PDB2CDextrapolator

A (relatively) simple extrapolation script for PDB2CD web server data, to allow it to be compatible with Dichroweb and other Circular Dichroism tools.

PDB2CD is a webserver (http://pdb2cd.cryst.bbk.ac.uk/) which predicts/simulates Circular Dichroism spectral data, however it only does this up to 240 nm. This makes it incompatible with Dichroweb (http://dichroweb.cryst.bbk.ac.uk/html/home.shtml), the webserver which analyses the same kind of data, from experiments. Many of the reference sets require 260 nm worth of data though, even if they dont use it within the analysis.

PDB2CDextrapolate.py

This python script takes in the plain text output of PDB2CD spectra, handles all the file manipulation and returns some extended spectral data from simple curve fitting via a Finite Difference Taylor Series. PDB2CD data looks like this:

#################################
# Created By PDB2CD             #
# 1/01/70 00:00:00              #
# Version 1.0                   #
# Author: Dr. Lazaros Mavridis  #
# E-mail: l.mavridis@qmul.ac.uk #
#################################

Data for the run: 1abc
----------

Wavelength	CD
175	-2.065
176	-1.974
177	-1.929
...
238	-0.203
239	-0.155
240	-0.123

Installation

None required, just clone this repository and run the script. The exception is if you wish to use the simple matplotlib functionality embedded in one of the methods to visualise the extrapolation (-p|--plot) - if so you'll need to make sure you've installed the module before.

$ python -m pip install matplotlib

is usually sufficient.

Execution

There are a few different funtionalities build in to the script. The script takes the following options:

-s | --spectrum - The input file from PDB2CD (plain text format).

-b | --bibliography - Display some salient references and exit (you cannot use this option with other options).

-f | --forecast - The number of periods (x axis increments) to extend the data by. Default of 20 nm in 1 nm increments.

-o | --outfile - Have the script write a separate new file for the extended spectrum. Prints to screen by default.

-v | --verbose - Output some useful info about variable values and progress messages. Supports 2 levels of verbosity at present (-v,-vv).

-p | --plot - Invoke matplotlib at the end of the script to visualise the extended spectrum. Requires matplotlib to be preinstalled - see above.

-d | --delta - The span of data from which gradients are calculated, this is a default of 3 x-increments. IMPORTANT - see the note below about usage.

A basic script invocation would be:

$ python PDB2CDextrapolate.py -s 1abc.txt

To view the plot and output a new file:

$ python PDB2CDextrapolate.py -s 1abc.txt -o ~/path/to/outputfile.txt -p

The Delta parameter and the Taylor expansion:

Delta, the interval along X to perform the finite difference calculations on has to have a minimum value of 3 so that the average gradient and difference calculations can work. The script by default will use 3 data points, and calculate the first 2 derivative terms of the Taylor series (the first term is just itself):

Therefore order of the series used is always delta - 1 .

This is because each successive derivative calculation, relies on the differences of the previous, which reduces the dimensions of the array you calculate from by 1 each time (eventually you'd have an empty array, and the average calculations which divide by the len(array), would give a divide-by-zero error.

The most the script will use is the 3rd derivative, which requires at least 5 data points. If the default is used, the third derivative is simply set at 0.

Disclaimers: