htmd.dock module#
- htmd.dock.dock(protein, ligand, center=None, extent=None, numposes=20, babelexe='obabel', vinaexe=None)#
Perform molecular docking using AutoDock Vina.
If
centerandextentare not provided, docking is performed over the whole protein.- Parameters:
protein (
Molecule) – Molecule object representing the receptor.ligand (
Molecule) – Molecule object representing the ligand to dock.center (
list|tuple|ndarray|None) – 3-element vector for the centre of the search bounding box.extent (
list|tuple|ndarray|None) – 3-element vector for the linear extent of the search bounding box.numposes (
int) – Number of poses to return. Vina cannot return more than 20 poses.babelexe (
str) – Path to the babel executable.vinaexe (
str|None) – Path to the AutoDock Vina executable.
- Returns:
scores (
numpy.ndarray) – A (num_poses, 3) array containing kcal, rmsd lb, and rmsd ub for each pose.
Examples
>>> poses, scoring = dock(protein, ligand) >>> poses, scoring = dock(protein, ligand, center=[ 10., 5., 12. ], extent=[ 15., 15., 15. ] )