File Formats

Input can be parsed in a variety of file formats that are autodetected:

>>> FileParser('compound.sdf')

['RDKit MolObject']

The full list of file formats that cocktail-shaker supports parsing:

sdf       # 2D Structure file format

Output can be returned in a variety of file formats that are specified your enumerated compounds and your desired file extension:

>>> FileWriter('test'', compounds, '.mol2')

Writes all the compounds to 1 mol2 file.

The full list of file formats:

alc         # Alchemy format
cdxml       # CambridgeSoft ChemDraw XML format
cerius      # MSI Cerius II format
charmm      # Chemistry at Harvard Macromolecular Mechanics file format
cif         # Crystallographic Information File
cml         # Chemical Markup Language
gjf         # Gaussian input data file
gromacs     # GROMACS file format
hyperchem   # HyperChem file format
jme         # Java Molecule Editor format
maestro     # Schroedinger MacroModel structure file format
mol         # Symyx molecule file
mol2        # Tripos Sybyl MOL2 format
pdb         # Protein Data Bank
sdf         # 2D formatted structure data files
sdf3000     # Symyx Structure Data Format 3000
sln         # SYBYL Line Notation
xyz         # xyz file format