Package cinfony :: Module cdk

Module cdk


cdk - A Cinfony module for accessing the CDK from CPython and Jython

Global variables:
  cdk - the underlying CDK Java library (org.openscience.cdk)
  informats - a dictionary of supported input formats
  outformats - a dictionary of supported output formats
  descs - a list of supported descriptors
  fps - a list of supported fingerprint types
  forcefields - a list of supported forcefields

Classes
	Outputfile Represent a file to which output is to be sent.
	Molecule Represent a cdkjpype Molecule.
	Fingerprint A Molecular Fingerprint.
	Atom Represent a cdkjpype Atom.
	Smarts A Smarts Pattern Matcher
	MoleculeData Store molecule data in a dictionary-type object

Functions

readfile(format, filename)
Iterate over the molecules in a file.

source code

readstring(format, string)
Read in a molecule from a string.

source code

Variables
	cdk = `JPackage("org").openscience.cdk`
	descs = `['hBondacceptors', 'weight', 'ip', 'CPSA', 'autoCorrel...` A list of supported descriptors
	fps = `['pubchem', 'daylight', 'extended', 'estate', 'maccs', '...` A list of supported fingerprint types
	informats = `{'inchi': 'InChI', 'mol': 'MDL MOL', 'sdf': 'MDL S...` A dictionary of supported input formats
	outformats = `{'inchi': 'InChI', 'inchikey': 'InChIKey', 'mol':...` A dictionary of supported output formats
	forcefields = `[u'mm2', u'mmff94']` A list of supported forcefields
	__package__ = `'cinfony'`

Function Details

readfile(format, filename)

source code

Iterate over the molecules in a file.

Required parameters:
   format - see the informats variable for a list of available
            input formats
   filename

You can access the first molecule in a file using the next() method
of the iterator:
    mol = readfile("smi", "myfile.smi").next()

You can make a list of the molecules in a file using:
    mols = list(readfile("smi", "myfile.smi"))

You can iterate over the molecules in a file as shown in the
following code snippet:
>>> atomtotal = 0
>>> for mol in readfile("sdf", "head.sdf"):
...     atomtotal += len(mol.atoms)
...
>>> print atomtotal
43

readstring(format, string)

source code

Read in a molecule from a string.

Required parameters:
   format - see the informats variable for a list of available
            input formats
   string

Example:
>>> input = "C1=CC=CS1"
>>> mymol = readstring("smi", input)
>>> len(mymol.atoms)
5

Variables Details

descs

A list of supported descriptors

Value:

['hBondacceptors',
 'weight',
 'ip',
 'CPSA',
 'autoCorrelationPolarizability',
 'kierHallSmarts',
 'zagrebIndex',
 'wienerNumbers',
...

fps

A list of supported fingerprint types

Value:

['pubchem',
 'daylight',
 'extended',
 'estate',
 'maccs',
 'klekota-roth',
 'graph',
 'substructure',
...

informats

A dictionary of supported input formats

Value:

{'inchi': 'InChI',
 'mol': 'MDL MOL',
 'sdf': 'MDL SDF',
 'smi': 'SMILES'}

outformats

A dictionary of supported output formats

Value:

{'inchi': 'InChI',
 'inchikey': 'InChIKey',
 'mol': 'MDL MOL',
 'mol2': 'MOL2',
 'sdf': 'MDL SDF',
 'smi': 'SMILES'}