Biomolecular Calculator

Calculation of Biomolecular Dimensions

Usage

Using script for pdbs in a directory to create vina config files in bulk

# Single File In a Directory for Specific residues (residues are optional, if not provided it will work for whole the structure)
python /path/to/vina.py -b /path/to/base/directory -s xyz.pdb -res ALA ASN TRP

# Using File Name pattern(s) or using multiple files, both will work
python /path/to/vina.py -b /path/to/base/directory -s *.pdb *xyz.pdb m*.pdb -res ALA ASN TRP

# Giving Spacing
python /path/to/vina.py -b /path/to/base/directory -s *.pdb *xyz.pdb m*.pdb -res HETATM -spc 10

Check Options or parameters

python /path/to/vina.py -h python /path/to/vina.py --help

Setting different VINA Option

python /path/to/vina.py [OTHER OPTIONS] --exhaustiveness 15 --cpu 2

Features for calculating grid for autodock VINA

• Calculates grid size of a given PDB

• Using coordinates
• Adding spacing around the coordinates

• Calculates grid around selected residues

• Fitting the coordinates
• Adding spacing around the coordinates

Ref and downloades

• https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html
• https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL
• https://pymolwiki.org/index.php/Windows_Install

Notes

• Created using Python 3.9.5, not tested with other versions of python
• For any other calculation, feel free to comment