schrodinger.structutils.smilesfilter module

A group of functions and classes to help filtering structure files on unique SMILES strings.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.structutils.smilesfilter.remove_dupes(smiles_generator, struct_iterator, put_unique, put_dupes=None, error_handler=None, reporter=None)

Process structures from the provided structure iterator ‘struct_iterator’ using the ‘smiles_generator’ to compute unique SMILES strings. Unique structures are passed to the ‘put_unique’ callback and duplicates to ‘put_dupes’ (if provided).

Parameters:

• struct_iterator (iterator return Structure objects) – Any iterator returning Structure objects (such as a StructureReader) will work.
• put_dupes (callable) – These functions will be called with (structure, SMILES string) arguments in the appropriate situation.
• error_handler (callable) – A callable that takes (index, structure, exception) for cases where SMILES generation generates a RuntimeError.
• reporter (FilterReporter) – If present, information will be logged.

schrodinger.structutils.smilesfilter.add_smiles(smiles_generator, struct_iterator, put_output, error_handler=None)

Calculate SMILES strings with ‘smiles_generator’ for each structure in ‘struct_iterator’.

Parameters

smiles_generator (SmilesGenerator)

struct_iterator (iterator return Structure objects)

Any iterator returning Structure objects (such as a StructureReader) will work.

put_output (callable)

This function will be called with (structure, SMILES string) arguments when a SMILES string can be calculated.

error_handler (callable)

A callback function that takes (index, structure, exception) and is called in cases where SMILES generation generates a RuntimeError.

class schrodinger.structutils.smilesfilter.FilterReporter(logger)

Bases: object

A class to handle reporting of results from the remove_dupes function.

__init__(logger)

Parameters

logger (logging.Logger)

The logger instance that will be used to output messages.

logResult(index, orig_index, title, smiles, dupe_index)

Log messages for a given result.

Parameters

index (int)

Index of the current structure.

orig_index (int)

Index of the unique structure of which the current one is a duplicate.

title (str)

Title of the current structure.

smiles (str)

SMILES string of the structure.

dupe_index (int)

Index of the duplicate structure in the saved duplicates file.

summarize(total, unique, duplicates, error_count)

Generate a summary of the filter results.

Parameters

total (int)

Total number of structures filtered.

unique (int)

Number of unique structures found.

duplicates (int)

Number of duplicates found.

error_count (int)

Number of structures generating errors in SMILES conversion.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.smilesfilter', '__doc__': '\n A class to handle reporting of results from the remove_dupes function.\n ', '__init__': <function FilterReporter.__init__>, 'logResult': <function FilterReporter.logResult>, 'summarize': <function FilterReporter.summarize>, '__dict__': <attribute '__dict__' of 'FilterReporter' objects>, '__weakref__': <attribute '__weakref__' of 'FilterReporter' objects>})

__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.structutils.smilesfilter'

__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.structutils.smilesfilter.SmilesErrorHandler(logger, struct_writer=None, message=None)

Bases: object

A class that acts as an error handler for cases where SMILES generation fails. It is used as a callable that takes arguments of (index, struct, exception).

__init__(logger, struct_writer=None, message=None)

Parameters

logger (logging.Logger)

The logger instance that will be used to output messages.

struct_writer (obj with append method)

An instance that will log structures that have errors. Any instance with an append method (such as a StructureWriter or list) can be used.

message (str)

The message to use as the logging template. It should have format conversion specifiers for (index, structure title, exception) (types of int, str, exception).

__call__(index, struct, exception)

This logs the message to the object’s ‘logger’ attribute and appends the structure to the object’s ‘struct_writer’, which can be anything with an append method.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.smilesfilter', '__doc__': '\n A class that acts as an error handler for cases where SMILES generation\n fails. It is used as a callable that takes arguments of (index, struct,\n exception).\n\n ', '__init__': <function SmilesErrorHandler.__init__>, '__call__': <function SmilesErrorHandler.__call__>, '__dict__': <attribute '__dict__' of 'SmilesErrorHandler' objects>, '__weakref__': <attribute '__weakref__' of 'SmilesErrorHandler' objects>})

__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.structutils.smilesfilter'

__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)