The align_vector_to_box_axis.py Python3 script has been written to align a user-definable vector, provided by two groups defined in the index file, along one of the three axes (x, y, or z). The tool takes as input a .gro file, the index names of the two groups defining the vector, and information along which axis to align.
usage: align_vector_to_box_axis.py [-h] -f GRO -n NDX -g1 GROUP1 -g2 GROUP2 [–axis {x,y,z}] [-gc GROUP_CENTER]
[–center-target CENTER_TARGET] -o OUTPUT
options:
-h, --help show this help message and exit
-f GRO, --gro GRO Input .gro file
-n NDX, --ndx NDX Input .ndx file
-g1 GROUP1, --group1 GROUP1
First group name in .ndx
-g2 GROUP2, --group2 GROUP2
Second group name in .ndx
–axis {x,y,z} Target axis for alignment (default: x)
-gc GROUP_CENTER, --group-center GROUP_CENTER
Third group name in .ndx whose COM will be moved to the chosen target
–center-target CENTER_TARGET
Target position for third-group COM: “box”, “origin”, or “x,y,z” in nm
-o OUTPUT, --output OUTPUT
Output rotated .gro file
The script can be downloaded from GitHub - UAMCAntwerpen/Align_vector_to_box_axis: This Python script aligns two groups of Gromaces protein structure (.gro) to one of the axis (x, y, or z) · GitHub
Contact person: Hans De Winter