rmsf_calculator.calculate_rmsf_per_trajectory(topology: str, trajectory: str, reference: MDAnalysis.Universe, column_name: str) → pandas.DataFrame

Compute per-residue RMSF for a single trajectory.

pyqmmm.md.rmsf_calculator.parse_rmsf_input_file(file_path: pathlib.Path)
Returns:

  • n_cpus (int | None)

  • topology (str)

  • reference (str)

  • trajectories (list[tuple[str, str]])

pyqmmm.md.rmsf_calculator.print_example_input() → None
pyqmmm.md.rmsf_calculator.main() → None