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 0x7f5b444f3de0>)
Number of aliphatic carboxylic acids
source code
 
fr_Al_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3bb0>)
Number of aliphatic hydroxyl groups
source code
 
fr_Al_OH_noTert(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2bb0>)
Number of aliphatic hydroxyl groups excluding tert-OH
source code
 
fr_ArN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e7130>)
Number of N functional groups attached to aromatics
source code
 
fr_Ar_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3e50>)
Number of Aromatic carboxylic acide
source code
 
fr_Ar_N(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0360>)
Number of aromatic nitrogens
source code
 
fr_Ar_NH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e03d0>)
Number of aromatic amines
source code
 
fr_Ar_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3c20>)
Number of aromatic hydroxyl groups
source code
 
fr_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3ec0>)
Number of carboxylic acids
source code
 
fr_COO2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3f30>)
Number of carboxylic acids
source code
 
fr_C_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3ad0>)
Number of carbonyl O
source code
 
fr_C_O_noCOO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3b40>)
Number of carbonyl O, excluding COOH
source code
 
fr_C_S(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0ec0>)
Number of thiocarbonyl
source code
 
fr_HOCCN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e70c0>)
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 0x7f5b441e04b0>)
Number of Imines
source code
 
fr_NH0(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e02f0>)
Number of Tertiary amines
source code
 
fr_NH1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0280>)
Number of Secondary amines
source code
 
fr_NH2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0210>)
Number of Primary amines
source code
 
fr_N_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e06e0>)
Number of hydroxylamine groups
source code
 
fr_Ndealkylation1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2e50>)
Number of XCCNR groups
source code
 
fr_Ndealkylation2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2f30>)
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 0x7f5b441e0ad0>)
Number of H-pyrrole nitrogens
source code
 
fr_SH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0e50>)
Number of thiol groups
source code
 
fr_aldehyde(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0130>)
Number of aldehydes
source code
 
fr_alkyl_carbamate(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2fa0>)
Number of alkyl carbamates (subject to hydrolysis)
source code
 
fr_alkyl_halide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0d70>)
Number of alkyl halides
source code
 
fr_allylic_oxid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2de0>)
Number of allylic oxidation sites excluding steroid dienone
source code
 
fr_amide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0910>)
Number of amides
source code
 
fr_amidine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e09f0>)
Number of amidine groups
source code
 
fr_aniline(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0440>)
Number of anilines
source code
 
fr_aryl_methyl(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2ec0>)
Number of aryl methyl sites for hydroxylation
source code
 
fr_azide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e08a0>)
Number of azide groups
source code
 
fr_azo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e07c0>)
Number of azo groups
source code
 
fr_barbitur(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2130>)
Number of barbiturate groups
source code
 
fr_benzene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2910>)
Number of benzene rings
source code
 
fr_benzodiazepine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2d70>)
Number of benzodiazepines with no additional fused rings
source code
 
fr_bicyclic(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e28a0>)
Bicyclic
source code
 
fr_diazo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0830>)
Number of diazo groups
source code
 
fr_dihydropyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2b40>)
Number of dihydropyridines
source code
 
fr_epoxide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e27c0>)
Number of epoxide rings
source code
 
fr_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3d70>)
Number of esters
source code
 
fr_ether(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0050>)
Number of ether oxygens (including phenoxy)
source code
 
fr_furan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e22f0>)
Number of furan rings
source code
 
fr_guanido(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0a60>)
Number of guanidine groups
source code
 
fr_halogen(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0d00>)
Number of halogens
source code
 
fr_hdrzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0590>)
Number of hydrazine groups
source code
 
fr_hdrzone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0600>)
Number of hydrazone groups
source code
 
fr_imidazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2280>)
Number of imidazole rings
source code
 
fr_imide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0b40>)
Number of imide groups
source code
 
fr_isocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0bb0>)
Number of isocyanates
source code
 
fr_isothiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0c20>)
Number of isothiocyanates
source code
 
fr_ketone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3fa0>)
Number of ketones
source code
 
fr_ketone_Topliss(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e7050>)
Number of ketones excluding diaryl, a,b-unsat.
source code
 
fr_lactam(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2670>)
Number of beta lactams
source code
 
fr_lactone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e26e0>)
Number of cyclic esters (lactones)
source code
 
fr_methoxy(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3d00>)
Number of methoxy groups -OCH3
source code
 
fr_morpholine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2600>)
Number of morpholine rings
source code
 
fr_nitrile(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0520>)
Number of nitriles
source code
 
fr_nitro(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0750>)
Number of nitro groups
source code
 
fr_nitro_arom(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2a60>)
Number of nitro benzene ring substituents
source code
 
fr_nitro_arom_nonortho(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2ad0>)
Number of non-ortho nitro benzene ring substituents
source code
 
fr_nitroso(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0670>)
Number of nitroso groups, excluding NO2
source code
 
fr_oxazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2440>)
Number of oxazole rings
source code
 
fr_oxime(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b444f3c90>)
Number of oxime groups
source code
 
fr_para_hydroxylation(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2d00>)
Number of para-hydroxylation sites
source code
 
fr_phenol(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e00c0>)
Number of phenols
source code
 
fr_phenol_noOrthoHbond(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2c90>)
Number of phenolic OH excluding ortho intramolecular Hbond substituents
source code
 
fr_phos_acid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2980>)
Number of phosphoric acid groups
source code
 
fr_phos_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e29f0>)
Number of phosphoric ester groups
source code
 
fr_piperdine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2520>)
Number of piperdine rings
source code
 
fr_piperzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2590>)
Number of piperzine rings
source code
 
fr_priamide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0980>)
Number of primary amides
source code
 
fr_prisulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e20c0>)
Number of primary sulfonamides
source code
 
fr_pyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e24b0>)
Number of pyridine rings
source code
 
fr_quatN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e01a0>)
Number of quarternary nitrogens
source code
 
fr_sulfide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0de0>)
Number of thioether
source code
 
fr_sulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2050>)
Number of sulfonamides
source code
 
fr_sulfone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0fa0>)
Number of sulfone groups
source code
 
fr_term_acetylene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2210>)
Number of terminal acetylenes
source code
 
fr_tetrazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2750>)
Number of tetrazole rings
source code
 
fr_thiazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e23d0>)
Number of thiazole rings
source code
 
fr_thiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e0c90>)
Number of thiocyanates
source code
 
fr_thiophene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2360>)
Number of thiophene rings
source code
 
fr_unbrch_alkane(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f5b441e2830>)
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 0x7f5b441e21a0>)
Number of urea groups
source code
Variables [hide private]
  defaultPatternFileName = '/scratch/old_versions/RDKit_2014_09_...
  fns = [('fr_C_O', <function <lambda> at 0x7f5b441d67d0>), ('fr...
  fn = None
hash(x)
  __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 0x7f5b441e7050>)

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


Variables Details [hide private]

defaultPatternFileName

Value:
'/scratch/old_versions/RDKit_2014_09_1/Data/FragmentDescriptors.csv'

fns

Value:
[]