Polyphony. Python code for the analysis of protein structure ensembles.

Copyright (C) 2013 William R. Pitt

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

Usage: Do principal component analysis on given property for given alignment and report important residue positions for first principal component as a Jalview feature file

-h, --help show this help message and exit
-f FILE, --file=FILE
 name of a fasta file created with create_fasta_file.py
-p PROPERTY, --property=PROPERTY
 type of property to calculate, can be [backbone|sidech ain|phipsi|bfactor|sequence|calphas|crystal_contacts|p ockets|distance1000]
-g GROUPS, --groups=GROUPS
 optional group by sequence identity cutoff. Use by specifying a percentage to use e.g. 90
-u, --update use this option if you want to recalculate property data