Chemical Groups¶

The medchem.groups module contains a large list of chemical and functional groups to classify compounds. Its easy-to-use API allows you to specify either a whole family or a subset of chemical groups. For example, you can load all the known hinge binders motifs with ChemicalGroup("hinge_binders*").

In [2]:

import datamol as dm
import pandas as pd

import medchem
from medchem.groups import ChemicalGroup

import datamol as dm import pandas as pd import medchem from medchem.groups import ChemicalGroup

List the available chemical and functional groups¶

List the default chemical groups

In [3]:

medchem.groups.list_default_chemical_groups()

medchem.groups.list_default_chemical_groups()

Out[3]:

['emerging_perfluoroalkyls',
 'montmorillonite_adsorption',
 'common_monomer_repeating_units',
 'electrophilic_warheads_for_kinases',
 'common_warhead_covalent_inhibitors',
 'rings_in_drugs',
 'iupac_blue_book_rings',
 'phase_2_hetereocyclic_rings',
 'privileged_scaffolds',
 'iupac_blue_book',
 'common_rgroup_replacements',
 'braf_inhibitors',
 'privileged_kinase_inhibitor_scaffolds',
 'common_organic_solvents',
 'amino_acid_protecting_groups',
 'schedule_one',
 'schedule_two',
 'schedule_three',
 'schedule_four',
 'schedule_five',
 'interstellar_space',
 'vitamins',
 'open_smiles',
 'amino_acids',
 'pihkal',
 'aggregator',
 'basic_groups',
 'extended_groups',
 'hinge_binders']

List common functional group names. The list is too long to we only show a few elements.

In [4]:

medchem.groups.list_functional_group_names()[40:50]

medchem.groups.list_functional_group_names()[40:50]

Out[4]:

['Enediols',
 'Ethers',
 'Dialkylethers',
 'Alkylarylethers',
 'Diarylethers',
 'Thioethers',
 'Disulfides',
 'Peroxides',
 'Hydroperoxides',
 'Hydrazine derivatives']

You can also retrieve a dict of functional group to their SMARTS. Here again we only show a small subset.

In [5]:

fg_map = medchem.groups.get_functional_group_map()

dict(list(fg_map.items())[:10])

fg_map = medchem.groups.get_functional_group_map() dict(list(fg_map.items())[:10])

Out[5]:

{'1,2 – Aminophenols': 'c([OH1])c[NX3]([#1,#6])[#1,#6]',
 '1,2 – Aminothiophenols': 'c([SH1])c[NX3]([#1,#6])[#1,#6]',
 '1,2 – Diphenols': 'c([OH1])c([OH1])',
 '1,2 – Dithiophenols': 'c([SH1])c([SH1])',
 '1,2,3,4-Oxatriazoles (HS)': '[oR1]1[nR1][nR1][nR1][cR1]1',
 '1,2,3,4-Thiatriazoles (HS)': '[sR1]1[nR1][nR1][nR1][cR1]1',
 '1,2,3,5-Oxatriazoles (HS)': '[oR1]1[nR1][nR1][cR1][nR1]1',
 '1,2,3,5-Thiatriazoles (HS)': '[sR1]1[nR1][nR1][cR1][nR1]1',
 '1,2,3-Oxadiazoles (HS)': '[oR1]1[nR1][nR1][cR1][cR1]1',
 '1,2,3-Triazoles (HS)': '[nR1]1[nR1][nR1][cR1][cR1]1'}

Load one ore more groups and filter a list of molecules¶

In [6]:

group = ChemicalGroup(groups=["basic_groups", "rings_in_drugs"])

group

group = ChemicalGroup(groups=["basic_groups", "rings_in_drugs"]) group

Out[6]:

<medchem.groups._groups.ChemicalGroup at 0x7f6f82ffdf10>

The groups are part of a hierarchy you can explore with:

In [7]:

group.list_hierarchy_groups()

group.list_hierarchy_groups()

Out[7]:

['medicinal_chemistry.rings.rings_in_drugs.rings_in_drugs',
 'medicinal_chemistry.functional_groups.basic_groups']

Check whether a molecule match with the created group.

In [8]:

mol = dm.to_mol("CCS(=O)(=O)N1CC(C1)(CC#N)N2C=C(C=N2)C3=C4C=CNC4=NC=N3")

mol

mol = dm.to_mol("CCS(=O)(=O)N1CC(C1)(CC#N)N2C=C(C=N2)C3=C4C=CNC4=NC=N3") mol

Out[8]:

In [9]:

group.get_matches(mol, use_smiles=True)

group.get_matches(mol, use_smiles=True)

Out[9]:

	name	smiles	smarts	group	matches
204	diazine	C1=NC=CC=N1	[#6]1:[#7]:[#6]:[#6]:[#6]:[#7]:1	rings_in_drugs	((24, 23, 22, 18, 17, 25),)
234	1H-pyrazole	N1=CC=CN1	[#7]1:[#6]:[#6]:[#6]:[#7H]:1	rings_in_drugs	((12, 13, 14, 15, 16),)
257	1H-pyrrole	C1=CC=CN1	[#6]1:[#6]:[#6]:[#6]:[#7H]:1	rings_in_drugs	((20, 19, 18, 22, 21),)

You can also display all the filters for a given group.

In [10]:

group.data.head()

group.data.head()

Out[10]:

	name	smiles	smarts	group	hierarchy	mol_smarts	mol
191	benzene	C1=CC=CC=C1	[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1	rings_in_drugs	medicinal_chemistry.rings.rings_in_drugs.rings...	<rdkit.Chem.rdchem.Mol object at 0x7f6f80cc6ea0>	<rdkit.Chem.rdchem.Mol object at 0x7f6f80bc6570>
192	pyridine	C1=CC=CN=C1	[#6]1:[#6]:[#6]:[#6]:[#7]:[#6]:1	rings_in_drugs	medicinal_chemistry.rings.rings_in_drugs.rings...	<rdkit.Chem.rdchem.Mol object at 0x7f6f80cc6f80>	<rdkit.Chem.rdchem.Mol object at 0x7f6f80bc5e70>
193	piperidine	N1CCCCC1	[#7]1-[#6]-[#6]-[#6]-[#6]-[#6]-1	rings_in_drugs	medicinal_chemistry.rings.rings_in_drugs.rings...	<rdkit.Chem.rdchem.Mol object at 0x7f6f80cc6e30>	<rdkit.Chem.rdchem.Mol object at 0x7f6f80bc6340>
194	piperazine	N1CCNCC1	[#7]1-[#6]-[#6]-[#7]-[#6]-[#6]-1	rings_in_drugs	medicinal_chemistry.rings.rings_in_drugs.rings...	<rdkit.Chem.rdchem.Mol object at 0x7f6f80cc6dc0>	<rdkit.Chem.rdchem.Mol object at 0x7f6f80bc5cb0>
195	cyclohexane	C1CCCCC1	[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1	rings_in_drugs	medicinal_chemistry.rings.rings_in_drugs.rings...	<rdkit.Chem.rdchem.Mol object at 0x7f6f80cc6d50>	<rdkit.Chem.rdchem.Mol object at 0x7f6f80bc6810>

Load groups from a hierarchy¶

Groups are organized as a hierarchy. It's possible to load many groups at once.

In [11]:

medchem.groups.list_default_chemical_groups(hierarchy=True)[:20]

medchem.groups.list_default_chemical_groups(hierarchy=True)[:20]

Out[11]:

['environment.emerging_perfluoroalkyls.emerging_perfluoroalkyls',
 'materials.clay.montmorillonite_adsorption.montmorillonite_adsorption',
 'materials.polymers.common_monomer_repeating_units.common_monomer_repeating_units',
 'medicinal_chemistry.warheads.electrophillic_warheads_for_kinases.electrophilic_warheads_for_kinases',
 'medicinal_chemistry.warheads.common_warheads_covalent_inhibitors.common_warhead_covalent_inhibitors',
 'medicinal_chemistry.rings.rings_in_drugs.rings_in_drugs',
 'medicinal_chemistry.rings.iupac_blue_book_rings.iupac_blue_book_rings',
 'medicinal_chemistry.rings.phase_2_hetereocyclic_rings.phase_2_hetereocyclic_rings',
 'medicinal_chemistry.scaffolds.privileged_scaffolds.privileged_scaffolds',
 'medicinal_chemistry.scaffolds.iupac_blue_book_substituents.iupac_blue_book',
 'medicinal_chemistry.scaffolds.common_r_group_replacements.common_rgroup_replacements',
 'proteins.kinases.braf.inhibitors.braf_inhibitors',
 'proteins.kinases.scaffolds.privileged_kinase_inhibtors.privileged_kinase_inhibitor_scaffolds',
 'organic_synthesis.solvents.common_organic_solvents.common_organic_solvents',
 'organic_synthesis.protecting_groups.amino_acid_protecting_groups.amino_acid_protecting_groups',
 'narcotics.schedule_one.schedule_one',
 'narcotics.schedule_two.schedule_two',
 'narcotics.schedule_three.schedule_three',
 'narcotics.schedule_four.schedule_four',
 'narcotics.schedule_five.schedule_five']

For example you can load all the hinge binder groups with:

In [12]:

group = ChemicalGroup("hinge_binders*")

group.list_hierarchy_groups()[:10]

group = ChemicalGroup("hinge_binders*") group.list_hierarchy_groups()[:10]

Out[12]:

['medicinal_chemistry.chemotype.kinases.NAK.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.ABL.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.ACK.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.STKR.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.AKT.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.ALK.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.AUR.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.GRK.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.RAF.hinge_binders',
 'medicinal_chemistry.chemotype.kinases.SRC.hinge_binders']

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