schrodinger.application.phase.packages.shape_binary_utils module

class schrodinger.application.phase.packages.shape_binary_utils.ShapeFileWriter(filename, metadata='')

Bases: contextlib.AbstractContextManager

__init__(filename, metadata='')
Parameters:
  • filename (str) – File name (expected to exist if metadata is empty).
  • metadata (str) – Text to be stored as file-scope “metadata”. If empty, “append” opening mode is assumed. If not empty, existing file with the same name will be truncated.
__exit__(exc_type, exc_value, traceback)

Raise any exception triggered within the runtime context.

append(title, shapes)

Appends shapes to the associated binary file.

Parameters:
  • title (str) – Title of the shapes.
  • shapes (list(shape.ShapeStructure)) – List of shape.ShapeStructure instances (may have different number of spheres).
__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.shape_binary_utils', '__init__': <function ShapeFileWriter.__init__>, '__exit__': <function ShapeFileWriter.__exit__>, '_check': <function ShapeFileWriter._check>, 'append': <function ShapeFileWriter.append>, '__doc__': None, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__enter__()

Return self upon entering the runtime context.

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.phase.packages.shape_binary_utils'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.phase.packages.shape_binary_utils.ShapeFileReader(filename, block_size=10000)

Bases: contextlib.AbstractContextManager

__init__(filename, block_size=10000)
Parameters:
  • filename (str) – File name.
  • block_size (int) – Number of (title, structures) entries to read in one scoop.
__exit__(exc_type, exc_value, traceback)

Raise any exception triggered within the runtime context.

metadata

File-scope metadata from the associated “shape binary” file.

__iter__()

Yields blocks of named blocks of shape structures.

Returns:Blocks of shapes and their titles. The titles is a vector of (name, number-of-shape-structures) pairs, and shapes is a vector of shape.ShapeStructure instances. len(shapes) == titles[0][1] + titles[1][1] + … + titles[N][1]
Return type:(shape.ShapeStructureVector, shape.ShapeBlockTitleVector)
__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.shape_binary_utils', '__init__': <function ShapeFileReader.__init__>, '__exit__': <function ShapeFileReader.__exit__>, 'metadata': <property object>, '__iter__': <function ShapeFileReader.__iter__>, '__doc__': None, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__enter__()

Return self upon entering the runtime context.

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.phase.packages.shape_binary_utils'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)