HelixAngle

Python module: Calculation of helices angle during a MD

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		module_helix_angle.py (16-Sept-2015) 	version 1.00   

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Copyright (c) Emmanuel Edouard MOUTOUSSAMY M2BI

Contents

1. Introduction
2. Necessary packages and software
3. Examples
4. Contact

#1. Introduction

This packages allow to determine differents angles between alpha-helix: - Helix - helix angle - Helix - Helix bundle angle - helix - Helix torsion angle

The helix position can be given by the user or calculated with the dssp program. The computing time depends of the size of the protein.

This packages contain 6 functions :

1. PDBHelix_vs_helix(top,traj,output = 0,limits = 0): Compute helix -helix angle for a pdb file. A topology and a trajectory file are obligatory. If you want to write the results in an outpufile, the output argument must be "w". And if you want to give the helix position, limits must be a list which contain the helix position (ex. limits = [(12,45),(56,75)]).

2. PDBHelix_vs_helixBundle(top,traj,output = 0,limits = 0): Compute helix - helixBundle angle for a pdb file. The arguments is the same than 1.

3. PDBHelix_torsion_angle(top,traj,output = 0): Compute helix - helixBundle angle for a pdb file.

4. MDHelix_vs_helix(top,traj,output = 0,limits = 0): Compute Helix-helix angle during a MD simulation. If output = "w", the results is write in an output file.

5. MDHelix_vs_helixBundle(top,traj,output = 0,limits = 0): Compute Helix-helixBundle angle during a MD simulation. The arguments is the same than 4.

6. MDHelix_torsion_angle(top,traj,output = 0): Compute Helix torsion angle during a MD simulation. The arguments is the same than 4.

#2. Necessary packages and software

The necessary packages are : modules python: -SYS (basic python package) -OS (basic python package)

-NUMPY (http://www.numpy.org): Debian / Ubuntu : sudo apt-get install python-numpy Mac OSX-MAVERICK (via MacPorts) : sudo port install py27-numpy

-MATPLOTLIB (http://matplotlib.org): Debian / Ubuntu : sudo apt-get install python-matplotlib Mac OSX-MAVERICK (via MacPorts) : sudo port install py27-matplotlib

-MDAnalysis : Debian / Ubuntu : pip install MDAnalysis Mac OSX-MAVERICK : pip install MDAnalysis

!Caution : the mkdssp program is essential for some options !!!! http://pkgs.org/download/mkDSSP

#3. Example

the example file contain differents uses of this program. For run example.py, Uncomment the lines that your want to test and type :

./example.py

The data file contain :

• a pdb file : 1H6I.pdb

#4. Contact

For all questions or informations: e.e.moutoussamy@gmail.com