LaBOX

An automatic ligand-based grid box size calculation tool for molecular docking.
Supported file formats include .pdb, .pdbqt, .sdf and .mol2.
Revamped from LABOGRID.

Usage
╰─○ LaBOX.py [-l] <filename>

Argument
╰─○ Command description:
        -l  ligand filename (supported: pdb, pdbqt, sdf, mol2)
        -h  help
        -a  about
╰─○ Optional parameters:
        -s  scale factor (default is 2)
        -c  grid box center

Return
╰─○ Grid Box Center: X  {value} Y  {value} Z  {value}
    Grid Box Size  : W  {value} H  {value} D  {value}

Method

NOTE: The values have been rounded to three decimals for accuracy, and additional testing will be conducted to refine the optimal scale factor.

1. The min() and max() functions were employed to identify the minimum and maximum X, Y, and Z atomic coordinates of a ligand.
2. The statistics.mean() function was used to compute the X, Y, and Z coordinates of the center of the gridbox based on the values obtained in step 1.
3. The absolute difference (abs(subtraction)) between the minimum and maximum X, Y, and Z coordinates was used to determine the dimensions (width, length, and depth) of the gridbox.
4. A default scale factor of 2 was applied to adjust the size of the gridbox based on the dimensions obtained in step 3.

Bug

If you encounter any bugs, please report the issue to https://github.com/RyanZR/LaBOX/issues.

License

The script is licensed under MIT, see the LICENSE file for details.