Function Index

Callable Python interfaces are grouped below by task. Analysis wrappers accept the same input files as their command-line counterparts. Lower-level numerical functions operate on arrays or PQAnalysis objects and do not parse command-line arguments. For worked recipes, see Learn the Python API. The bundled files are in Example data.

Analysis workflows

rdf(input_file[, md_format, export_files])	Calculates the radial distribution function (RDF) using a given input file.
msd(input_file[, md_format, export_files])	Calculates the mean square displacement (MSD) using a given input file.
vacf(input_file[, md_format, export_files])	Calculates the velocity auto-correlation function (VACF) using a given input file.
vibrations(input_file[, export_files])	Run vibrational analysis from an input file.
check_momentum(trajectory_files[, output, ...])	Calculate the total linear momentum norm per frame and write it.
build_spectrum(input_file[, output, alpha, ...])	Broaden a two-column stick spectrum file and write the result.

Numerical methods

apodization_window(n_points, time_step[, ...])	Calculates the one-sided legacy apodization window.
vacf_spectrum(time, correlation[, ftsize, ...])	Calculates the legacy cosine-transform spectrum of a correlation function.
alpha_from_fwhm(fwhm)	Convert a Gaussian full width at half maximum to the exponent alpha.
fwhm_from_alpha(alpha)	Convert a Gaussian exponent alpha to the full width at half maximum.
wavenumber_grid([wavenumber_min, ...])	Build the regular wavenumber grid of the broadened spectrum.
broaden(wavenumbers, intensities, grid[, ...])	Broaden a stick spectrum on a wavenumber grid.
calculate(atom_masses, atom_coords, hessian)	Calculate wavenumbers, force constants, reduced masses and normal modes.
read_hessian_file(filename)	Read a plain square Hessian matrix.
select_mode_indices(wavenumbers[, modes, ...])	Select mode indices from a user-facing one-based mode selection.

Analysis tables

infer_output_format(filename)	Infer a requested output format from a recognized filename suffix.
read_analysis_table(filename)	Read native, CSV, TSV or XVG analysis data by content.
write_analysis_table(table, file, output_format)	Write an analysis table to an open text stream.
convert_analysis_output(input_file, output_files)	Convert one analysis table to one or more output files.

Structure and trajectory I/O

read_trajectory(filename[, md_format, ...])	API function for reading a trajectory from a file.
read_trajectory_generator(filename[, ...])	API function for building a frame generator from a trajectory file.
write_trajectory(traj[, filename, ...])	Wrapper for TrajectoryWriter to write a trajectory to a file.
calculate_frames_of_trajectory_file(filename)	Calculate the number of frames in a trajectory file.
read_restart_file(filename[, ...])	API function for reading a restart file.
write_restart_file(atomic_system[, ...])	Write an atomic system to a restart file.
read_gen_file(filename)	Function to read a gen file.
write_gen_file(system[, filename, periodic, ...])	Function to write a gen file.
read_topology_file(filename)	Function to read a topology file.
write_topology_file(bonded_topology[, ...])	Wrapper function to write a topology file.
read_box(filename)	Reads a data-style box file.
read_optimizer_file(filename)	Read a PQ optimizer output file.
write(object_to_write[, filename, mode])	API write wrapper function for writing different objects to a file.
write_box(traj[, filename, output_format])	Writes the given trajectory to the file in a selected box file format.
check_trajectory_pbc(cells)	Checks no cell in the trajectory is Cell() i.e. checks if the trajectory is never in vacuum.
check_trajectory_vacuum(cells)	Checks if all cells of the trajectory are in vacuum i.e. cell = Cell().

Format conversion

rst2xyz(restart_file[, output, print_box, ...])	Converts a restart file to a xyz file and prints it to stdout or writes it to a file.
xyz2rst(xyz_file[, velocity_file, ...])	Converts a xyz file to a restart file and prints it to stdout or writes it to a file.
xyz2gen(xyz_file[, output, periodic, mode, ...])	Converts a xyz file to a gen file and prints it to stdout or writes it to a file.
gen2xyz(gen_file[, output, md_format, ...])	Converts a gen file to a xyz file and prints it to stdout or writes it to a file.
traj2box(trajectory_files, vmd[, output, mode])	Converts multiple trajectory files to a box file and prints it to stdout or writes it to a file.
traj2extxyz(trajectory_files[, output, ...])	Converts one or more PQ xyz trajectory files to extended xyz format and prints it to stdout or writes it to a file.
traj2qmcfc(trajectory_files[, output, mode])	Converts multiple trajectory files from a PQ format to a QMCFC format and prints it to stdout or writes it to a file.

See Package Reference for classes, enums, exceptions and the generated module hierarchy.