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