Reference

qaa.__main__

Command-line interface.

qaa.cli

qaa.cli Module

Module that contains the command line app.

Why does this file exist, and why not put this in __main__?

You might be tempted to import things from __main__ later, but that will cause problems: the code will get executed twice:

• When you run python -mqaa python will execute __main__.py as a script. That means there won’t be any qaa.__main__ in sys.modules.

• When you import __main__ it will get executed again (as a module) because there’s no qaa.__main__ in sys.modules.

Also see (1) from http://click.pocoo.org/5/setuptools/#setuptools-integration

qaa.commands

qaa.commands.cmd_align Module

Align trajectories to their average structure.

qaa.commands.cmd_cluster Module

Cluster data into regions.

Functions

create_logging_dict(logfile)	Configure the logger.
find_closest_point(point, data)	Locate a point in the data closest to the point.

qaa.commands.cmd_pca Module

Subcommand to find the principal components of a trajectory.

qaa.commands.cmd_qaa Module

CLI to compute quasi-anharmonic analysis.

qaa.decomposition

qaa.decomposition.jade Module

Module to find signals using the Jade ICA method.

This module contains the function, _jade, which does blind source separation of real signals. The original Python code can be found at https://github.com/gvacaliuc/jade_c/blob/master/jade.py

Classes

BaseEstimator()	Base class for all estimators in scikit-learn.
Float(*args, **kwargs)	A numpy float.
JadeICA(*[, n_components])	Perform blind source separation using joint diagonalization.
NDArray(*args, **kwargs)	NDArray is a representation of numpy.ndarray.
TransformerMixin()	Mixin class for all transformers in scikit-learn.
combinations(iterable, r)	Return successive r-length combinations of elements in the iterable.

qaa.libs

qaa.libs.align Module

Functions to align coordinate files.

Functions

align_trajectory(mobile, reference, *[, …])	Align mobile to reference using the Kabsch method.
rmse(mobile, reference)	Calculate the root-mean-square error between two arrays.

qaa.libs.figure Module

Draw and save figures for QAA.

Classes

Figure(*[, azim, elevation])	Create a plot of 2D and 3D plots.
Path(*args, **kwargs)	PurePath subclass that can make system calls.

qaa.libs.kabsch Module

Align a trajectory using the Kabsch method.

Notes

Kabsch functions originally from https://github.com/charnley/rmsd/blob/master/rmsd/calculate_rmsd.py

Classes

BaseEstimator()	Base class for all estimators in scikit-learn.
Float(*args, **kwargs)	A numpy float.
Kabsch([verbose])	Kabsch alignment method.
NDArray(*args, **kwargs)	NDArray is a representation of numpy.ndarray.
StandardScaler(*[, copy, with_mean, with_std])	Standardize features by removing the mean and scaling to unit variance
TransformerMixin()	Mixin class for all transformers in scikit-learn.

qaa.libs.utils Module

Various utilities.

Functions

get_average_structure(topology, trajectory, *)	Compute the average structure of a trajectory.
get_positions(topology, trajectory, *[, …])	Read a molecular dynamics trajectory and retrieve the coordinates.
in_units_of(quantity, units_in, units_out[, …])	Convert a numerical quantity between unit systems.
reshape_positions(positions)	Reshape a n * m * 3 trajectory to a n * (m * 3) 2D matrix.
rmse(mobile, reference)	Calculate the root-mean-square error between two arrays.