schrodinger.analysis.visanalysis.volumedatastructureutils module

schrodinger.analysis.visanalysis.volumedatastructureutils.BoundingInformation(st, resolution=None, extend=(0.0, 0.0, 0.0))[source]

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.

Parameters

  • st (schrodinger.structure.Structure) – The structure to be processed by the function.

  • resolution (iterable) – The resolution to use, specified in world-coordinates.

  • extend (iterable) – 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.

Returns

These are the values of N, resolution and origin required by a new VolumeData instance.

Return type

C{tuple< iterable< int, 3 >, iterable< float, 3 >, iterable< float, 3 > >

schrodinger.analysis.visanalysis.volumedatastructureutils.BoundingInformationL(sts, resolution=None, extend=(0.0, 0.0, 0.0))[source]

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.

Parameters

  • sts (iterable) – The set of structures to be processed. (This could be a StructureReader instance).

  • resolution (iterable) – The resolution to use, specified in world-coordinates.

  • extend (iterable) – 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.

Returns

These are the values of N, resolution and origin required by a new VolumeData instance.

Return type

C{tuple< iterable< int, 3 >, iterable< float, 3 >, iterable< float, 3 > >

schrodinger.analysis.visanalysis.volumedatastructureutils.VDWMask(atoms, N=None, resolution=None, origin=None, vdwScale=1.0)[source]

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

  • atoms (iterable over schrodinger.structure.StructureAtom) – Atoms to be considered.

  • N (iterable) – The parameters to use when sizing the output VolumeData

  • resolution (iterable) – The parameters to use when sizing the output VolumeData

  • origin (iterable) – The parameters to use when sizing the output VolumeData

  • vdwScale (float) – A scaling factor for the atomic vdW-radii

Returns

The calculated vdW-mask

Return type

VolumeData