rdkit.Chem.Fragments

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 0x7fc441c8f3d0>) Number of aliphatic carboxylic acids | source code
fr_Al_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f1a0>) Number of aliphatic hydroxyl groups | source code
fr_Al_OH_noTert(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b1a0>) Number of aliphatic hydroxyl groups excluding tert-OH | source code
fr_ArN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b6e0>) Number of N functional groups attached to aromatics | source code
fr_Ar_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f440>) Number of Aromatic carboxylic acide | source code
fr_Ar_N(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f910>) Number of aromatic nitrogens | source code
fr_Ar_NH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f980>) Number of aromatic amines | source code
fr_Ar_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f210>) Number of aromatic hydroxyl groups | source code
fr_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f4b0>) Number of carboxylic acids | source code
fr_COO2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f520>) Number of carboxylic acids | source code
fr_C_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f0c0>) Number of carbonyl O | source code
fr_C_O_noCOO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f130>) Number of carbonyl O, excluding COOH | source code
fr_C_S(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c954b0>) Number of thiocarbonyl | source code
fr_HOCCN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b670>) 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 0x7fc441c8fa60>) Number of Imines | source code
fr_NH0(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f8a0>) Number of Tertiary amines | source code
fr_NH1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f830>) Number of Secondary amines | source code
fr_NH2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f7c0>) Number of Primary amines | source code
fr_N_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fc90>) Number of hydroxylamine groups | source code
fr_Ndealkylation1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b440>) Number of XCCNR groups | source code
fr_Ndealkylation2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b520>) 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 0x7fc441c950c0>) Number of H-pyrrole nitrogens | source code
fr_SH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95440>) Number of thiol groups | source code
fr_aldehyde(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f6e0>) Number of aldehydes | source code
fr_alkyl_carbamate(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b590>) Number of alkyl carbamates (subject to hydrolysis) | source code
fr_alkyl_halide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95360>) Number of alkyl halides | source code
fr_allylic_oxid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b3d0>) Number of allylic oxidation sites excluding steroid dienone | source code
fr_amide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fec0>) Number of amides | source code
fr_amidine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8ffa0>) Number of amidine groups | source code
fr_aniline(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f9f0>) Number of anilines | source code
fr_aryl_methyl(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b4b0>) Number of aryl methyl sites for hydroxylation | source code
fr_azide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fe50>) Number of azide groups | source code
fr_azo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fd70>) Number of azo groups | source code
fr_barbitur(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c956e0>) Number of barbiturate groups | source code
fr_benzene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95ec0>) Number of benzene rings | source code
fr_benzodiazepine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b360>) Number of benzodiazepines with no additional fused rings | source code
fr_bicyclic(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95e50>) Bicyclic | source code
fr_diazo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fde0>) Number of diazo groups | source code
fr_dihydropyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b130>) Number of dihydropyridines | source code
fr_epoxide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95d70>) Number of epoxide rings | source code
fr_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f360>) Number of esters | source code
fr_ether(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f600>) Number of ether oxygens (including phenoxy) | source code
fr_furan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c958a0>) Number of furan rings | source code
fr_guanido(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95050>) Number of guanidine groups | source code
fr_halogen(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c952f0>) Number of halogens | source code
fr_hdrzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fb40>) Number of hydrazine groups | source code
fr_hdrzone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fbb0>) Number of hydrazone groups | source code
fr_imidazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95830>) Number of imidazole rings | source code
fr_imide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95130>) Number of imide groups | source code
fr_isocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c951a0>) Number of isocyanates | source code
fr_isothiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95210>) Number of isothiocyanates | source code
fr_ketone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f590>) Number of ketones | source code
fr_ketone_Topliss(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b600>) Number of ketones excluding diaryl, a,b-unsat. | source code
fr_lactam(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95c20>) Number of beta lactams | source code
fr_lactone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95c90>) Number of cyclic esters (lactones) | source code
fr_methoxy(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f2f0>) Number of methoxy groups -OCH3 | source code
fr_morpholine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95bb0>) Number of morpholine rings | source code
fr_nitrile(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fad0>) Number of nitriles | source code
fr_nitro(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fd00>) Number of nitro groups | source code
fr_nitro_arom(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b050>) Number of nitro benzene ring substituents | source code
fr_nitro_arom_nonortho(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b0c0>) Number of non-ortho nitro benzene ring substituents | source code
fr_nitroso(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8fc20>) Number of nitroso groups, excluding NO2 | source code
fr_oxazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c959f0>) Number of oxazole rings | source code
fr_oxime(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f280>) Number of oxime groups | source code
fr_para_hydroxylation(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b2f0>) Number of para-hydroxylation sites | source code
fr_phenol(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f670>) Number of phenols | source code
fr_phenol_noOrthoHbond(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c9b280>) Number of phenolic OH excluding ortho intramolecular Hbond substituents | source code
fr_phos_acid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95f30>) Number of phosphoric acid groups | source code
fr_phos_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95fa0>) Number of phosphoric ester groups | source code
fr_piperdine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95ad0>) Number of piperdine rings | source code
fr_piperzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95b40>) Number of piperzine rings | source code
fr_priamide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8ff30>) Number of primary amides | source code
fr_prisulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95670>) Number of primary sulfonamides | source code
fr_pyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95a60>) Number of pyridine rings | source code
fr_quatN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c8f750>) Number of quarternary nitrogens | source code
fr_sulfide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c953d0>) Number of thioether | source code
fr_sulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95600>) Number of sulfonamides | source code
fr_sulfone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95590>) Number of sulfone groups | source code
fr_term_acetylene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c957c0>) Number of terminal acetylenes | source code
fr_tetrazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95d00>) Number of tetrazole rings | source code
fr_thiazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95980>) Number of thiazole rings | source code
fr_thiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95280>) Number of thiocyanates | source code
fr_thiophene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95910>) Number of thiophene rings | source code
fr_unbrch_alkane(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object at 0x7fc441c95de0>) 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 0x7fc441c95750>) Number of urea groups | source code

Variables | [hide private]
| defaultPatternFileName = ``'``/scratch/RDKit_git/Data/FragmentDesc``...``
| fns = ``[``(``'``fr_C_O``'``,` <function <lambda> at 0x7fc441c6d5f0>`)``,` `(``'``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 0x7fc441c9b600>) | source code
    Number of ketones excluding diaryl, a,b-unsat. dienones, heteroatom on Calpha

Variables Details | [hide private]

  ### defaultPatternFileName Value:
      '/scratch/RDKit_git/Data/FragmentDescriptors.csv'

  ### fns Value:
      []