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Cinfony
Package cinfony :: Module jchem :: Class Molecule
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Class Molecule

source code

object --+
         |
        Molecule

Represent a JChem Molecule.

Required parameters:
   Molecule -- a JChem Molecule or any type of cinfony Molecule

Attributes:
   atoms, data, exactmass, formula, molwt, title

Methods:
   addh(), calcfp(), calcdesc(), draw(), removeh(), write()

The underlying JChem Molecule can be accessed using the attribute:
   Molecule
The associated JChem MolHandler can be accessed using the attribute:
   MolHandler
Instance Methods
 
__init__(self, Molecule)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
__iter__(self)
Iterate over the Atoms of the Molecule.		 source code
 
__str__(self)
str(x)		 source code
 
addh(self)
Add hydrogens.		 source code
 
removeh(self)
Remove hydrogens.		 source code
 
write(self, format='smi', filename=None, overwrite=False)
Write the molecule to a file or return a string.		 source code
 
calcfp(self, fp='ecfp')
Calculate a molecular fingerprint.		 source code
 
calcdesc(self, descnames=[])
Calculate descriptor values.		 source code
 
make3D(self)
Generate 3D coordinates.		 source code
 
draw(self, show=True, filename=None, update=False, usecoords=False)
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
  atoms
  data
  formula
  exactmass
  molwt
  title

Inherited from object: __class__

Method Details

__init__(self, Molecule)
(Constructor)

source code 

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

Overrides: object.__init__
(inherited documentation)

__iter__(self)

source code  
Iterate over the Atoms of the Molecule.

This allows constructions such as the following:
   for atom in mymol:
       print atom

__str__(self)
(Informal representation operator)

source code 

str(x)

Overrides: object.__str__
(inherited documentation)

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.

calcfp(self, fp='ecfp')

source code  
Calculate a molecular fingerprint.

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

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.

make3D(self)

source code 

Generate 3D coordinates.

Hydrogens are added, and a low energy conformer is found using the MMFF94 forcefield.


Property Details

atoms

Get Method:
unreachable.atoms(self)

data

Get Method:
unreachable.data(self)

formula

Get Method:
unreachable.formula(self)

exactmass

Get Method:
unreachable.exactmass(self)

molwt

Get Method:
unreachable.molwt(self)

title

Get Method:
_gettitle(self)
Set Method:
_settitle(self, val)

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