Package schrodinger :: Module structure :: Class SmilesStructure

Class SmilesStructure

object --+
         |
        SmilesStructure

SMILES representation of a Structure that is returned by SmilesReader and SmilesCsvReader. When written to a SMILES-formatted file, properties other than the title are not retained.

Instance Methods

[hide private]

__init__(self, pattern, properties=None)
x.__init__(...) initializes x; see help(type(x)) for signature

__str__(self)
Return a string representation of this structure.

write(self, filename)
Write the structure to a SMILES formatted file.

append(self, filename)
Append the structure to a SMILES formatted file.

_writeSmiles(self, fh)

_writeSmilesCsv(self, filename, append)

getDistortedStructure(self)
Return a (potentially distorted) Structure object for this SMILES.

Structure.Structure

get2dStructure(self)
Return a 2D Structure object for this SMILES.

Structure.Structure

get3dStructure(self, require_stereo=True)
Return a 3D Structure object for this SMILES with all hydrogens added.

neutralize(self)
Neutralize this SMILES structure.

_getSmilesTitle(self)

_setSmilesTitle(self, title)

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Variables

[hide private]

mmsmiles_initialized = False
hash(x)

Properties

[hide private]

title

Inherited from object: __class__

Method Details

[hide private]

init(self, pattern, properties=None)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

Return a string representation of this structure.

Overrides: object.__str__

getDistortedStructure(self)

Return a (potentially distorted) Structure object for this SMILES. Deprecated; use get3dStructure() method instead.

get2dStructure(self)

Return a 2D Structure object for this SMILES. The structure will have only 2D coordinates, with stereo annotation properties for chiral atoms with specified chirality. NOTE: Use for 2D applications only.

Returns: Structure.Structure: 2D structure.

get3dStructure(self, require_stereo=True)

Return a 3D Structure object for this SMILES with all hydrogens added.

Parameters:

require_stereo (bool) - Whether to require all chiral centers to have defined stereochemistry via annotation properties. Defaults to True. UndefinedStereochemistry exception is raised if any chiral atom has ambiguous chirality. If set to False, ambiguous chiralities will be expanded arbitrarily.

Returns: Structure.Structure

Volumized 3D structure.

Property Details

[hide private]

title

Get Method:: _getSmilesTitle(self)
Set Method:: _setSmilesTitle(self, title)

Class SmilesStructure

__init__(self, pattern, properties=None) (Constructor)

__str__(self) (Informal representation operator)

getDistortedStructure(self)

get2dStructure(self)

get3dStructure(self, require_stereo=True)

title

init(self, pattern, properties=None)
(Constructor)

str(self)
(Informal representation operator)