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 0x7f7935f14d00>)
Number of aliphatic carboxylic acids
source code
 
fr_Al_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14ad0>)
Number of aliphatic hydroxyl groups
source code
 
fr_Al_OH_noTert(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3ad0>)
Number of aliphatic hydroxyl groups excluding tert-OH
source code
 
fr_ArN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f09050>)
Number of N functional groups attached to aromatics
source code
 
fr_Ar_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14d70>)
Number of Aromatic carboxylic acide
source code
 
fr_Ar_N(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd280>)
Number of aromatic nitrogens
source code
 
fr_Ar_NH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd2f0>)
Number of aromatic amines
source code
 
fr_Ar_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14b40>)
Number of aromatic hydroxyl groups
source code
 
fr_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14de0>)
Number of carboxylic acids
source code
 
fr_COO2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14e50>)
Number of carboxylic acids
source code
 
fr_C_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f149f0>)
Number of carbonyl O
source code
 
fr_C_O_noCOO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14a60>)
Number of carbonyl O, excluding COOH
source code
 
fr_C_S(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdde0>)
Number of thiocarbonyl
source code
 
fr_HOCCN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3fa0>)
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 0x7f7936cbd3d0>)
Number of Imines
source code
 
fr_NH0(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd210>)
Number of Tertiary amines
source code
 
fr_NH1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd1a0>)
Number of Secondary amines
source code
 
fr_NH2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd130>)
Number of Primary amines
source code
 
fr_N_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd600>)
Number of hydroxylamine groups
source code
 
fr_Ndealkylation1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3d70>)
Number of XCCNR groups
source code
 
fr_Ndealkylation2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3e50>)
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 0x7f7936cbd9f0>)
Number of H-pyrrole nitrogens
source code
 
fr_SH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdd70>)
Number of thiol groups
source code
 
fr_aldehyde(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd050>)
Number of aldehydes
source code
 
fr_alkyl_carbamate(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3ec0>)
Number of alkyl carbamates (subject to hydrolysis)
source code
 
fr_alkyl_halide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdc90>)
Number of alkyl halides
source code
 
fr_allylic_oxid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3d00>)
Number of allylic oxidation sites excluding steroid dienone
source code
 
fr_amide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd830>)
Number of amides
source code
 
fr_amidine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd910>)
Number of amidine groups
source code
 
fr_aniline(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd360>)
Number of anilines
source code
 
fr_aryl_methyl(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3de0>)
Number of aryl methyl sites for hydroxylation
source code
 
fr_azide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd7c0>)
Number of azide groups
source code
 
fr_azo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd6e0>)
Number of azo groups
source code
 
fr_barbitur(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3050>)
Number of barbiturate groups
source code
 
fr_benzene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3830>)
Number of benzene rings
source code
 
fr_benzodiazepine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3c90>)
Number of benzodiazepines with no additional fused rings
source code
 
fr_bicyclic(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc37c0>)
Bicyclic
source code
 
fr_diazo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd750>)
Number of diazo groups
source code
 
fr_dihydropyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3a60>)
Number of dihydropyridines
source code
 
fr_epoxide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc36e0>)
Number of epoxide rings
source code
 
fr_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14c90>)
Number of esters
source code
 
fr_ether(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14f30>)
Number of ether oxygens (including phenoxy)
source code
 
fr_furan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3210>)
Number of furan rings
source code
 
fr_guanido(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd980>)
Number of guanidine groups
source code
 
fr_halogen(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdc20>)
Number of halogens
source code
 
fr_hdrzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd4b0>)
Number of hydrazine groups
source code
 
fr_hdrzone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd520>)
Number of hydrazone groups
source code
 
fr_imidazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc31a0>)
Number of imidazole rings
source code
 
fr_imide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbda60>)
Number of imide groups
source code
 
fr_isocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdad0>)
Number of isocyanates
source code
 
fr_isothiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdb40>)
Number of isothiocyanates
source code
 
fr_ketone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14ec0>)
Number of ketones
source code
 
fr_ketone_Topliss(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3f30>)
Number of ketones excluding diaryl, a,b-unsat.
source code
 
fr_lactam(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3590>)
Number of beta lactams
source code
 
fr_lactone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3600>)
Number of cyclic esters (lactones)
source code
 
fr_methoxy(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14c20>)
Number of methoxy groups -OCH3
source code
 
fr_morpholine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3520>)
Number of morpholine rings
source code
 
fr_nitrile(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd440>)
Number of nitriles
source code
 
fr_nitro(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd670>)
Number of nitro groups
source code
 
fr_nitro_arom(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3980>)
Number of nitro benzene ring substituents
source code
 
fr_nitro_arom_nonortho(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc39f0>)
Number of non-ortho nitro benzene ring substituents
source code
 
fr_nitroso(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd590>)
Number of nitroso groups, excluding NO2
source code
 
fr_oxazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3360>)
Number of oxazole rings
source code
 
fr_oxime(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14bb0>)
Number of oxime groups
source code
 
fr_para_hydroxylation(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3c20>)
Number of para-hydroxylation sites
source code
 
fr_phenol(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7935f14fa0>)
Number of phenols
source code
 
fr_phenol_noOrthoHbond(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3bb0>)
Number of phenolic OH excluding ortho intramolecular Hbond substituents
source code
 
fr_phos_acid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc38a0>)
Number of phosphoric acid groups
source code
 
fr_phos_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3910>)
Number of phosphoric ester groups
source code
 
fr_piperdine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3440>)
Number of piperdine rings
source code
 
fr_piperzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc34b0>)
Number of piperzine rings
source code
 
fr_priamide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd8a0>)
Number of primary amides
source code
 
fr_prisulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdfa0>)
Number of primary sulfonamides
source code
 
fr_pyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc33d0>)
Number of pyridine rings
source code
 
fr_quatN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbd0c0>)
Number of quarternary nitrogens
source code
 
fr_sulfide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdd00>)
Number of thioether
source code
 
fr_sulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdf30>)
Number of sulfonamides
source code
 
fr_sulfone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdec0>)
Number of sulfone groups
source code
 
fr_term_acetylene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3130>)
Number of terminal acetylenes
source code
 
fr_tetrazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3670>)
Number of tetrazole rings
source code
 
fr_thiazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc32f0>)
Number of thiazole rings
source code
 
fr_thiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cbdbb0>)
Number of thiocyanates
source code
 
fr_thiophene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3280>)
Number of thiophene rings
source code
 
fr_unbrch_alkane(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7f7936cc3750>)
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 0x7f7936cc30c0>)
Number of urea groups
source code
Variables [hide private]
  defaultPatternFileName = '/home/vagrant/RDKit_git/Data/Fragmen...
  fns = [('fr_C_O', <function <lambda> at 0x7f7936cbf2a8>), ('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 0x7f7936cc3f30>)

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


Variables Details [hide private]

defaultPatternFileName

Value:
'/home/vagrant/RDKit_git/Data/FragmentDescriptors.csv'

fns

Value:
[]