PCA

Welcome to Polymer Chain Analyzer, the toolkit for geometric study of polymer chains. The project includes:

• PCA library
• Applications
• Tools for visualization

The detail description of the project comming soon in User Manual.

License

PCA project is distributed under Apache-2.0 license (see LICENSE and NOTICE(comes soon)).

Cite

Cite by the DOI:

And make a reference to the paper: arXiv:1705.09603.

PCA Library

This is the independent core of the project. To install the library run:

PCA/PCA_lib$ make

from the PCA_lib folder.

To make the library accessible from any folder on your computer you should run an initialisation session from the root folder PCA:

PCA$ source init_session.sh

This you have to do every time when start new terminal session!

There is automatically generated library documentation in PCA_lib/documentation.

Applications

You can find 3 different independent programs in applications folder. You can write your own application or change already existent ones. All applications use PCA library. If you did correctly the previous step, then you can copy and put applications in any folder on your computer. To compile the project do

myApplication$ make

from the folder with your application.

Run the program without arguments and it will tell you about itself and what values it expects:

myApplication$ ./pca

By default there are 2 important points:

• All output files go to folder results/ which you should have in the folder with application
• All input files should be stored in PCA/data/ folder.

These terms can be changed in main.cpp.

Tools for Visualization

There are two kind of tools:

• Matlab functions for visualization chains
• GNUplot script for plotting dependence of observables

Put the tool you want to use in the root of application. Matlab functions works with all applications in applications.

Matlab

If you have Matlab you can call from the workspace:

>> showConfiguration ('myPolymer')

for plot the original chain, or:

>> showConfiguration ('myPolymer', 10)

for the chain after 10 steps of rescaling procedure.

>> makeScalingMovie('myPolymer',5)

will make an avi file with scaling procedure, where each frame will be the 5th step of scaling procedure. Skip the second argument for drawing each step of the procedure.

GNUplot

If you have GNUplot you can call

myApplication$ gnuplot -e "polymerName='myPolymer'" -e "k=10" plotObservable.gnu

for plotting dependence of Observable on scaling step for default value of k. It works for totalAngle and various_k projects.

Data Format

The program uses the special file format .pca:

<x_firts_atom>    <y_first_atom>    <z_first_atom>
<x_second_atom>   <y_second_atom>   <z_second_atom>

 ...               ...               ...
 
<x_last_atom>     <y_last_atom>     <z_last_atom>

If you want several chains are taken for the statistics, put all of them in one file and separete them with one or more empty lines. All such blocks should have the same number of atoms:

<block 1 with N lines>
    <empty line>
<block 2 with N lines>
    <empty line>
...

All the input data should go to PCA/data.

You can see, there are already several pca files for proteins from PDB. To convert pdb-format to pca-format, this program was used: https://github.com/Anny-Moon/pdb2xyz