Package rdkit :: Package Chem :: Module Fragments
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Module Fragments

source code

functions to match a bunch of fragment descriptors from a file

No user-servicable parts inside.  ;-)

Functions [hide private]
 
_CountMatches(mol, patt, unique=True) source code
 
_LoadPatterns(fileName=None) source code
 
fr_Al_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e61b4>)
Number of aliphatic carboxylic acids
source code
 
fr_Al_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37d8e9c>)
Number of aliphatic hydroxyl groups
source code
 
fr_Al_OH_noTert(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb224>)
Number of aliphatic hydroxyl groups excluding tert-OH
source code
 
fr_ArN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb64c>)
Number of N functional groups attached to aromatics
source code
 
fr_Ar_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e625c>)
Number of Aromatic carboxylic acide
source code
 
fr_Ar_N(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e679c>)
Number of aromatic nitrogens
source code
 
fr_Ar_NH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e672c>)
Number of aromatic amines
source code
 
fr_Ar_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37d8f44>)
Number of aromatic hydroxyl groups
source code
 
fr_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6224>)
Number of carboxylic acids
source code
 
fr_COO2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e62cc>)
Number of carboxylic acids
source code
 
fr_C_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37d8d84>)
Number of carbonyl O
source code
 
fr_C_O_noCOO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37d8df4>)
Number of carbonyl O, excluding COOH
source code
 
fr_C_S(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4374>)
Number of thiocarbonyl
source code
 
fr_HOCCN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb6bc>)
Number of C(OH)CCN-Ctert-alkyl or C(OH)CCNcyclic
source code
 
fr_Imine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e68b4>)
Number of Imines
source code
 
fr_NH0(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e664c>)
Number of Tertiary amines
source code
 
fr_NH1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6684>)
Number of Secondary amines
source code
 
fr_NH2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6534>)
Number of Primary amines
source code
 
fr_N_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6b54>)
Number of hydroxylamine groups
source code
 
fr_Ndealkylation1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb48c>)
Number of XCCNR groups
source code
 
fr_Ndealkylation2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb4fc>)
Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)
source code
 
fr_Nhpyrrole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6f7c>)
Number of H-pyrrole nitrogens
source code
 
fr_SH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4304>)
Number of thiol groups
source code
 
fr_aldehyde(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e64c4>)
Number of aldehydes
source code
 
fr_alkyl_carbamate(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb56c>)
Number of alkyl carbamates (subject to hydrolysis)
source code
 
fr_alkyl_halide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4224>)
Number of alkyl halides
source code
 
fr_allylic_oxid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb3ac>)
Number of allylic oxidation sites excluding steroid dienone
source code
 
fr_amide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6d4c>)
Number of amides
source code
 
fr_amidine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6e2c>)
Number of amidine groups
source code
 
fr_aniline(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6844>)
Number of anilines
source code
 
fr_aryl_methyl(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb41c>)
Number of aryl methyl sites for hydroxylation
source code
 
fr_azide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6cdc>)
Number of azide groups
source code
 
fr_azo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6bfc>)
Number of azo groups
source code
 
fr_barbitur(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e464c>)
Number of barbiturate groups
source code
 
fr_benzene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4e64>)
Number of benzene rings
source code
 
fr_benzodiazepine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb294>)
Number of benzodiazepines with no additional fused rings
source code
 
fr_bicyclic(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4d84>)
Bicyclic
source code
 
fr_diazo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6c6c>)
Number of diazo groups
source code
 
fr_dihydropyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb17c>)
Number of dihydropyridines
source code
 
fr_epoxide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4d14>)
Number of epoxide rings
source code
 
fr_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e610c>)
Number of esters
source code
 
fr_ether(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e63e4>)
Number of ether oxygens (including phenoxy)
source code
 
fr_furan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e480c>)
Number of furan rings
source code
 
fr_guanido(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6ed4>)
Number of guanidine groups
source code
 
fr_halogen(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e41b4>)
Number of halogens
source code
 
fr_hdrzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e69cc>)
Number of hydrazine groups
source code
 
fr_hdrzone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6994>)
Number of hydrazone groups
source code
 
fr_imidazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e46f4>)
Number of imidazole rings
source code
 
fr_imide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6f44>)
Number of imide groups
source code
 
fr_isocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4064>)
Number of isocyanates
source code
 
fr_isothiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e40d4>)
Number of isothiocyanates
source code
 
fr_ketone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6374>)
Number of ketones
source code
 
fr_ketone_Topliss(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb5dc>)
Number of ketones excluding diaryl, a,b-unsat.
source code
 
fr_lactam(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4b1c>)
Number of beta lactams
source code
 
fr_lactone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4c34>)
Number of cyclic esters (lactones)
source code
 
fr_methoxy(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6064>)
Number of methoxy groups -OCH3
source code
 
fr_morpholine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4b54>)
Number of morpholine rings
source code
 
fr_nitrile(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6924>)
Number of nitriles
source code
 
fr_nitro(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6ae4>)
Number of nitro groups
source code
 
fr_nitro_arom(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4fb4>)
Number of nitro benzene ring substituents
source code
 
fr_nitro_arom_nonortho(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb0d4>)
Number of non-ortho nitro benzene ring substituents
source code
 
fr_nitroso(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6a3c>)
Number of nitroso groups, excluding NO2
source code
 
fr_oxazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e495c>)
Number of oxazole rings
source code
 
fr_oxime(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37d8fb4>)
Number of oxime groups
source code
 
fr_para_hydroxylation(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb33c>)
Number of para-hydroxylation sites
source code
 
fr_phenol(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6454>)
Number of phenols
source code
 
fr_phenol_noOrthoHbond(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb144>)
Number of phenolic OH excluding ortho intramolecular Hbond substituents
source code
 
fr_phos_acid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4f44>)
Number of phosphoric acid groups
source code
 
fr_phos_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb02c>)
Number of phosphoric ester groups
source code
 
fr_piperdine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4a3c>)
Number of piperdine rings
source code
 
fr_piperzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4aac>)
Number of piperzine rings
source code
 
fr_priamide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e6dbc>)
Number of primary amides
source code
 
fr_prisulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e45a4>)
Number of primary sulfonamides
source code
 
fr_pyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e49cc>)
Number of pyridine rings
source code
 
fr_quatN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e65a4>)
Number of quarternary nitrogens
source code
 
fr_sulfide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4294>)
Number of thioether
source code
 
fr_sulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e44c4>)
Number of sulfonamides
source code
 
fr_sulfone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4454>)
Number of sulfone groups
source code
 
fr_term_acetylene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4764>)
Number of terminal acetylenes
source code
 
fr_tetrazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4ca4>)
Number of tetrazole rings
source code
 
fr_thiazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e48ec>)
Number of thiazole rings
source code
 
fr_thiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4144>)
Number of thiocyanates
source code
 
fr_thiophene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e487c>)
Number of thiophene rings
source code
 
fr_unbrch_alkane(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4dbc>)
Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)
source code
 
fr_urea(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37e4534>)
Number of urea groups
source code
Variables [hide private]
  defaultPatternFileName = '/builddir/build/BUILD/rdkit-Release_...
  fns = [('fr_C_O', <function <lambda> at 0xf37d8dbc>), ('fr_C_O...
  fn = None
  __package__ = 'rdkit.Chem'
  name = 'fr_HOCCN'

Imports: os, RDConfig, Chem


Function Details [hide private]

fr_ketone_Topliss(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0xf37eb5dc>)

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


Variables Details [hide private]

defaultPatternFileName

Value:
'/builddir/build/BUILD/rdkit-Release_2016_03_5/python2/Data/FragmentDe\
scriptors.csv'

fns

Value:
[]