Molecule Exportation

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Introduction

After loading a molecule, you can convert it to a different format using a to_ method of Molecule.

For instance, use to_smiles to output a SMILES, use to_mol2 for a MOL2 output, and use to_rdkit for an RDKit object.

Thus, file format conversion typically involves two steps:

1. Load using a from_* method
2. Export using a to_* method

from simmate.toolkit import Molecule

# step 1: LOAD
molecule = Molecule.from_sdf_file("example.sdf")

# step 2: EXPORT
molecule.to_png_file("output.png")

Note

For exporting numerous molecules or handling large files, refer to our "Many Molecules" section.

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Basic Exportation

Files

File-based outputs accept a filename as a string or a pathlib.Path object.

molecule = Molecule.to_sdf_file("example.sdf")

TYPE	METHOD
Image	to_png_file
SDF (aka CTAB)	to_sdf_file

Tip

Each of these methods has a corresponding submethod for exporting to a string, as detailed in the section below. For instance, to_sdf outputs a string, while to_sdf_file writes a .sdf file.

Warning

Writing numerous files (with many molecules in each) can be slow using these methods. Refer to the "many molecules" section for optimized writing of thousands or millions of molecules.

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Raw Text / Strings

Instead of writing to a file, you can also obtain the converted format as a python variable (string) for use elsewhere.

my_smiles = molecule.to_smiles()

TYPE	METHOD
INCHI	to_inchi
INCHI Key	to_inchi_key
SMILES	to_smiles
SMILES (kekulized)	to_smiles(kekulize=True)
SMILES (CX-extended)	to_cx_smiles
SDF (aka CTAB)	to_sdf

Tip

Each of these methods has a corresponding submethod for exporting directly to a file, as detailed in the section above. For instance, to_sdf outputs a string, while to_sdf_file writes a .sdf file.

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Python Objects

Methods are available to convert to other popular python objects, such as those from RDKit.

molecule.to_rdkit()

TYPE	METHOD
RDKit Mol object	to_rdkit
RDKit Mol object written as binary	to_binary

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