Module pi

Compute the squared distance between two centroids. Using the squared distance saves the sqrt compute cycles.

Parameters:

• cent1 (Centroid object) - first centroid
• cent2 (Centroid object) - second centroid

Returns: float

the squared distance between the two centroids.

Determine if any positive centers are within a specified distance cutoff of any aromatic ring centroids. For those positive center/ring contacts, determine if the positive center is located on the face of the ring rather than the edge.

Code example:

   import interactions
   from schrodinger import structure
   recep = None
   for struct in structure.StructureReader(input_file):
       if not recep:
           recep = struct
           # Precalculate receptor rings and cations to save time
           rings = interactions.gather_rings(recep)
           cations = interactions.get_receptor_positive_centroids(recep)
       else:
           picats = interactions.find_pi_cation_interactions(recep,
                                       rings1=rings, cations1=cations,
                                       struct2=struct)

Parameters:

• struct1 (schrodinger.structure.Structure object) - Receptor structure if for a ligand-receptor complex, or the first of two structures to compute pi-cations for
• struct2 (schrodinger.structure.Structure object) - Ligand structure if for a ligand-receptor complex, or the second of two structures, or None if the first structure should be search for intramolecular interactions.
• rings1 (list of SSSR (from gather_rings)) - SSSR of struct1. If not passed, will be computed.
• rings2 (list of SSSR (from gather_rings)) - SSSR of struct2. If not passed, will be computed.
• skip_unknown - UNUSED and deprecated.

Returns: list

list of CationPiInteraction interaction objects:

   # CationPiInteraction properties:
   cation_structure: structure that contains the cation
   pi_structure: structure that contains the pi group
   cation_centroid: Centroid of the positive charge
   pi_centroid: Centroid of the pi group
   distance: distance between the centroids
   angle: angle in degrees between the centroids

Find all pi-pi interactions between the rings in struct1 and struct2 (or within struct1 if only 1 structure is given). Interactions are classified as to whether they are face-to-face or edge-to-face.

Code example:

   import interactions
   from schrodinger import structure
   recep = None
   for struct in structure.StructureReader(input_file):
       if not recep:
           recep = struct
           # Precalculate receptor rings to save time
           rings = interactions.gather_rings(recep)
       else:
           pipi = interactions.find_pi_pi_interactions(recep,
                                       rings1=rings, struct2=struct)

Parameters:

• struct1 (schrodinger.structure.Structure object) - first of two structures to compute pi-pi interactions for
• struct2 (schrodinger.structure.Structure object) - second of two structures to compute pi-pi interactions for. If not given, struct1 will be searched for intramolecular interactions.
• rings1 (list of SSSR (from gather_rings)) - SSSR of struct1 If not passed, will be computed.
• rings2 (list of SSSR (from gather_rings)) - SSSR of struct2. If not passed, will be computed.
• max_angle (float) - The maximum angle allowed for a face-to-face interaction. (The minimum angle allowed for edge-to-face interactions will be 90 - max_angle.)
• max_ftf_dist (float) - The maximum distance allowed between the centroids of face-to-face rings
• max_etf_dist (float) - The maximum distance allowed between the centroids of edge-to-face rings

Returns: list of PiPiInteraction objects

a PiPiInteraction object for each interaction found. Properties of a PiPiInteraction object are:

• struct1: structure that contains the first ring
• struct2: structure that contains the second ring
• ring1: Centroid of the first ring
• ring2: Centroid of the second ring
• distance: distance between the centroids
• angle: angle in degrees between the two ring planes
• face_to_face: True if the interaction is face to face, False if it is edge to face

__doc__

Value:

""" A module for detecting pi-pi and pi-cation interactions. Code example for pi-cation interactions:: from schrodinger.structutils import interactions from schrodinger import structure recep = None for struct in structure.StructureReader(input_file): ...