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
    else:
        picats = interactions.find_pi_cation_interactions(recep,
                                    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
    else:
        pipi = interactions.find_pi_pi_interactions(recep, 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 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¶

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

pi_structure¶

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

cation_centroid¶

Ivar: Centroid of the positive charge
Type: Centroid object

pi_centroid¶

Ivar: Centroid of the pi group
Type: Centroid object

property distance¶

Ivar: distance between the centroids
Type: float

property angle¶

Ivar: angle in degrees between the centroids
Type: float

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

property distance¶

Returns: distance between the centroids
Return type: float

property angle¶

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

schrodinger.structutils.interactions.pi.find_pi_cation_interactions(struct1, struct2=None, atoms1=None, atoms2=None, skip_unknown=None, params=None)¶

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
    else:
        picats = interactions.find_pi_cation_interactions(recep,
                                    struct2=struct)

Parameters

struct1 (schrodinger.structure.Structure object) – first structure to compute pi-cation interactions for
struct2 (schrodinger.structure.Structure object) – second structure to compute pi-cation interactions for or or None if the first structure should be used.
atoms1 (list of atom indices) – atoms in struct1 defining the selection to be examined. If not passed, all atoms will be used.
atoms2 (list of atom indices) – atoms in struct2 defining the selection to be examined. If not passed, all atoms will be used. If struct2 is not specified struct1 will be used.
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, atoms1=None, atoms2=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
    else:
        pipi = interactions.find_pi_pi_interactions(recep, 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.
atoms1 (list of atom indices) – atoms in struct1 defining the rings that will be examined. If not passed, all atoms will be used.
atoms2 (list of atom indices) – atoms in struct2 defining the rings that will be examined. If not passed, all atoms will be used. struct2 must be specified if this argument is used.
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.