Package schrodinger :: Package analysis :: Package visanalysis :: Module volumedatastructureutils

Module volumedatastructureutils

Functions

BoundingInformation(st, resolution=None, extend=(0.0,0.0,0.0))
This function calculates values for N, resolution and origin for a VolumeData instance that would enclose the specified structure.

BoundingInformationL(sts, resolution=None, extend=(0.0,0.0,0.0))
This function calculates values for N, resolution and origin for a VolumeData instance that would enclose the specified set of structures.

VolumeData

VDWMask(st, N=None, resolution=None, origin=None, vdwScale=1.0)
This function creates a new VolumeData instance that stores a vdW-mask for the specified molecule.

Variables

[hide private]

_DOWN_COLUMNS = 0

_ACROSS_ROWS = 1

Function Details

[hide private]

BoundingInformation(st, resolution=None, extend=(0.0,0.0,0.0))


This function calculates values for N, resolution and origin for a
VolumeData instance that would enclose the specified structure. The
function accepts an optional extend value, which enlarges the overall
VolumeData by the specified amount in each direction.

@param st: The structure to be processed by the function.
@type st: C{L{schrodinger.structure.Structure}}
@param resolution: The resolution to use, specified in world-coordinates.
@type resolution: C{iterable< float, 3 >}
@param extend: How much to extend the VolumeData around the molecule. 
The default value will ensure that the minimum X, Y, Z coordinate just fit 
within the VolumeData i.e. no account will be made for atomic volume.
@type extend: C{iterable< float, 3 >}

@return: These are the values of N, resolution and origin required by a new 
VolumeData instance.
@rtype: C{tuple< iterable< int, 3 >, iterable< float, 3 >, 
iterable< float, 3 > >

BoundingInformationL(sts, resolution=None, extend=(0.0,0.0,0.0))


This function calculates values for N, resolution and origin for a
VolumeData instance that would enclose the specified set of structures.
The function accepts an optional extend value, which enlarges the overall
VolumeData by the specified amount in each direction.

@param sts: The set of structures to be processed. (This could be a 
StructureReader instance).
@type sts: C{iterable< schrodinger.structure.Structure >}
@param resolution: The resolution to use, specified in world-coordinates.
@type resolution: C{iterable< float, 3 >}
@param extend: How much to extend the VolumeData around the molecule. 
The default value will ensure that the minimum X, Y, Z coordinate just fit 
within the VolumeData i.e. no account will be made for atomic volume.
@type extend: C{iterable< float, 3 >}

@return: These are the values of N, resolution and origin required by a new 
VolumeData instance.
@rtype: C{tuple< iterable< int, 3 >, iterable< float, 3 >, 
iterable< float, 3 > >

VDWMask(st, N=None, resolution=None, origin=None, vdwScale=1.0)

This function creates a new VolumeData instance that stores a vdW-mask for the specified molecule. A vdW-mask stores 1.0 for data-point within the vdW-surface of the molecule and 0.0 elsewhere.

Parameters:

st (schrodinger.structure.Structure) - The molecule
N (iterable< int, 3 >) - The parameters to use when sizing the output VolumeData
resolution (iterable< float, 3 >) - The parameters to use when sizing the output VolumeData
origin (iterable< float, 3 >) - The parameters to use when sizing the output VolumeData
vdwScale (float) - A scaling factor for the atomic vdW-radii

Returns: VolumeData

The calculated vdW-mask