11.4. XVG auxiliary reader — MDAnalysis.auxiliary.XVG

xvg files are produced by Gromacs during simulation or analysis, formatted for plotting data with Grace.

Data is column-formatted; time/data selection is enabled by providing column indices.

Note

By default, the time of each step is assumed to be stored in the first column, in units of ps.

class MDAnalysis.auxiliary.XVG.XVGStep(time_selector=0, data_selector=None, **kwargs)[source]

AuxStep class for .xvg file format.

Extends the base AuxStep class to allow selection of time and data-of-interest fields (by column index) from the full set of data read each step.

Parameters:

  • time_selector (int | None, optional) – Index of column in .xvg file storing time, assumed to be in ps. Default value is 0 (i.e. first column).

  • data_selector (list of int | None, optional) – List of indices of columns in .xvg file containing data of interest to be stored in data. Default value is None.

  • **kwargs – Other AuxStep options.

See also

AuxStep

11.4.1. XVG Readers

The default XVGReader reads and stores the full contents of the .xvg file on initialisation, while a second reader (XVGFileReader) that reads steps one at a time as required is also provided for when a lower memory footprint is desired.

Note

Data is assumed to be time-ordered.

Multiple datasets, separated in the .xvg file by ‘&’, are currently not supported (the readers will stop at the first line starting ‘&’).

class MDAnalysis.auxiliary.XVG.XVGReader(filename, **kwargs)[source]

Auxiliary reader to read data from an .xvg file.

Default reader for .xvg files. All data from the file will be read and stored on initialisation.

Parameters:

  • filename (str) – Location of the file containing the auxiliary data.

  • **kwargs – Other AuxReader options.

See also

AuxReader

Note

The file is assumed to be of a size such that reading and storing the full contents is practical.

read_all_times()[source]

Get NumPy array of time at each step.

Returns:

Time at each step.

Return type:

NumPy array of float

class MDAnalysis.auxiliary.XVG.XVGFileReader(filename, **kwargs)[source]

Auxiliary reader to read (one step at a time) from an .xvg file.

An alternative XVG reader which reads each step from the .xvg file as needed (rather than reading and storing all from the start), for a lower memory footprint.

Parameters:

  • filename (str) – Location of the file containing the auxiliary data.

  • **kwargs – Other AuxReader options.

See also

AuxFileReader

Note

The default reader for .xvg files is XVGReader.

read_all_times()[source]

Iterate through all steps to build times list.

Returns:

Time of each step

Return type:

NumPy array of float

MDAnalysis.auxiliary.XVG.uncomment(lines)[source]

Remove comments from lines in an .xvg file

Parameters:

lines (list of str) – Lines as directly read from .xvg file

Yields:

str – The next non-comment line, with any trailing comments removed