Package schrodinger :: Package application :: Package matsci :: Module amorphous :: Class XYZVolumeGraph

Class XYZVolumeGraph

object --+
         |
        XYZVolumeGraph

Create a networkx graph to search the voids in structure.

Instance Methods

[hide private]

__init__(self, struct, spacing=2.0, scaffold=None)
Create networkx graph based on the structure PBC or coordinates.

tuple

getNodeXYZ(self, node)
Convert networkx node (tuple of X, Y, Z index) to XYZ coordinates

removeOverlappedNodes(self, atom_ids=None, vdw_scale=1.0)
Remove all nodes that overlap a bitset-on atom (all atoms by default) in current structure.

tuple

voids(self)
A generator that returns groups of connected nodes that define voids in the structure.

tuple

getLargestVoid(self)
Get the largest void.

tuple

getBuriedNode(self, blob)
A generator that returns nodes that is buried inside the blob of connected nodes.

tuple

getBuriedXYZ(self, blob)
Like getBuriedNode but return the xyz coordinates.

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, struct, spacing=2.0, scaffold=None)
(Constructor)

Create networkx graph based on the structure PBC or coordinates.

Parameters:

struct (schrodinger.structure.Structure) - The structure to compute the graph over
spacing (float) - The approximate spacing (Angstroms) between graph nodes. The actual grid spacing will be adjusted in each direction to ensure uniform grid point distribution, and the actual spacing used in each direction can be found in the self.xyz_spacings list
scaffold (Scaffold or None) - a structure that occupies space as a cluster of molecules.

Overrides: object.__init__

getNodeXYZ(self, node)

Convert networkx node (tuple of X, Y, Z index) to XYZ coordinates

Parameters:

node (tuple) - the node to convert

Returns: tuple

A tuple of x, y z coordinates in Angstroms

removeOverlappedNodes(self, atom_ids=None, vdw_scale=1.0)

Remove all nodes that overlap a bitset-on atom (all atoms by default) in current structure.

Parameters:

atom_ids (set or None) - if not None, only check clashes for atoms in this set
vdw_scale (float) - VDW scale factor to use

voids(self)

A generator that returns groups of connected nodes that define voids in the structure.

Returns: tuple: Each returned value is a set of nodes that are all connected and define a void blob. The sets are returned in order of size, largest to smallest

getLargestVoid(self)

Get the largest void.

Returns: tuple: The set of nodes that form the largest void in the structure

getBuriedNode(self, blob)

A generator that returns nodes that is buried inside the blob of connected nodes. Buried nodes have lots of connections to other nodes.

Parameters:

blob (a set of tuples) - Each item of the set is a node

Returns: tuple

The buried node

getBuriedXYZ(self, blob)

Like getBuriedNode but return the xyz coordinates.

Parameters:

blob (a set of tuples) - Each item of the set is a node

Returns: tuple

A tuple of x, y z coordinates in Angstroms

Class XYZVolumeGraph

__init__(self, struct, spacing=2.0, scaffold=None) (Constructor)

getNodeXYZ(self, node)

removeOverlappedNodes(self, atom_ids=None, vdw_scale=1.0)

voids(self)

getLargestVoid(self)

getBuriedNode(self, blob)

getBuriedXYZ(self, blob)

init(self, struct, spacing=2.0, scaffold=None)
(Constructor)