File API Documentation

This page provides an overview of how cocktail-shaker operates reading and writing files. To see the files that cocktail-shaker supports, refer to file formats.

The FileParser Module

You instantiate a FileParser by providing the exact path to a file with the extension included. cocktail-shaker is smart enough to detect the file extension and allocate its specific parsing. If the file being parsed is not supported, then FileNotSupportedError will be raised instead.

>>> from cocktail_shaker import FileParser
>>> molecules = FileParser('compounds.sdf')
>>> print (molecules)
>>> ['c1cc(CCCO)ccc1']

FileParser will then return a list of SMILES.

file_path

The path to a file

The FileWriter Module

The FileWriter module uses the NIH web cactus resolver under the hood to generate the 2D or 3D data. By issuing requests of the compound in SMILES and returning a XML formatted data struct of the 2D/3D coordinates in whatever chemical format indicated by the user. Unfortunately, the cactus resolver can only process one api call at a time and not bulk requests. This means that sending combinations worth of 1000+ -> 1000+ api requests might not be in your best interest and eventually the server will deny any requests.

This feature is still in development so use at your own discretion.

You instantiate a FileWriter by providing the path to the file, compounds to be written, and the extension you would like the files in. If the file being written is not supported, then FileNotSupportedError will be raised instead.

>>> from cocktail_shaker import Cocktail, FileWriter
>>> from cocktail_shaker import PeptideBuilder
>>> peptide_backbone = PeptideBuilder(2)
>>> cocktail = Cocktail(peptide_backbone,ligand_library = ['Br', 'I'])
>>> combinations = cocktail.shake()
>>> FileWriter('new_compounds', combinations, 'sdf')
Generates an SDF File....

However, if you would like to generate the files into separate files, then you can pass in the fragmentation parameter.

>>> from cocktail_shaker import Cocktail, FileWriter
>>> from cocktail_shaker import PeptideBuilder
>>> peptide_backbone = PeptideBuilder(2)
>>> cocktail = Cocktail(peptide_backbone,ligand_library = ['Br', 'I'])
>>> combinations = cocktail.shake()
>>> FileWriter('new_compounds', combinations, 'sdf', fragmentation=2)
Generates 2 SDF Files....

name

The path to a file

molecules

List of RDKit molecules you would like to write.

option

The extension of the file you would like to write

fragmentation(optional)

How many files you would like to produce.