Usage

qaa

Run main command-line interface.

qaa [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

align

Align a trajectory to average structure using Kabsch fitting.

qaa align [OPTIONS]

Options

-s, --top <FILE>

Topology

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.top

-f, --traj <FILE>

Trajectory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.nc

-r, --ref <FILE>

Average structure of trajectory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/average.pdb

-o, --outfile <FILE>

Aligned trajectory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/aligned.nc

-l, --logfile <LOG>

Log file

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/align_traj.log

--dt <OFFSET>

Trajectory output offset (0 = single step)

Default

0

-m, --mask <mask>

Atom selection

Default

ca

Options

ca | cab | back | side | noh | all

--tol <tol>

Error tolerance

Default

0.001

-v, --verbose

Noisy output

cluster

Perform cluster analysis on the provided data.

qaa cluster [OPTIONS]

Options

-s, --top <FILE>

Topology

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.top

-f, --traj <FILE>

Trajectory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.nc

-i, --infile <FILE>

Data file for analysis

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.csv

-o, --outdir <DIR>

Clustered image file

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs

-l, --logfile <LOG>

Log file

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/image.log

--axes <AXES>

Components

Default

0, 1, 2

--ica, --pca

Type of data

--gmm, --kmeans

Clustering method

--iter <MAXITER>

Maximum number of iterations for clustering

Default

200

--tol <TOL>

Maximum tolerance for clustering

Default

0.001

-n, --nclusters <n_clusters>

Number of cluster centers to plot

Default

3

--dp <n_points>

Number of points to skip for plotting

Default

1

--save

Save structures from corresponding cluster center

-v, --verbose

Noisy output

cluster

Visualize the data.

qaa cluster [OPTIONS]

Options

-i, --infile <FILE>

Data file for analysis

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.csv

--label <FILE>

Cluster labels

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/labels.npy

-c, --centroid <FILE>

Cluster labels

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/centroids.csv

-o, --outfile <FILE>

Image file

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/cluster.png

-l, --logfile <LOG>

Log file

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/plot.log

--axes <AXES>

Components to plot

--ica, --pca

Type of data

--dpi <DPI>

Resolution of the figure

Default

600

--azim <AZIMUTH>

Azimuth rotation of 3D plot

Default

120

--elev <ELEVATION>

Elevation of 3D plot

Default

30

--cluster

Cluster analysis

-v, --verbose

Noisy output

pca

Calculate principal components for a trajectory.

qaa pca [OPTIONS]

Options

-s, --top <FILE>

Topology

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.top

-f, --traj <FILE>

Trajectory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.nc

-o, --outdir <DIR>

Output directory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs

-l, --logfile <LOG>

Log file

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/align_traj.log

--dt <OFFSET>

Trajectory output offset (0 = single step)

Default

0

-m, --mask <mask>

Atom selection

Default

ca

Options

ca | cab | back | side | noh | all

-n, --nmodes <NMODES>

Number of eigenmodes (0 = all components)

Default

0

-w, --whiten

Whitens the data

--bias, --no-bias

Calculate with population bias (N vs N-1

--dpi <dpi>

Resolution of the figure

Default

600

--it <image_type>

Image type

Default

png

Options

png | pdf | svg | jpg

-v, --verbose

Noisy output

qaa

Perform quasi-anharmonic analysis on a trajectory.

qaa qaa [OPTIONS]

Options

-s, --top <FILE>

Topology

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.top

-f, --traj <FILE>

Trajectory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/input.nc

-o, --outdir <DIR>

Output directory

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs

-l, --logfile <LOG>

Log file

Default

/home/docs/checkouts/readthedocs.org/user_builds/pyqaa/checkouts/latest/docs/align_traj.log

--dt <OFFSET>

Trajectory output offset (0 = single step)

Default

0

-m, --mask <mask>

Atom selection

Default

ca

Options

ca | cab | back | side | noh | all

-n, --nmodes <NMODES>

Number of eigenmodes (0 = all components)

Default

0

--jade, --fastica

QAA method

-w, --whiten

Whitens the data

--iter <MAXITER>

Maximum number of iterations for FastICA

Default

200

--tol <TOL>

Maximum number of iterations for FastICA

Default

0.001

-v, --verbose

Noisy output