Module ringspear

Create a infrastructure DistanceCell that obeys the given periodic boundary size.

Parameters:

• struct (schrodinger.structure.Structure) - The structure to create the distance cell for
• dist (float) - The distance threshold for the distance cell
• pbc (None, infrastructure.PBC, or list) - If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors:

     * a, b, c : box lengths
     * a, b, c, alpha, beta, gamma box : box lengths and angles
     * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
  

Returns: (schrodinger.infra.structure.DistanceCell, schrodinger.infra.structure.PBC or None)

A distance cell object that obeys the given PBC conditions. Note that this is a different type of object than an mmct distance cell and has a completely different API. The second value returned is the PBC object used to create the distance cell or None if no PBC was used.

Raises:

• ValueError - If the pbc needs to be constructed and the parameters don't match an available constructor

Check for ring spears - rings that have bonds passing through the face of the ring.

Parameters:

• ring_struct (schrodinger.structure.Structure) - The structure containing the rings to check for spearing
• spear_struct (schrodinger.structure.Structure) - The structure to check if any bonds spear a ring in ring_struct. If not given, ring_struct will be used - i.e. intrastructure ring spears will be searched for.
• atoms (list) - List of atom indexes to check to see if they spear a ring. Should be indexes from spear_struct if spear_struct is given, otherwise indexes from ring_struct. If not given, all atoms will be checked.
• rings (iterable of schrodinger.structure._Ring) - _Ring objects to check to see if they are speared. If not given, all rings in the ring_struct.ring iterator will be used. Use this parameter if you have an optimized method of finding rings in ring_struct or if they are already known.
• 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 a 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.
• dist (float) - The distance from the centroid to use when making a first rough cut pass to eliminate atoms that are too far away from a ring to spear it. The default value is the module constant ROUGH_CUT_DISTANCE. This value is ignored if distorted is True.
• pbc (None, infrastructure.PBC, or list) - If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors:

     * a, b, c : box lengths
     * a, b, c, alpha, beta, gamma box : box lengths and angles
     * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
  

• max_ring_size (int or None) - The maximum size ring that will be checked for ring spears. The default value prevents macrocycles from being checked. Set to None to include all rings

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.

Raises:

• ValueError - If the pbc needs to be constructed and the parameters don't match an available constructor

__doc__

Value:

""" Functions and classes useful for finding ring spears. A ring spear is when a bond between two atoms external to a ring passes through the face of t he ring. The bond may be a single bond or a higher-order bond, and it may be cy clic or acyclic. Thus, ring catenation is also found. ...