Class PiStackFinder

object --+
         |
        PiStackFinder

Find pi-pi interactions in proteins

Instance Methods

[hide private]

__init__(self, max_stack_dist=4.0)
Initialize a new object using the specified interaction cutoffs

iter

piStacksIterator(self, struc, group_strucs)
Create an iterator that iterates through all pi stacking between two groups of atoms

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Methods

[hide private]

iter

createIter(cls, struc, group_strucs, max_stack_dist=4.0)
A convenience function to initalize the class and return an iterator

Class Variables

[hide private]

set NON_AROMATIC_RES = set(['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GL...
A set of residue types that don't contain aromatic side chains

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, max_stack_dist=4.0)
(Constructor)

Initialize a new object using the specified interaction cutoffs

Parameters:

max_stack_dist (float) - The maximum distance between two ring centroids allowed for face-face interactions.

Overrides: object.__init__

createIter(cls, struc, group_strucs, max_stack_dist=4.0)
Class Method

A convenience function to initalize the class and return an iterator

Parameters:

struc (schrodinger.structure.Structure) - The structure being analyzed
group_strucs (list) - A list of [Structure object for group 1, Structure object for group 2]
max_stack_dist (float) - The maximum distance between two ring centroids allowed for face-face interactions.

Returns: iter

An iterator that produces tuples of two atom number lists, representing (the ring atoms from group 1 involved in the stacking, the ring atoms from group 2 involved in the stacking

piStacksIterator(self, struc, group_strucs)

Create an iterator that iterates through all pi stacking between two groups of atoms

Parameters:

struc (schrodinger.structure.Structure) - The structure being analyzed
group_strucs (list) - A list of [Structure object for group 1, Structure object for group 2]

Returns: iter

An iterator that produces tuples of two atom number lists, representing (the ring atoms from group 1 involved in the stacking, the ring atoms from group 2 involved in the stacking

Class Variable Details

[hide private]

NON_AROMATIC_RES

A set of residue types that don't contain aromatic side chains

Type:: set

Value:

set(['ALA',
     'ARG',
     'ASN',
     'ASP',
     'CYS',
     'GLN',
     'GLU',
     'GLY',
...

Class PiStackFinder

__init__(self, max_stack_dist=4.0) (Constructor)

createIter(cls, struc, group_strucs, max_stack_dist=4.0) Class Method

piStacksIterator(self, struc, group_strucs)

NON_AROMATIC_RES

init(self, max_stack_dist=4.0)
(Constructor)

createIter(cls, struc, group_strucs, max_stack_dist=4.0)
Class Method