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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=1) source code
 
_LoadPatterns(fileName=None) source code
 
fr_Al_COO(x, y=1, z=<Chem.rdchem.Mol object at 0x8730144>)
Number of aliphatic carboxylic acids		 source code
 
fr_Al_OH(x, y=1, z=<Chem.rdchem.Mol object at 0x8722e64>)
Number of aliphatic hydroxyl groups		 source code
 
fr_Al_OH_noTert(x, y=1, z=<Chem.rdchem.Mol object at 0x873448c>)
Number of aliphatic hydroxyl groups excluding tert-OH		 source code
 
fr_ArN(x, y=1, z=<Chem.rdchem.Mol object at 0x873487c>)
Number of N functional groups attached to aromatics		 source code
 
fr_Ar_COO(x, y=1, z=<Chem.rdchem.Mol object at 0x873010c>)
Number of Aromatic carboxylic acide		 source code
 
fr_Ar_N(x, y=1, z=<Chem.rdchem.Mol object at 0x87307d4>)
Number of aromatic nitrogens		 source code
 
fr_Ar_NH(x, y=1, z=<Chem.rdchem.Mol object at 0x873087c>)
Number of aromatic amines		 source code
 
fr_Ar_OH(x, y=1, z=<Chem.rdchem.Mol object at 0x8722ed4>)
Number of aromatic hydroxyl groups		 source code
 
fr_COO(x, y=1, z=<Chem.rdchem.Mol object at 0x8730294>)
Number of carboxylic acids		 source code
 
fr_COO2(x, y=1, z=<Chem.rdchem.Mol object at 0x873025c>)
Number of carboxylic acids		 source code
 
fr_C_O(x, y=1, z=<Chem.rdchem.Mol object at 0x8722c34>)
Number of carbonyl O		 source code
 
fr_C_O_noCOO(x, y=1, z=<Chem.rdchem.Mol object at 0x8722df4>)
Number of carbonyl O, excluding COOH		 source code
 
fr_C_S(x, y=1, z=<Chem.rdchem.Mol object at 0x87314c4>)
Number of thiocarbonyl		 source code
 
fr_HOCCN(x, y=1, z=<Chem.rdchem.Mol object at 0x87348ec>)
Number of C(OH)CCN-Ctert-alkyl or C(OH)CCNcyclic		 source code
 
fr_Imine(x, y=1, z=<Chem.rdchem.Mol object at 0x8730924>)
Number of Imines		 source code
 
fr_NH0(x, y=1, z=<Chem.rdchem.Mol object at 0x873072c>)
Number of Tertiary amines		 source code
 
fr_NH1(x, y=1, z=<Chem.rdchem.Mol object at 0x8730684>)
Number of Secondary amines		 source code
 
fr_NH2(x, y=1, z=<Chem.rdchem.Mol object at 0x87305dc>)
Number of Primary amines		 source code
 
fr_N_O(x, y=1, z=<Chem.rdchem.Mol object at 0x8730c34>)
Number of hydroxylamine groups		 source code
 
fr_Ndealkylation1(x, y=1, z=<Chem.rdchem.Mol object at 0x87346bc>)
Number of XCCNR groups		 source code
 
fr_Ndealkylation2(x, y=1, z=<Chem.rdchem.Mol object at 0x873472c>)
Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)		 source code
 
fr_Nhpyrrole(x, y=1, z=<Chem.rdchem.Mol object at 0x87310d4>)
Number of H-pyrrole nitrogens		 source code
 
fr_SH(x, y=1, z=<Chem.rdchem.Mol object at 0x8731454>)
Number of thiol groups		 source code
 
fr_aldehyde(x, y=1, z=<Chem.rdchem.Mol object at 0x873048c>)
Number of aldehydes		 source code
 
fr_alkyl_carbamate(x, y=1, z=<Chem.rdchem.Mol object at 0x873479c>)
Number of alkyl carbamates (subject to hydrolysis)		 source code
 
fr_alkyl_halide(x, y=1, z=<Chem.rdchem.Mol object at 0x87313ac>)
Number of alkyl halides		 source code
 
fr_allylic_oxid(x, y=1, z=<Chem.rdchem.Mol object at 0x87345dc>)
Number of allylic oxidation sites excluding steroid dienone		 source code
 
fr_amide(x, y=1, z=<Chem.rdchem.Mol object at 0x8730e2c>)
Number of amides		 source code
 
fr_amidine(x, y=1, z=<Chem.rdchem.Mol object at 0x8730e9c>)
Number of amidine groups		 source code
 
fr_aniline(x, y=1, z=<Chem.rdchem.Mol object at 0x8730844>)
Number of anilines		 source code
 
fr_aryl_methyl(x, y=1, z=<Chem.rdchem.Mol object at 0x873464c>)
Number of aryl methyl sites for hydroxylation		 source code
 
fr_azide(x, y=1, z=<Chem.rdchem.Mol object at 0x8730dbc>)
Number of azide groups		 source code
 
fr_azo(x, y=1, z=<Chem.rdchem.Mol object at 0x8730cdc>)
Number of azo groups		 source code
 
fr_barbitur(x, y=1, z=<Chem.rdchem.Mol object at 0x873179c>)
Number of barbiturate groups		 source code
 
fr_benzene(x, y=1, z=<Chem.rdchem.Mol object at 0x8734144>)
Number of benzene rings		 source code
 
fr_benzodiazepine(x, y=1, z=<Chem.rdchem.Mol object at 0x87344fc>)
Number of benzodiazepines with no additional fused rings		 source code
 
fr_bicyclic(x, y=1, z=<Chem.rdchem.Mol object at 0x8734064>)
Bicyclic		 source code
 
fr_diazo(x, y=1, z=<Chem.rdchem.Mol object at 0x8730d4c>)
Number of diazo groups		 source code
 
fr_dihydropyridine(x, y=1, z=<Chem.rdchem.Mol object at 0x87343e4>)
Number of dihydropyridines		 source code
 
fr_epoxide(x, y=1, z=<Chem.rdchem.Mol object at 0x8731ed4>)
Number of epoxide rings		 source code
 
fr_ester(x, y=1, z=<Chem.rdchem.Mol object at 0x873009c>)
Number of esters		 source code
 
fr_ether(x, y=1, z=<Chem.rdchem.Mol object at 0x87303ac>)
Number of ether oxygens (including phenoxy)		 source code
 
fr_furan(x, y=1, z=<Chem.rdchem.Mol object at 0x8731924>)
Number of furan rings		 source code
 
fr_guanido(x, y=1, z=<Chem.rdchem.Mol object at 0x873102c>)
Number of guanidine groups		 source code
 
fr_halogen(x, y=1, z=<Chem.rdchem.Mol object at 0x8731304>)
Number of halogens		 source code
 
fr_hdrzine(x, y=1, z=<Chem.rdchem.Mol object at 0x8730a74>)
Number of hydrazine groups		 source code
 
fr_hdrzone(x, y=1, z=<Chem.rdchem.Mol object at 0x8730b54>)
Number of hydrazone groups		 source code
 
fr_imidazole(x, y=1, z=<Chem.rdchem.Mol object at 0x873195c>)
Number of imidazole rings		 source code
 
fr_imide(x, y=1, z=<Chem.rdchem.Mol object at 0x873109c>)
Number of imide groups		 source code
 
fr_isocyan(x, y=1, z=<Chem.rdchem.Mol object at 0x873117c>)
Number of isocyanates		 source code
 
fr_isothiocyan(x, y=1, z=<Chem.rdchem.Mol object at 0x873125c>)
Number of isothiocyanates		 source code
 
fr_ketone(x, y=1, z=<Chem.rdchem.Mol object at 0x8730304>)
Number of ketones		 source code
 
fr_ketone_Topliss(x, y=1, z=<Chem.rdchem.Mol object at 0x873480c>)
Number of ketones excluding diaryl, a,b-unsat.		 source code
 
fr_lactam(x, y=1, z=<Chem.rdchem.Mol object at 0x8731d84>)
Number of beta lactams		 source code
 
fr_lactone(x, y=1, z=<Chem.rdchem.Mol object at 0x8731e64>)
Number of cyclic esters (lactones)		 source code
 
fr_methoxy(x, y=1, z=<Chem.rdchem.Mol object at 0x8722fb4>)
Number of methoxy groups -OCH3		 source code
 
fr_morpholine(x, y=1, z=<Chem.rdchem.Mol object at 0x8731dbc>)
Number of morpholine rings		 source code
 
fr_nitrile(x, y=1, z=<Chem.rdchem.Mol object at 0x8730994>)
Number of nitriles		 source code
 
fr_nitro(x, y=1, z=<Chem.rdchem.Mol object at 0x8730bc4>)
Number of nitro groups		 source code
 
fr_nitro_arom(x, y=1, z=<Chem.rdchem.Mol object at 0x8734294>)
Number of nitro benzene ring substituents		 source code
 
fr_nitro_arom_nonortho(x, y=1, z=<Chem.rdchem.Mol object at 0x8734304>)
Number of non-ortho nitro benzene ring substituents		 source code
 
fr_nitroso(x, y=1, z=<Chem.rdchem.Mol object at 0x8730ae4>)
Number of nitroso groups, excluding NO2		 source code
 
fr_oxazole(x, y=1, z=<Chem.rdchem.Mol object at 0x8731ae4>)
Number of oxazole rings		 source code
 
fr_oxime(x, y=1, z=<Chem.rdchem.Mol object at 0x8722f44>)
Number of oxime groups		 source code
 
fr_para_hydroxylation(x, y=1, z=<Chem.rdchem.Mol object at 0x873456c>)
Number of para-hydroxylation sites		 source code
 
fr_phenol(x, y=1, z=<Chem.rdchem.Mol object at 0x873041c>)
Number of phenols		 source code
 
fr_phenol_noOrthoHbond(x, y=1, z=<Chem.rdchem.Mol object at 0x8734374>)
Number of phenolic OH excluding ortho intramolecular Hbond substituents		 source code
 
fr_phos_acid(x, y=1, z=<Chem.rdchem.Mol object at 0x87341b4>)
Number of phosphoric acid groups		 source code
 
fr_phos_ester(x, y=1, z=<Chem.rdchem.Mol object at 0x8734224>)
Number of phosphoric ester groups		 source code
 
fr_piperdine(x, y=1, z=<Chem.rdchem.Mol object at 0x8731c6c>)
Number of piperdine rings		 source code
 
fr_piperzine(x, y=1, z=<Chem.rdchem.Mol object at 0x8731d14>)
Number of piperzine rings		 source code
 
fr_priamide(x, y=1, z=<Chem.rdchem.Mol object at 0x8730ed4>)
Number of primary amides		 source code
 
fr_prisulfonamd(x, y=1, z=<Chem.rdchem.Mol object at 0x87316f4>)
Number of primary sulfonamides		 source code
 
fr_pyridine(x, y=1, z=<Chem.rdchem.Mol object at 0x8731b54>)
Number of pyridine rings		 source code
 
fr_quatN(x, y=1, z=<Chem.rdchem.Mol object at 0x8730534>)
Number of quarternary nitrogens		 source code
 
fr_sulfide(x, y=1, z=<Chem.rdchem.Mol object at 0x8731374>)
Number of thioether		 source code
 
fr_sulfonamd(x, y=1, z=<Chem.rdchem.Mol object at 0x87315dc>)
Number of sulfonamides		 source code
 
fr_sulfone(x, y=1, z=<Chem.rdchem.Mol object at 0x8731534>)
Number of sulfone groups		 source code
 
fr_term_acetylene(x, y=1, z=<Chem.rdchem.Mol object at 0x87318b4>)
Number of terminal acetylenes		 source code
 
fr_tetrazole(x, y=1, z=<Chem.rdchem.Mol object at 0x8731f44>)
Number of tetrazole rings		 source code
 
fr_thiazole(x, y=1, z=<Chem.rdchem.Mol object at 0x8731a04>)
Number of thiazole rings		 source code
 
fr_thiocyan(x, y=1, z=<Chem.rdchem.Mol object at 0x87311ec>)
Number of thiocyanates		 source code
 
fr_thiophene(x, y=1, z=<Chem.rdchem.Mol object at 0x8731a74>)
Number of thiophene rings		 source code
 
fr_unbrch_alkane(x, y=1, z=<Chem.rdchem.Mol object at 0x8731fb4>)
Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)		 source code
 
fr_urea(x, y=1, z=<Chem.rdchem.Mol object at 0x8731684>)
Number of urea groups		 source code
Variables [hide private]
  defaultPatternFileName = '/scratch/RDKit_Q32008_1/Data/Fragmen...
  fns = [('fr_C_O', <function <lambda> at 0x8722dbc>), ('fr_C_O_...
  fn = None
  name = 'fr_HOCCN'
Function Details [hide private]

fr_ketone_Topliss(x, y=1, z=<Chem.rdchem.Mol object at 0x873480c>)

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

Variables Details [hide private]

defaultPatternFileName

Value:
'/scratch/RDKit_Q32008_1/Data/FragmentDescriptors.csv'

fns

Value:
[]

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