rdkit.Chem.Fragments module — The RDKit 2016.09.1 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 quarternary 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