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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS
 

DATCLASS manual

datclass

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© ATSAS Team, 2012-2018

Table of Contents

Manual

The following sections shortly describe how to run DATCLASS from the command-line on any of the supported platforms, the required input and runtime output

Introduction

DATCLASS applies machine learning methods to rapidly classify the particle shape and estimate Molecular Weight (Da) and Dmax (A) from SAXS patterns. Possible shape classes are:

  • compact
  • extended
  • flat
  • ring
  • compact-hollow
  • hollow-sphere
  • random-chain
  • unknown

Please note that no parameter estimates are provided for objects classified as either "random-chain" or "unknown". The output will show "N/A" instead.

DATCLASS requires external files to run. If DATCLASS reports:

error: shape classifier initialization failed

please verify your installation and/or make sure that the ATSAS environment variable is set correctly.

Running datclass

Usage:

$ datclass [OPTIONS] <DATAFILE(S)>

OPTIONS known by DATCLASS are described in next section, the required argument(s) FILE(S) in the section on input files.

Command-line arguments and options

DATCLASS requires the following command line arguments:

ArgumentDescription
FILE(S) Data files in any of the supported formats.

Absolute as well as relative paths to data files are accepted. Up to one of the input files may also be given as '-', in this case input is read from stdin instead of a file.

DATCLASS recognizes following command-line options:

Short optionLong optionDescription
--rg Experimental Radius of Gyration in the units of the data. This option is mandatory for experimental data files.
--i0 Experimental forward scattering in the units of the data. This option is mandatory for experimental data files.
--first=<N> Index of the first point to be used. Default: 1.
--query=<N> Query and print the N nearest neighbours of the input data and exit. Default: N=5.
--features Print feature vector of input data and exit.
-v --version Print version information and exit.
-h --help Print a summary of arguments and options and exit.

Runtime output

DATCLASS output consists of one result line for each input file with the following values: shape classification, MW (Da), Dmax (A), file name.

datclass input files

FILE may come in any supported file format that provides a scattering vector, experimental intensity and experimental errors.

If FILE is a GNOM output file, reciprocal space Rg and I0 stated in the file are used, but may be overridden by the corresponding command-line options.

Example

$ datclass --rg=3 --i0=65.1 bsa.dat
compact      77594     103.48   bsa.dat

  Last modified: January 25, 2018

© BioSAXS group 2018