A python package for DNA structural analysis
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.
G4Analysis -p coor_file -f traj_file -o output_file --rise/twist/rmsd [--begin/end/skip]
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
- Rewrited Simple_atom and modified some bugs.
- Add G4_area.py to calculate the area of four O6 atoms in the G-quartet.
- For B-DNA. helical parameters and dihedral parameters.
- For G-quadruplex, rise, twist and RMSD_z for G-quartets.