Loading a Molecule¶
Introduction¶
To load a molecule, call a from_ method of Molecule.
For instance, from_smiles for a SMILES input, from_mol2 for a MOL2 input, and from_rdkit for an RDKit object. Choose the method that corresponds to your input type, or use the from_dynamic strategy if you're unsure or have a variety of input types.
Tip
from_dynamic is the simplest and most convenient method, but it may not always work! If you know your molecule's format, use the specific method for it.
Dynamic Loading¶
Dynamic loading examines your input and determines how to convert it into a Molecule object. It performs checks and then calls one of the methods detailed on this page.
from simmate.toolkit import Molecule
# try this with a filename, a smiles string, SDF string, rdkit object, ...
input_01 = "example_molecule.sdf"
input_02 = "example_molecule.csv"
input_03 = "C1=CC(=C(C=C1CCN)O)O"
# The from_dynamic method will determine the format and convert it
for new_input in [input_01, input_02, input_03]
molecule = Molecule.from_dynamic(new_input)
Note
from_dynamic also checks if we already have a Molecule object and returns it if we do.
Basic Loading¶
Files¶
File-based inputs accept a filename as a string or a pathlib.Path object.
from simmate.toolkit import Molecule
molecule = Molecule.from_sdf_file("example.sdf")
| TYPE | METHOD |
|---|---|
| (dynamic loading) | from_file |
| CSV | from_csv_file |
| SMILES (any type) | from_smiles_file |
| SDF (aka CTAB) | from_sdf_file |
| MOL2 | from_mol2_file |
Tip
Each of these methods has a corresponding submethod for loading this format directly from text/str, detailed in the section below. For instance, from_smiles takes a string, while from_smiles_file takes a .smi file.
Raw text / strings¶
You can read a python string variable directly. These methods are primarily used for testing and debugging.
from simmate.toolkit import Molecule
molecule = Molecule.from_smiles("C1=CC(=C(C=C1CCN)O)O")
| TYPE | METHOD |
|---|---|
| INCHI | from_inchi |
| SMILES | from_smiles |
| SMARTS | from_smarts |
| SDF (aka CTAB) | from_sdf |
| MOL2 | from_mol2 |
Tip
Each of these methods has a corresponding submethod for loading this format directly from a file, detailed in the section above. For instance, from_smiles takes a string, while from_smiles_file takes a .smi file.
Python Objects¶
Methods are available to convert other popular python objects, such as those from RDKit
from simmate.toolkit import Molecule
from rdkit import Chem
# Smiles -> RDKit -> Simmate
rdkit_mol = Chem.MolFromSmiles("Cc1ccccc1")
molecule = Molecule.from_rdkit(rdkit_mol)
# !!! NOT RECOMMENDED !!!
# Smiles -> Simmate
molecule = Molecule.from_smiles("Cc1ccccc1")
# !!! RECOMMENDED !!!
| TYPE | METHOD |
|---|---|
| RDKit Mol object | from_rdkit |
| RDKit Mol object written as binary | from_binary |
| Simmate (aka nothing needs to be done) | from_dynamic |
pathlib.Path |
see from_file section above |
Database Entries¶
Warning
Loading from database metadata is still in progress. Refer to our guides on Python ORM
to access datasets as Molecule objects quickly.
For example:
from simmate.database import connect
from simmate.datasets.models import CortevaCore
molecule_db = CortevaCore.objects.get(id=123)
molecule = molecule_db.to_toolkit()