Class SpearRing

Create a SpearRing object

Parameters:

• struct (schrodinger.structure.Structure) - The structure that contains this ring
• ring (schrodinger.structure._Ring) - The _Ring object that represents this ring
• pbc (schrodinger.infra.structure.PBC) - The periodic boundary condition to use if any or None if there is no PBC to use

Overrides: object.__init__

Get the ring centroid. Accounts for the fact that the ring might be broken across the periodic boundary condition

Parameters:

• struct (schrodinger.structure.Structure) - The structure that contains this ring

Returns: numpy.array, numpy.array

A 3-float numpy array giving the [X, Y, Z] coordinates of the ring centroid, and a numpy array of the XYZ coordinates of each ring atom taking into account the PBC so that the coordinates are not split by the PBC. The coordinate list is in the same order as the ring_indexes property.

Find the average normal vector to the ring plane and compute the radius of the ring.

The average normal vector is the average of the normal vectors computed for each pair of adjacent ring atoms and the ring centroid.

The radius is defined as the largest centroid-ring atom distance

Parameters:

• struct (schrodinger.structure.Structure) - The structure that contains this ring

Returns: numpy.array, numpy.array, float

The average normal vector to the plane of the ring translated so its base is at the origin, the average normal vector to the plane of the ring translated so its base is at the ring centroid, the radius of the ring.

Get a rotation matrix that rotates the ring to be aligned with the positive Z-axis when the ring centroid is at the origin.

Returns: numpy.array

A 4x4 numpy array containing the rotation matrix that aligns the ring normal vector to the positive Z-axis

Check for ring spears - bonds that pass through the face of the ring. It does not matter if the spearing bond is a single or multiple bond, or if it is part of another ring.

Parameters:

• orig_struct (schrodinger.structure.Structure) - The structure to check if any bonds spear this ring in ring_struct.
• atoms (list) - List of atom indexes to check to see if they spear this ring.
• is_ring_struct (bool) - Whether orig_struct contains this ring. If True, the atoms with the same index as the indexes of this ring will not be considered for spearing calculations.
• distorted (bool) - If False (default), the structure will be assumed to have reasonable bond lengths, and optimizations will be used to dramatically speed up spear-finding in large structures by eliminating atoms that cannot possibly spear this ring. If True, atom distances will not be used to optimize spear-finding - significantly increasing the time required.
• first_only (bool) - Whether to return after finding the first ring spear, or whether all ring spears should be found.
• cell (schrodinger.infra.structure.DistanceCell) - schrodinger.infra.structure.DistanceCell object created using pbc. cell is used for rough-cutting atoms too far away from the ring. If not provided, a cell will be created based on the value (or lack of value) of pbc. Pre-creating the cell for a structure and passing it to this method for all rings saves significant time. See also the pbc parameter.
• dist (float) - The distance from the ring centroid at which atoms will be rough cut and eliminated from spearing consideration. This is only used if cell is not provided.

Returns: list

A list of found ring-spears, each item is a Spear object. An empty list is returned if no spears are found, and if first_only is True the list will be at most 1 item long.

Apply the same translation and rotation to the structure as would be required to place the ring centroid at the origin with the ring in the XY plane.

Parameters:

• struct (schrodinger.structure.Structure) - The structure to be centered and rotated. It does not matter if this structure does not contain the ring.

Returns: None

Returns nothing - the input structure is modified directly

Quickly weed out any atoms that are too far away from the ring centroid to spear the ring.

This method differs from the rough cut method, which uses a larger spherical cutoff based on the centroid. This uses a cubic cutoff, which allows the dimensions to be smaller since the sphere has to large enough to maintain sufficient distance near the edges of the ring.

This method also uses smaller distances for smaller atoms

Parameters:

• struct (schrodinger.structure.Structure) - The structure to modify directly be deleting atoms that are weeded out

Returns: None

Nothing is returned, the input structure is modified directly

Add an atom property to all atoms with the atom's current index. This allows the original index to be retrieved even after atom indexes have been modified via atom extraction or deletion.

Find where the bond from atom1 to atom2 intersects the XY (z=0) plane.

The equation for a 3d line that passes through points p0=(x0, y0, z0) and p1=(x1, y1, z1) can be written:

   x-x0   y-y0   z-z0
   ---- = ---- = ----
    a       b     c

where (a, b, c) is the vector from p0 - p1.

if z = 0, then x = x0 - a(z0/c) and y = y0 - b(z0/c)

Parameters:

• atom1 (schrodinger.structure._StructureAtom) - The first atom in the bond to check
• atom2 (schrodinger.structure._StructureAtom) - The second atom in the bond to check

Returns: (float, float) or None

The (x,y) location where the bond intersects the ring plane, or None if there is no intersection (the bond is parallel or nearly parallel to the ring plane).