Chemical Reactions¶

Tutorial¶

This tutorial will show you how to:

1. Define reactions from SMARTS or Blocks
2. Basic reactions examples
3. Fragment replacement examples

In [2]:

import datamol as dm

import datamol as dm

In [3]:

# Define a reaction from rxn block finle
rxn = dm.reactions.rxn_from_block_file("data/ReactionBlock.rxn", sanitize=True)
rxn

# Define a reaction from rxn block finle rxn = dm.reactions.rxn_from_block_file("data/ReactionBlock.rxn", sanitize=True) rxn

Out[3]:

In [4]:

dm.reactions.is_reaction_ok(rxn, enable_logs=True)

dm.reactions.is_reaction_ok(rxn, enable_logs=True)

2022-10-14 12:30:01.734 | INFO     | datamol.reactions._reactions:is_reaction_ok:147 - Number of warnings:0
2022-10-14 12:30:01.735 | INFO     | datamol.reactions._reactions:is_reaction_ok:148 - Number of preprocessing errors: 0
2022-10-14 12:30:01.735 | INFO     | datamol.reactions._reactions:is_reaction_ok:149 - Number of reactants in reaction: 2
2022-10-14 12:30:01.736 | INFO     | datamol.reactions._reactions:is_reaction_ok:150 - Number of products in reaction: 1
2022-10-14 12:30:01.736 | INFO     | datamol.reactions._reactions:is_reaction_ok:151 - Preprocess labels added:((), ())

Out[4]:

True

In [5]:

# Apply reaction and snitize the products
prod_mols = dm.reactions.apply_reaction(
    rxn=rxn,
    reactants=(dm.to_mol("CC(=O)O"), dm.to_mol("NC")),
    as_smiles=False,
    sanitize=True,
    single_output=False,
)
dm.to_image(prod_mols, use_svg=False)

# Apply reaction and snitize the products prod_mols = dm.reactions.apply_reaction( rxn=rxn, reactants=(dm.to_mol("CC(=O)O"), dm.to_mol("NC")), as_smiles=False, sanitize=True, single_output=False, ) dm.to_image(prod_mols, use_svg=False)

Out[5]:

In [6]:

# Return a single product in SMILES and keep the open attachment points
prod_smi_att = dm.reactions.apply_reaction(
    rxn=rxn,
    reactants=(dm.to_mol("[2*]CC(=O)O"), dm.to_mol("NC[1*]")),
    as_smiles=False,
    sanitize=True,
    single_output=True,
    rm_attach=False,
)
prod_smi_att

# Return a single product in SMILES and keep the open attachment points prod_smi_att = dm.reactions.apply_reaction( rxn=rxn, reactants=(dm.to_mol("[2*]CC(=O)O"), dm.to_mol("NC[1*]")), as_smiles=False, sanitize=True, single_output=True, rm_attach=False, ) prod_smi_att

Out[6]:

In [7]:

# Return a single product in SMILES without any open attachment points
prod_smi = dm.reactions.apply_reaction(
    rxn=rxn,
    reactants=(dm.to_mol("[2*]CC(=O)O"), dm.to_mol("NC[1*]")),
    as_smiles=False,
    sanitize=True,
    single_output=True,
    rm_attach=True,
)
prod_smi

# Return a single product in SMILES without any open attachment points prod_smi = dm.reactions.apply_reaction( rxn=rxn, reactants=(dm.to_mol("[2*]CC(=O)O"), dm.to_mol("NC[1*]")), as_smiles=False, sanitize=True, single_output=True, rm_attach=True, ) prod_smi

Out[7]:

In [8]:

scaffold = dm.to_mol("O=C(NCc1ccnc([2*])c1)[1*]")
frag1 = dm.to_mol("[1*]OC1CCC1")
frag2 = dm.to_mol("[2*]N1CCCC1")
dm.to_image([scaffold, frag1, frag2], use_svg=False)

scaffold = dm.to_mol("O=C(NCc1ccnc([2*])c1)[1*]") frag1 = dm.to_mol("[1*]OC1CCC1") frag2 = dm.to_mol("[2*]N1CCCC1") dm.to_image([scaffold, frag1, frag2], use_svg=False)

Out[8]:

In [9]:

# Define reaction with SMARTS and apply reaction on the specified attachment points

rxn1 = dm.reactions.rxn_from_smarts("[1*][*:1].[1*][*:2]>>[*:1][*:2]")
res1 = dm.reactions.apply_reaction(rxn1, (dm.to_mol(frag1), dm.to_mol(scaffold)), rm_attach=True)
dm.to_image(res1, use_svg=False)

# Define reaction with SMARTS and apply reaction on the specified attachment points rxn1 = dm.reactions.rxn_from_smarts("[1*][*:1].[1*][*:2]>>[*:1][*:2]") res1 = dm.reactions.apply_reaction(rxn1, (dm.to_mol(frag1), dm.to_mol(scaffold)), rm_attach=True) dm.to_image(res1, use_svg=False)

Out[9]:

In [10]:

# One reaction to attach multiple specified attchment points
rxn2 = dm.reactions.rxn_from_smarts("[1*][*:1].[2*][*:4].([1*][*:2].[2*][*:3])>>([*:1][*:2].[*:3][*:4])")
res2 = dm.reactions.apply_reaction(rxn2, (frag1, frag2, scaffold))
dm.to_image(res2, use_svg=False)

# One reaction to attach multiple specified attchment points rxn2 = dm.reactions.rxn_from_smarts("[1*][*:1].[2*][*:4].([1*][*:2].[2*][*:3])>>([*:1][*:2].[*:3][*:4])") res2 = dm.reactions.apply_reaction(rxn2, (frag1, frag2, scaffold)) dm.to_image(res2, use_svg=False)

Out[10]:

References¶

• RDKit Documentation