htmd.dock module

htmd.dock.dock(protein, ligand, center=None, extent=None, numposes=20, babelexe='obabel', vinaexe=None)

Molecular docking, using Vina

If centre and extent are not provided, docking will be performed over the whole protein

Parameters

  • protein (Molecule object) – Molecule object representing the receptor

  • ligand (Molecule object) – Molecule object representing the ligand to dock

  • center (list) – 3-vec centre of of the search bounding box (optional)

  • extent (list) – 3-vec linear extent of the search bounding box (optional)

  • numposes (int) – Number of poses to return. Vina cannot return more than 20 poses.

  • babelexe (str) – Path to babel executable.

  • vinaexe (str) – Path to AutoDock Vina executable.

Returns

  • poses – Molecule object representing the N<10 best poses

  • scores – 3x num_poses matrix containing kcal, rmsd lb, rmsd ub

Examples

>>> poses, scoring = dock(protein, ligand)
>>> poses, scoring = dock(protein, ligand, center=[ 10., 5., 12. ], extent=[ 15., 15., 15. ] )