schrodinger.application.desmond.image_generator module

class schrodinger.application.desmond.image_generator.ImageGenerator

Bases: object

A base class to generate 2D structure image file from SMILES

__init__()

Initialize self. See help(type(self)) for accurate signature.

getSupportedFormats()

generate(smiles, image, format=None)

Generating 2D image file from SMILES string :type smiles: string :param smiles: SMILES string representing molecule structure. :type image: string :param image: The output image file name of 2D structure. :type format: string :param format: output format of the image file. By default,

the output format will be deduced from the output image file name.

register(format, generator)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.image_generator', '__doc__': '\n A base class to generate 2D structure image file from SMILES\n ', '__init__': <function ImageGenerator.__init__>, 'getSupportedFormats': <function ImageGenerator.getSupportedFormats>, 'generate': <function ImageGenerator.generate>, 'register': <function ImageGenerator.register>, '__dict__': <attribute '__dict__' of 'ImageGenerator' objects>, '__weakref__': <attribute '__weakref__' of 'ImageGenerator' 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.application.desmond.image_generator'

__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.desmond.image_generator.SchrodImageGenerator

Bases: schrodinger.application.desmond.image_generator.ImageGenerator

A class to generate 2D structure image file from SMILES using Schrodinger toolkit.

__init__()

Initialize self. See help(type(self)) for accurate signature.

setBoundingRect(x, y, width, height)

smiles2mol(smiles)

mol2svg(mol, svg_fname)

smiles2svg(smiles, svg_fname)

mol2image(mol, image_fname, hl_atoms=[], hl_bonds=[])

smiles2image(smiles, image_fname)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.image_generator', '__doc__': '\n A class to generate 2D structure image file from SMILES using Schrodinger\n toolkit.\n ', '__init__': <function SchrodImageGenerator.__init__>, 'setBoundingRect': <function SchrodImageGenerator.setBoundingRect>, '_load_modules': <function SchrodImageGenerator._load_modules>, 'smiles2mol': <function SchrodImageGenerator.smiles2mol>, 'mol2svg': <function SchrodImageGenerator.mol2svg>, 'smiles2svg': <function SchrodImageGenerator.smiles2svg>, 'mol2image': <function SchrodImageGenerator.mol2image>, 'smiles2image': <function SchrodImageGenerator.smiles2image>, 'setCoorGenMode': <function SchrodImageGenerator.setCoorGenMode>})

__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.desmond.image_generator'

__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)

generate(smiles, image, format=None)

Generating 2D image file from SMILES string :type smiles: string :param smiles: SMILES string representing molecule structure. :type image: string :param image: The output image file name of 2D structure. :type format: string :param format: output format of the image file. By default,

the output format will be deduced from the output image file name.

getSupportedFormats()

register(format, generator)

setCoorGenMode(mode)