Clean

Algorithms to clean a field of points.

point_in_hull(point, hull, tolerance=1e-12)

Determines if a point is contained in a hull. A point is in the hull if and only if for every equation (describing the facets), the dot product between the point and the normal vector (eq[:-1]) plus the offset (eq[-1]) is less than or equal to zero. You may want to compare to a small, positive constant tolerance = 1e-12 rather than to zero because of issues of numerical precision (otherwise, you may find that a vertex of the convex hull is not in the convex hull).

PARAMETER	DESCRIPTION
point	coordinates of the point to be considered. TYPE: Sequence[float]
hull	Convex hulls in N dimensions. TYPE: ConvexHull
tolerance	tolerance for the calculation. TYPE: float DEFAULT: 1e-12

RETURNS	DESCRIPTION
bool	Returns True if point in hull, False otherwise

remove_convex_fop(fop_trimmed, trimmed_alpha)

Uses a convex hull to trim points from the field of points that are outside of the protein pocket.

PARAMETER	DESCRIPTION
fop	Field of points XYZ coordinates with no atom clashes.
trimmed_alpha	alpha atoms to define the convex hull. TYPE: Sequence[Sequence[float]]

RETURNS	DESCRIPTION
points_in_hull	FOP trimmed of points outside the convex hull defined by the protein. TYPE: Sequence[Sequence[float]]

remove_fop_atom_clash(fop, atoms_points, vdw_radius=2.6)

Removes points that clash with atoms within the field of points.

PARAMETER	DESCRIPTION
fop	Field of points XYZ coordinates. TYPE: Sequence[Sequence[float]]
atoms_points	coordinates of atoms within the field of points. TYPE: list of lists
vdw_radius	Van der Waals radius for atoms to detect clashes. Defaults to the van der Waals radius of water and that of hydrogen atom. TYPE: float DEFAULT: 2.6

RETURNS	DESCRIPTION
Sequence[Sequence[float]]	A field of points without atom clashes.