schrodinger.application.phase.packages.shape_ligprep module

Thin LigPrep wrapper and related subroutines (for PHASE-2070).

class schrodinger.application.phase.packages.shape_ligprep.LigPrep(input_file, options='[]')

Bases: object

__init__(input_file, options='[]')

Parameters:

• input_file (str) – Input file name.
• options (str) – Ligprep command line options (in JSON format).

Raises:

RuntimeError – If something goes wrong.

close()

getInputReader(text=False)

Returns an iterator over the input file associated with the LigPrep instance. If text is False, the iterator returns structure.Structure instances. Otherwise the iterator is an _InputReader that returns (text, structure) tuples.

Parameters:text – Whether input text reading is desired. Ptype text:bool Returns:Iterator over input. Rype:StructureReader, ligprep SMILES reader or _InputReader

prepareStructure(ct)

Applies ligprep to ct.

Returns:(outcomes, failures, summary) tuple Return type:(list(structure.Structure), list(structure.Structure), dict)

yieldStructures(text=False)

Reads consecutive entries from the input file, applies LigPrep and yields resulting structures. Optionally also yields input text from which the structures were obtained. TODO: support “strip” – minimize text size, like keep only the SMILES itself.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.shape_ligprep', '__init__': <function LigPrep.__init__>, 'close': <function LigPrep.close>, 'getInputReader': <function LigPrep.getInputReader>, 'prepareStructure': <function LigPrep.prepareStructure>, 'yieldStructures': <function LigPrep.yieldStructures>, '__dict__': <attribute '__dict__' of 'LigPrep' objects>, '__weakref__': <attribute '__weakref__' of 'LigPrep' 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_ligprep'

__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_ligprep.add_ligprep_arguments(parser)

Registers ligprep-specific options.

Parameters:parser (argparse.ArgumentParser) – Command line argument parser.

schrodinger.application.phase.packages.shape_ligprep.validate_ligprep_arguments(args)

Validates ligprep-specific command line options.

Parameters:args (argparse.Namespace) – Populated argparse.Namespace instance. Returns:Tuple of validation success, and error message. Return type:bool, str

schrodinger.application.phase.packages.shape_ligprep.validate_ligprep_options(text)

Validates ligprep-specific command-line arguments.

Parameters:text (str) – Ligprep options as list of strings in JSON format. Returns:Tuple of validation success, and error message. Return type:bool, str