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htmd.pathplanning module#

class htmd.pathplanning.Tree(initialpoints)#

Bases: object

addPoint(point, parent, dist)#
htmd.pathplanning.parallelfunc(j, spherecoor, ligcoor, protcoor, step, colldist, outdist, distances)#
htmd.pathplanning.raytracing(mol, ligandsel, othersel='protein', step=1, colldist=2, outdist=8, ligcom=False, numsamples=2000, ratioexposed=0, vmd=True)#

Find the escape vector of a ligand from a pocket.

This function creates a sphere of points around the othersel atoms and traces a line from each atom of the ligand to each point on the sphere. If the line does not hit any othersel atoms within colldist it is checked if it exits the pocket by checking if any point on the line is outside the pocket. Thus we can calculate all the unimpeded vectors with which the ligand can reach the solvent. We then select the point of the surrounding sphere to which most ligand atoms can reach without hitting any othersel atoms within colldist and we consider this as the escape vector.

Parameters:

  • mol (Molecule) – The molecule to analyze.

  • ligandsel (str) – The selection string to use to identify the ligand.

  • othersel (str, optional) – The selection string to use to identify the other molecules which impede the escape of the ligand.

  • step (float, optional) – The step size to use for the line tracing.

  • colldist (float, optional) – The collision distance threshold to use for the line tracing.

  • outdist (float, optional) – The distance threshold to use to check if the line exits the pocket.

  • ligcom (bool, optional) – Whether to use the center of mass of the ligand or its individual atoms to trace the line.

  • numsamples (int, optional) – The number of points to sample on the surrounding sphere.

  • ratioexposed (float, optional) – The ratio of exposed ligand atoms that should be present on the escape vector. If set to a value greater than 0, the function will check if the number of exposed ligand atoms on the escape vector is greater than the specified ratio and raise an error if it is not.

  • vmd (bool, optional) – Whether to visualize the results using VMD.

Returns:

  • translation (np.ndarray) – The translation vector to apply if we want to align the molecule to the escape vector.

  • escape_vector (np.ndarray) – The escape vector, i.e. the vector which the ligand can use to reach the solvent without hitting any othersel atoms within colldist.

Examples

>>> from moleculekit.util import rotation_matrix_from_vectors
>>> translation, escape_vector = raytracing(mol, "resname LIG", "protein")
>>> rotmat = rotation_matrix_from_vectors(np.array([0, 0, 1]), escape_vector) # align z-axis with escape vector
>>> mol.moveBy(translation)
>>> mol.rotateBy(rotmat)
htmd.pathplanning.rrt(mol, ligandsel, step=1, maxiter=1000000, ligcom=False, colldist=2, outdist=8)#
htmd.pathplanning.rrtstarsmart(mol, ligandsel, step=1, maxiter=1000000, ligcom=False, colldist=2, outdist=8, radius=2.5)#
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