Package schrodinger :: Package analysis :: Package visanalysis :: Module volumedataio

[frames] | no frames]

Module volumedataio

Classes

[hide private]

_MMVol
The _MMVol class acts as a wrapper around low-level MMVol objects.

Functions

[hide private]

class object

Singleton(cls)
This function acts as a decorator to a class defintion.

_MMInitialiser()
_getinstance: Called to retrieve the singleton instance for the specified class.

VolumeData

LoadPickle(stream=None, filename=None)
This function retrieves a VolumeData instance from the specified Python Pickle file.

SavePickle(volumeData, stream=None, filename=None)
This function saves the specified VolumeData object to the specified file in Python Pickle format.

VolumeData

_MMVolToVolumeData(mmvol, handleNonOrthogonalAxes=False)
This function converts the specified mmvol object to a VolumeData instance.

VolumeData

LoadVisFile(filename)
This function retrieves a VolumeData object from a Schrodinger .vis file.

_VolumeDataToMMVol(volumeData, mmvol)
This function configures the specified mmvol object to be equivalent to the specified VolumeData.

SaveVisFile(volumeData, filename)
This function saves a VolumeData object to a Schrodinger .vis file.

SaveCCP4File(volumeData, filename)
This function saves a VolumeData object to a CCP4 file.

VolumeData

LoadCNSFile(filename)
This function loads a VolumeData object from a CNS file.

Variables

[hide private]

_X = 0
hash(x)

_Y = 1

_Z = 2

_VX = array([ 1., 0., 0.])

_VY = array([ 0., 1., 0.])

_VZ = array([ 0., 0., 1.])

_MUST_SPECIFY_FILE = 'Either stream or filename must be specif...

_NON_ORTHOGONAL = 'Non-orthogonal axes are currently not permi...

_DEFAULT_NAME = 'VolumeData'

_PYTHON = 'PYTHON'

_mmInitialiser = _MMInitialiser()

__package__ = 'schrodinger.analysis.visanalysis'

Function Details

[hide private]

Singleton(cls)

This function acts as a decorator to a class defintion. Its purpose is to ensure that only one instance of the class is ever accessible by the user. We use this single instance in place of global variables as it makes the code considerably more explicit.

Parameters:

cls (class object) - Specifies the class which is to become a singleton.

Returns: class object

The decorated class-object

LoadPickle(stream=None, filename=None)

This function retrieves a VolumeData instance from the specified Python Pickle file.

Parameters:

stream (file) - The stream containing the Pickle information. Overrides filename
filename (string) - The file containing a Pickle holding a VolumeData object. This argument is ignored if stream is not None.

Returns: VolumeData

The VolumeData object extracted from the Pickle.

SavePickle(volumeData, stream=None, filename=None)

This function saves the specified VolumeData object to the specified file in Python Pickle format.

Parameters:

volumeData (VolumeData) - The VolumeData object to be serialised
stream (file) - The stream to save the Pickle information to
filename (string) - The file to save the Pickle information to. This argument is ignored if stream is not None

_MMVolToVolumeData(mmvol, handleNonOrthogonalAxes=False)

This function converts the specified mmvol object to a VolumeData instance.

Parameters:

mmvol - The MMVol object to be loaded into a VolumeData instance
mmvol - MMVol handle
handleNonOrthogonalAxes (bool) - True if the function should handle non-orthogonal axes. False otherwise. [Currently this parameter is ignored and the function will throw an exception if it encounters non- orthogonal axes.

Returns: VolumeData

The newly constructed VolumeData instance

LoadVisFile(filename)

This function retrieves a VolumeData object from a Schrodinger .vis file.

Parameters:

filename (string) - A Schrodinger .vis file containing a valid mmvol object

Returns: VolumeData

The VolumeData extracted from the contents of the .vis file

_VolumeDataToMMVol(volumeData, mmvol)

This function configures the specified mmvol object to be equivalent to the specified VolumeData.

Parameters:

volumeData (VolumeData) - The VolumeData object to be converted
mmvol (MMVol handle) - A pre-allocated mmvol handle which awaits configuration

SaveVisFile(volumeData, filename)

This function saves a VolumeData object to a Schrodinger .vis file.

Parameters:

volumeData (volumeData) - The VolumeData to be serialised
filename (string) - Where to store the .vis file

SaveCCP4File(volumeData, filename)

This function saves a VolumeData object to a CCP4 file.

Parameters:

volumeData (VolumeData) - The VolumeData to be serialised
filename (string) - Where to store the .CCP4 file

LoadCNSFile(filename)

This function loads a VolumeData object from a CNS file.

Parameters:

filename (string) - The .cns formatted file

Returns: VolumeData

The VolumeData object extracted from the .cns file.

Variables Details

[hide private]

_MUST_SPECIFY_FILE

Value:

'Either stream or filename must be specified.'

_NON_ORTHOGONAL

Value:

'Non-orthogonal axes are currently not permitted.'