g4analysis

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Introduction

A python package for DNA structural analysis

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Usage

Files

Option	Type	Filename	Description
-p	Input	coor_file	Structure fie: gro pdb etc.
-f	Input	traj_file	Trajectory: xtc trr.
-o	Input	output_file	xvgr/xmgr file.
-i	Input	para_an.in	input parmarter file.

Other options

Option	Type	Value	Description
--helical	bool	False	Calculate the helical parameters of nucleic acids.
--dihedral	bool	False	Calculate the backbone dihedral parameters of nucleic acids.
--rise	bool	False	Calculate the distance of DNA bases groups.
--twist	bool	False	Calculate the twist of DNA bases groups.
--rmsd	bool	False	skip Calculate the RMSD of DNA bases groups.
--begin	int	0	First frame (ps) to read from trajectory.
--end	int	-1	Last frame (ps) to read from trajectory.
--skip	int	1	Get frames when frame MOD skip = 0
-h	bool	yes	Print help info and quit

Two modes to use this program.

Interactive Mode.

G4Analysis -p coor_file -f traj_file -o output_file --rise/twist/rmsd [--begin/end/skip]

Input File Mode.

G4Analysis -p coor_file -f traj_file -i input_file [--begin/end/skip]

para.in format:

group_1(ID1:ID2:...) group_2(ID1:ID2:...) result.xvg

version 0.2.0

• Rewrited Simple_atom and modified some bugs.
• Add G4_area.py to calculate the area of four O6 atoms in the G-quartet.

version 0.1.0

• For B-DNA. helical parameters and dihedral parameters.
• For G-quadruplex, rise, twist and RMSD_z for G-quartets.