schrodinger.application.phase.packages.shape_binary_utils module¶
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class
schrodinger.application.phase.packages.shape_binary_utils.
ShapeFileWriter
(filename, metadata, compress)¶ Bases:
contextlib.AbstractContextManager
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__init__
(filename, metadata, compress)¶ - 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.
compress (bool) – Compress the file using zlib.
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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).
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class
schrodinger.application.phase.packages.shape_binary_utils.
ShapeFileReader
(filename, block_size=10000)¶ Bases:
contextlib.AbstractContextManager
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__init__
(filename, block_size=10000)¶ - Parameters
filename (str) – File name.
block_size (int) – Number of (title, structures) entries to read in one scoop.
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property
metadata
¶ File-scope metadata from the associated “shape binary” file.
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getBlock
(shapes=None, titles=None)¶ Reads next block of shapes and their titles. Returns (None, None) on EOF, raises RuntimeError on errors. Uses memory associated with
shapes
and/ortitles
unless the parameter is None.- Parameters
shapes (shape.ShapeStructureVector) – SWIG-wrapped c++ std::vector<shape::ShapeStructure>.
titles (shape.ShapeBlockTitleVector) – SWIG-wrapped c++ std::vector<std::pair<std::string, size_t>>.
- Returns
Blocks of shapes and their titles. The
titles
is a vector of (name, number-of-shape-structures) pairs, andshapes
is a vector of shape.ShapeStructure instances. len(shapes) == titles[0][1] + titles[1][1] + … + titles[N][1]- Return type
(shape.ShapeStructureVector, shape.ShapeBlockTitleVector)
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class
schrodinger.application.phase.packages.shape_binary_utils.
SingularShapeFileReader
(filename)¶ Bases:
schrodinger.application.phase.packages.shape_binary_utils.ShapeFileReader
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__init__
(filename)¶ - Parameters
filename (str) – File name.
block_size (int) – Number of (title, structures) entries to read in one scoop.
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getBlock
(shapes=None, titles=None)¶ Reads next block of shapes and their titles. Returns (None, None) on EOF, raises RuntimeError on errors. Uses memory associated with
shapes
and/ortitles
unless the parameter is None.- Parameters
shapes (shape.ShapeStructureVector) – SWIG-wrapped c++ std::vector<shape::ShapeStructure>.
titles (shape.ShapeBlockTitleVector) – SWIG-wrapped c++ std::vector<std::pair<std::string, size_t>>.
- Returns
Blocks of shapes and their titles. The
titles
is a vector of (name, number-of-shape-structures) pairs, andshapes
is a vector of shape.ShapeStructure instances. len(shapes) == titles[0][1] + titles[1][1] + … + titles[N][1]- Return type
(shape.ShapeStructureVector, shape.ShapeBlockTitleVector)
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property
metadata
¶ File-scope metadata from the associated “shape binary” file.
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