rdkit.Chem.Fragments module — The RDKit 2025.09.6 documentation

# rdkit.Chem.Fragments module

functions to match a bunch of fragment descriptors from a file

No user-servicable parts inside. ;-)

rdkit.Chem.Fragments.fr_Al_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aliphatic carboxylic acids

rdkit.Chem.Fragments.fr_Al_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aliphatic hydroxyl groups

rdkit.Chem.Fragments.fr_Al_OH_noTert(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aliphatic hydroxyl groups excluding tert-OH

rdkit.Chem.Fragments.fr_ArN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of N functional groups attached to aromatics

rdkit.Chem.Fragments.fr_Ar_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of Aromatic carboxylic acide

rdkit.Chem.Fragments.fr_Ar_N(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aromatic nitrogens

rdkit.Chem.Fragments.fr_Ar_NH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aromatic amines

rdkit.Chem.Fragments.fr_Ar_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aromatic hydroxyl groups

rdkit.Chem.Fragments.fr_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of carboxylic acids

rdkit.Chem.Fragments.fr_COO2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of carboxylic acids

rdkit.Chem.Fragments.fr_C_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of carbonyl O

rdkit.Chem.Fragments.fr_C_O_noCOO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of carbonyl O, excluding COOH

rdkit.Chem.Fragments.fr_C_S(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of thiocarbonyl

rdkit.Chem.Fragments.fr_HOCCN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of C(OH)CCN-Ctert-alkyl or C(OH)CCNcyclic

rdkit.Chem.Fragments.fr_Imine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of Imines

rdkit.Chem.Fragments.fr_NH0(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of Tertiary amines

rdkit.Chem.Fragments.fr_NH1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of Secondary amines

rdkit.Chem.Fragments.fr_NH2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of Primary amines

rdkit.Chem.Fragments.fr_N_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of hydroxylamine groups

rdkit.Chem.Fragments.fr_Ndealkylation1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of XCCNR groups

rdkit.Chem.Fragments.fr_Ndealkylation2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)

rdkit.Chem.Fragments.fr_Nhpyrrole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of H-pyrrole nitrogens

rdkit.Chem.Fragments.fr_SH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of thiol groups

rdkit.Chem.Fragments.fr_aldehyde(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aldehydes

rdkit.Chem.Fragments.fr_alkyl_carbamate(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of alkyl carbamates (subject to hydrolysis)

rdkit.Chem.Fragments.fr_alkyl_halide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of alkyl halides

rdkit.Chem.Fragments.fr_allylic_oxid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of allylic oxidation sites excluding steroid dienone

rdkit.Chem.Fragments.fr_amide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of amides

rdkit.Chem.Fragments.fr_amidine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of amidine groups

rdkit.Chem.Fragments.fr_aniline(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of anilines

rdkit.Chem.Fragments.fr_aryl_methyl(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of aryl methyl sites for hydroxylation

rdkit.Chem.Fragments.fr_azide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of azide groups

rdkit.Chem.Fragments.fr_azo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of azo groups

rdkit.Chem.Fragments.fr_barbitur(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of barbiturate groups

rdkit.Chem.Fragments.fr_benzene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of benzene rings

rdkit.Chem.Fragments.fr_benzodiazepine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of benzodiazepines with no additional fused rings

rdkit.Chem.Fragments.fr_bicyclic(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Bicyclic

rdkit.Chem.Fragments.fr_diazo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of diazo groups

rdkit.Chem.Fragments.fr_dihydropyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of dihydropyridines

rdkit.Chem.Fragments.fr_epoxide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of epoxide rings

rdkit.Chem.Fragments.fr_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of esters

rdkit.Chem.Fragments.fr_ether(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of ether oxygens (including phenoxy)

rdkit.Chem.Fragments.fr_furan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of furan rings

rdkit.Chem.Fragments.fr_guanido(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of guanidine groups

rdkit.Chem.Fragments.fr_halogen(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of halogens

rdkit.Chem.Fragments.fr_hdrzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of hydrazine groups

rdkit.Chem.Fragments.fr_hdrzone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of hydrazone groups

rdkit.Chem.Fragments.fr_imidazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of imidazole rings

rdkit.Chem.Fragments.fr_imide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of imide groups

rdkit.Chem.Fragments.fr_isocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of isocyanates

rdkit.Chem.Fragments.fr_isothiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of isothiocyanates

rdkit.Chem.Fragments.fr_ketone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of ketones

rdkit.Chem.Fragments.fr_ketone_Topliss(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of ketones excluding diaryl, a,b-unsat. dienones, heteroatom on Calpha

rdkit.Chem.Fragments.fr_lactam(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of beta lactams

rdkit.Chem.Fragments.fr_lactone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of cyclic esters (lactones)

rdkit.Chem.Fragments.fr_methoxy(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of methoxy groups -OCH3

rdkit.Chem.Fragments.fr_morpholine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of morpholine rings

rdkit.Chem.Fragments.fr_nitrile(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of nitriles

rdkit.Chem.Fragments.fr_nitro(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of nitro groups

rdkit.Chem.Fragments.fr_nitro_arom(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of nitro benzene ring substituents

rdkit.Chem.Fragments.fr_nitro_arom_nonortho(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of non-ortho nitro benzene ring substituents

rdkit.Chem.Fragments.fr_nitroso(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of nitroso groups, excluding NO2

rdkit.Chem.Fragments.fr_oxazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of oxazole rings

rdkit.Chem.Fragments.fr_oxime(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of oxime groups

rdkit.Chem.Fragments.fr_para_hydroxylation(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of para-hydroxylation sites

rdkit.Chem.Fragments.fr_phenol(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of phenols

rdkit.Chem.Fragments.fr_phenol_noOrthoHbond(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of phenolic OH excluding ortho intramolecular Hbond substituents

rdkit.Chem.Fragments.fr_phos_acid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of phosphoric acid groups

rdkit.Chem.Fragments.fr_phos_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of phosphoric ester groups

rdkit.Chem.Fragments.fr_piperdine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of piperdine rings

rdkit.Chem.Fragments.fr_piperzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of piperzine rings

rdkit.Chem.Fragments.fr_priamide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of primary amides

rdkit.Chem.Fragments.fr_prisulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of primary sulfonamides

rdkit.Chem.Fragments.fr_pyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of pyridine rings

rdkit.Chem.Fragments.fr_quatN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of quaternary nitrogens

rdkit.Chem.Fragments.fr_sulfide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of thioether

rdkit.Chem.Fragments.fr_sulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of sulfonamides

rdkit.Chem.Fragments.fr_sulfone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of sulfone groups

rdkit.Chem.Fragments.fr_term_acetylene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of terminal acetylenes

rdkit.Chem.Fragments.fr_tetrazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of tetrazole rings

rdkit.Chem.Fragments.fr_thiazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of thiazole rings

rdkit.Chem.Fragments.fr_thiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of thiocyanates

rdkit.Chem.Fragments.fr_thiophene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of thiophene rings

rdkit.Chem.Fragments.fr_unbrch_alkane(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)

rdkit.Chem.Fragments.fr_urea(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>)

  Number of urea groups