schrodinger.application.phase.packages.shape_creation_logic module

Creation of “binary shape files” from several kind of sources (PHASE-2070).

schrodinger.application.phase.packages.shape_creation_logic.add_arguments(p)

Adds shape-creation-specific arguments to the parser.

Parameters:p (argparser.ArgumentParser) – Parser-like instance.

schrodinger.application.phase.packages.shape_creation_logic.validate_args(args)

Validates command-line arguments added by add_arguments.

Parameters:args (argparse.Namespace) – Namespace holding command line options. Returns:Tuple of validation success and error message. Return type:(bool, str)

schrodinger.application.phase.packages.shape_creation_logic.runtimize_paths(args)

Runtimizes input file paths for the command line arguments.

Parameters:args (argparse.Namespace) – Namespace populated with command line arguments.

schrodinger.application.phase.packages.shape_creation_logic.get_input_files(args)

Identifies input files among arguments (for job control purposes).

Parameters:args (argparse.Namespace) – Namespace populated with command line arguments.

schrodinger.application.phase.packages.shape_creation_logic.get_jobname_and_outfile(args)

Returns the job name and job name-derived output file name. If job name is not provided it gets derived from the input file name.

Parameters:args (argparse.Namespace) – Namespace populated with command line arguments. Returns:job name, output file name Return type:str, str

class schrodinger.application.phase.packages.shape_creation_logic.ShapeCreator(args)

Bases: object

__init__(args)

Expects validated and runtimized command line arguments.

Parameters:args (argparse.Namespace) – Namespace populated with command line arguments.

limit

source

reader_options

generator

getMetadata()

Returns JSON-able representation of the self.

__iter__()

Yields (ID, shapes) tuples

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.shape_creation_logic', '__init__': <function ShapeCreator.__init__>, 'limit': <property object>, 'source': <property object>, 'reader_options': <property object>, 'generator': <property object>, 'getMetadata': <function ShapeCreator.getMetadata>, '__iter__': <function ShapeCreator.__iter__>, '__dict__': <attribute '__dict__' of 'ShapeCreator' objects>, '__weakref__': <attribute '__weakref__' of 'ShapeCreator' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__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_creation_logic'

__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).

__subclasshook__()

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)

schrodinger.application.phase.packages.shape_creation_logic.execute(args)

The “main” subroutine for the “create” task.

Parameters:args (argparse.Namespace) – Namespace populated with command line arguments.