Package cinfony :: Module silverwebel :: Class Molecule

Class Molecule

object --+
         |
        Molecule

Represent a Webel Molecule.

Required parameter:
   smiles -- a SMILES string or any type of cinfony Molecule

Attributes:
   formula, molwt, title

Methods:
   calcfp(), calcdesc(), draw(), write() 
  
The underlying SMILES string can be accessed using the attribute:
   smiles

Instance Methods

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

source code

formula(self)

source code

molwt(self)

source code

calcdesc(self, descnames=[])
Calculate descriptor values.

source code

calcfp(self, fptype="std")
Calculate a molecular fingerprint.

source code

write(self, format="smi", filename=None, overwrite=False)
Write the molecule to a file or return a string.

source code

__str__(self)
str(x)

source code

draw(self)
Create a 2D depiction of the molecule.

source code

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

Properties
Inherited from `object`: `__class__`

Method Details

init(self, smiles)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

formula(self)

source code

Decorators:

@property

molwt(self)

source code

Decorators:

@property

calcdesc(self, descnames=[])

source code

Calculate descriptor values.

Optional parameter:
   descnames -- a list of names of descriptors

If descnames is not specified, all available descriptors are
calculated. See the descs variable for a list of available
descriptors.

calcfp(self, fptype="std")

source code

Calculate a molecular fingerprint.

Optional parameters:
   fptype -- the fingerprint type (default is "std"). See the
             fps variable for a list of of available fingerprint
             types.

write(self, format="smi", filename=None, overwrite=False)

source code

Write the molecule to a file or return a string.

Optional parameters:
   format -- see the informats variable for a list of available
             output formats (default is "smi")
   filename -- default is None
   overwite -- if the output file already exists, should it
               be overwritten? (default is False)

If a filename is specified, the result is written to a file.
Otherwise, a string is returned containing the result.

To write multiple molecules to the same file you should use
the Outputfile class.

str(self)
(Informal representation operator)

source code

str(x)

Overrides: object.__str__: (inherited documentation)

Class Molecule

__init__(self, smiles) (Constructor)

formula(self)

molwt(self)

calcdesc(self, descnames=[])

calcfp(self, fptype="std")

write(self, format="smi", filename=None, overwrite=False)

__str__(self) (Informal representation operator)

init(self, smiles)
(Constructor)

str(self)
(Informal representation operator)