schrodinger.structutils.interactions.pi module¶

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):
    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)

Code example for pi-pi interactions:

from schrodinger.structutils 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)

schrodinger.structutils.interactions.pi.squared_centroid_distance(cent1, cent2)¶

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
Return type:	float
Returns:	the squared distance between the two centroids.

schrodinger.structutils.interactions.pi.unit_vector_points(a, b)¶

schrodinger.structutils.interactions.pi.unit_vector(vec)¶

class schrodinger.structutils.interactions.pi.Centroid(atoms, xyz)¶

Bases: object

The object that stores data about a centroid

__init__(atoms, xyz)¶

Create a Centroid object

Parameters:	atoms (list of int) – the atom numbers involved in the centroid xyz (list of float) – the XYZ coordinates of the centroid

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.interactions.pi', '__doc__': '\n The object that stores data about a centroid\n ', '__init__': <function Centroid.__init__>, '__dict__': <attribute '__dict__' of 'Centroid' objects>, '__weakref__': <attribute '__weakref__' of 'Centroid' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.structutils.interactions.pi'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

class schrodinger.structutils.interactions.pi.CationPiInteraction(cation_structure, pi_structure, cation_centroid, pi_centroid)¶

Bases: object

The object that stores the data for a Cation-Pi interaction

__init__(cation_structure, pi_structure, cation_centroid, pi_centroid)¶

Create a CationPiInteraction object

Parameters:

cation_structure (schrodinger.structure.Structure object) – structure that contains the cation
pi_structure (schrodinger.structure.Structure object) – structure that contains the pi group
cation_centroid (Centroid object) – Centroid of the positive charge
pi_centroid (Centroid object) – Centroid of the pi group
distance (float) – distance between the centroids
angle (float) – angle in degrees between the centroids

cation_structure = None¶

Ivar:	structure that contains the cation
Type:	schrodinger.structure.Structure object

pi_structure = None¶

Ivar:	structure that contains the pi group
Type:	schrodinger.structure.Structure object

cation_centroid = None¶

Ivar:	Centroid of the positive charge
Type:	Centroid object

pi_centroid = None¶

Ivar:	Centroid of the pi group
Type:	Centroid object

distance¶

Ivar:	distance between the centroids
Type:	float

angle¶

Ivar:	angle in degrees between the centroids
Type:	float

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.interactions.pi', '__doc__': '\n The object that stores the data for a Cation-Pi interaction\n ', '__init__': <function CationPiInteraction.__init__>, 'distance': <property object>, 'angle': <property object>, '__dict__': <attribute '__dict__' of 'CationPiInteraction' objects>, '__weakref__': <attribute '__weakref__' of 'CationPiInteraction' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.structutils.interactions.pi'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

class schrodinger.structutils.interactions.pi.PiPiInteraction(struct1, struct2, ring1, ring2, face_to_face)¶

Bases: object

The object that stores the data for a Pi-Pi interaction

__init__(struct1, struct2, ring1, ring2, face_to_face)¶

Create a PiPiInteraction object

Parameters:

struct1 (schrodinger.structure.Structure object) – structure that contains the first ring
struct2 (schrodinger.structure.Structure object) – structure that contains the second ring
ring1 (Centroid object) – Centroid of the first ring
ring2 (Centroid object) – Centroid of the second ring
distance (float) – distance between the centroids
angle (float) – angle in degrees between the two ring planes
face_to_face (bool) – True if the interaction is face to face, False if it is edge to face

distance¶

Returns:	distance between the centroids
Return type:	float

angle¶

Returns:	angle in degrees between the centroids
Return type:	float

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.interactions.pi', '__doc__': '\n The object that stores the data for a Pi-Pi interaction\n ', '__init__': <function PiPiInteraction.__init__>, 'distance': <property object>, 'angle': <property object>, '__dict__': <attribute '__dict__' of 'PiPiInteraction' objects>, '__weakref__': <attribute '__weakref__' of 'PiPiInteraction' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.structutils.interactions.pi'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__¶: list of weak references to the object (if defined)

schrodinger.structutils.interactions.pi.find_pi_cation_interactions(struct1, struct2=None, rings1=None, rings2=None, skip_unknown=None, params=None, honor_pbc=True)¶

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. params (schrodinger.infra.structure.PiCationParams or NoneType) – Detailed parameters controlling the interaction criteria. If None, then the default values will be used.
Return type:	list
Returns:	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

schrodinger.structutils.interactions.pi.gather_rings(astruct, atom_subset=None)¶

schrodinger.structutils.interactions.pi.find_pi_pi_interactions(struct1, struct2=None, rings1=None, rings2=None, params=None, honor_pbc=True)¶

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. params (schrodinger.infra.structure.PiPiParams or NoneType) – Detailed parameters controlling the interaction criteria. If None, then the default values will be used.
Return type:	list of PiPiInteraction objects
Returns:	a PiPiInteraction object for each interaction found.

schrodinger.structutils.interactions.pi module¶

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