Molecular docking, using Vina
If centre and extent are not provided, docking will be performed over the whole protein
Molecule object) – Molecule object representing the receptor
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.
poses – Molecule object representing the N<10 best poses
scores – 3x num_poses matrix containing kcal, rmsd lb, rmsd ub
>>> poses, scoring = dock(protein, ligand) >>> poses, scoring = dock(protein, ligand, center=[ 10., 5., 12. ], extent=[ 15., 15., 15. ] )