schrodinger.application.phase.packages.conformer_reader module

Conformer structure reader, which extracts blocks of conformers from the given input based on perception options.

Copyright Schrodinger LLC, All Rights Reserved.

class schrodinger.application.phase.packages.conformer_reader.ConformerReaderOptions(args, preferred_subset)

Bases: object

__init__(args, preferred_subset)

Initializes command line options used to read conformer blocks.

Parameters:args (argparser.Namespace) – argparser.Namespace with command line options

asDict()

Intended for serialization support.

Returns:Dictionary that describes the instance. Return type:dict

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.conformer_reader', '__init__': <function ConformerReaderOptions.__init__>, 'asDict': <function ConformerReaderOptions.asDict>, '__dict__': <attribute '__dict__' of 'ConformerReaderOptions' objects>, '__weakref__': <attribute '__weakref__' of 'ConformerReaderOptions' 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.conformer_reader'

__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)

class schrodinger.application.phase.packages.conformer_reader.ConformerReader(source, options)

Bases: object

__init__(source, options)

Initializes…

Parameters:

• source (str) – conformer structure input source
• options (ConformerReaderOptions) – reader options derived from command line options

db_ids

None implies source other than PhaseDB.

close()

getConformers(want_IDs=False)

Yields blocks of conformers from the source.

If want_IDs is True, yields tuples of (ID, conformers). If reading from PhaseDB, IDs are stringified DB IDs; for structure file source – IDs are m2io text for the structures; for ligprepping operation – IDs are given by the input text.

Yield:conformers or (name, conformers) pairs Ytype:list(structure.Structure) or (str, list(structure.Structure))

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.conformer_reader', '__init__': <function ConformerReader.__init__>, 'db_ids': <property object>, 'close': <function ConformerReader.close>, 'getConformers': <function ConformerReader.getConformers>, '_getReaderFromPhaseDb': <function ConformerReader._getReaderFromPhaseDb>, '_getReaderFromFile': <function ConformerReader._getReaderFromFile>, '_getReaderFromLigprep': <function ConformerReader._getReaderFromLigprep>, '_getConformers': <function ConformerReader._getConformers>, '_busToText': <staticmethod object>, '__dict__': <attribute '__dict__' of 'ConformerReader' objects>, '__weakref__': <attribute '__weakref__' of 'ConformerReader' 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.conformer_reader'

__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.conformer_reader.add_file_options(parser)

Adds file screening options to the provided parser and returns the argument group object that holds those options.

Parameters:parser (argparser.ArgumentParser) – Argument parser object Returns:Argument group object Return type:argparse._ArgumentGroup

schrodinger.application.phase.packages.conformer_reader.add_confgen_options(parser, refine)

Adds conformer generation options to the provided parser and returns the argument group object that holds those options.

Parameters:

• parser (argparser.ArgumentParser) – Argument parser object
• refine (bool) – Flag to add -refine as mutually exclusive option to -flex

Returns:

Argument group object

Return type:

argparse._ArgumentGroup

schrodinger.application.phase.packages.conformer_reader.add_standard_confgen_options(argument_group, refine)

Adds standard conformer generation options to the provided argument group.

Parameters:

• argument_group (argparser._ArgumentGroup) – Argument group object
• refine (bool) – Set to True if argument_group supports -refine flag

schrodinger.application.phase.packages.conformer_reader.get_confgen_options(args)

Creates conformer generation options from the supplied parser.

Parameters:args (argparse.Namespace) – Command line arguments. Returned:Conformer generation options Return type:PhpConfOptions

schrodinger.application.phase.packages.conformer_reader.get_dict_from_confgen_options(confgen_options)

Creates/populates dictionary that describes the confgen_options (intended for serialization support).

Parameters:confgen_options (PhpConfOptions) – Conformer generation options. Returns:Dictionary that can be used to re-construct the options. Return type:dict(str,)

schrodinger.application.phase.packages.conformer_reader.get_confgen_options_from_dict(obj)

Instantiates conformer generation options from a dictionary.

Parameters:obj (dict(str,)) – Dictionary that describes the options. Returns:Conformer generation options. Return type:PhpConfOptions

schrodinger.application.phase.packages.conformer_reader.validate_confgen_conflicts(args)

Checks options for conflicts between file options and confgen options not detected by ArgumentParser.parse_args and returns an informative error message if a conflict is found.

Parameters:args (argparser.Namespace) – argparser.Namespace with command line options Returns:tuple of validity and error message if a conflict is found Return type:bool, str

schrodinger.application.phase.packages.conformer_reader.validate_confgen_nddo(args)

Checks for illegal use of -nddo flag.

Parameters:args (argparser.Namespace) – argparser.Namespace with command line arguments Returns:tuple of validity and non-empty error message if not valid Return type:bool, str