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>) Number of aliphatic carboxylic acids | source code
fr_Al_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of aliphatic hydroxyl groups | source code
fr_Al_OH_noTert(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of aliphatic hydroxyl groups excluding tert-OH | source code
fr_ArN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of N functional groups attached to aromatics | source code
fr_Ar_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of Aromatic carboxylic acide | source code
fr_Ar_N(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of aromatic nitrogens | source code
fr_Ar_NH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of aromatic amines | source code
fr_Ar_OH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of aromatic hydroxyl groups | source code
fr_COO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of carboxylic acids | source code
fr_COO2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of carboxylic acids | source code
fr_C_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of carbonyl O | source code
fr_C_O_noCOO(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of carbonyl O, excluding COOH | source code
fr_C_S(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of thiocarbonyl | source code
fr_HOCCN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of C(OH)CCN-Ctert-alkyl or C(OH)CCNcyclic | source code
fr_Imine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of Imines | source code
fr_NH0(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of Tertiary amines | source code
fr_NH1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of Secondary amines | source code
fr_NH2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of Primary amines | source code
fr_N_O(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of hydroxylamine groups | source code
fr_Ndealkylation1(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of XCCNR groups | source code
fr_Ndealkylation2(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) 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>) Number of H-pyrrole nitrogens | source code
fr_SH(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of thiol groups | source code
fr_aldehyde(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of aldehydes | source code
fr_alkyl_carbamate(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of alkyl carbamates (subject to hydrolysis) | source code
fr_alkyl_halide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of alkyl halides | source code
fr_allylic_oxid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of allylic oxidation sites excluding steroid dienone | source code
fr_amide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of amides | source code
fr_amidine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of amidine groups | source code
fr_aniline(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of anilines | source code
fr_aryl_methyl(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of aryl methyl sites for hydroxylation | source code
fr_azide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of azide groups | source code
fr_azo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of azo groups | source code
fr_barbitur(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of barbiturate groups | source code
fr_benzene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of benzene rings | source code
fr_benzodiazepine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of benzodiazepines with no additional fused rings | source code
fr_bicyclic(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Bicyclic | source code
fr_diazo(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of diazo groups | source code
fr_dihydropyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of dihydropyridines | source code
fr_epoxide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of epoxide rings | source code
fr_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of esters | source code
fr_ether(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of ether oxygens (including phenoxy) | source code
fr_furan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of furan rings | source code
fr_guanido(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of guanidine groups | source code
fr_halogen(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of halogens | source code
fr_hdrzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of hydrazine groups | source code
fr_hdrzone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of hydrazone groups | source code
fr_imidazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of imidazole rings | source code
fr_imide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of imide groups | source code
fr_isocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of isocyanates | source code
fr_isothiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of isothiocyanates | source code
fr_ketone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of ketones | source code
fr_ketone_Topliss(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of ketones excluding diaryl, a,b-unsat. | source code
fr_lactam(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of beta lactams | source code
fr_lactone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of cyclic esters (lactones) | source code
fr_methoxy(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of methoxy groups -OCH3 | source code
fr_morpholine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of morpholine rings | source code
fr_nitrile(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of nitriles | source code
fr_nitro(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of nitro groups | source code
fr_nitro_arom(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of nitro benzene ring substituents | source code
fr_nitro_arom_nonortho(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of non-ortho nitro benzene ring substituents | source code
fr_nitroso(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of nitroso groups, excluding NO2 | source code
fr_oxazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of oxazole rings | source code
fr_oxime(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of oxime groups | source code
fr_para_hydroxylation(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of para-hydroxylation sites | source code
fr_phenol(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of phenols | source code
fr_phenol_noOrthoHbond(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of phenolic OH excluding ortho intramolecular Hbond substituents | source code
fr_phos_acid(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of phosphoric acid groups | source code
fr_phos_ester(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of phosphoric ester groups | source code
fr_piperdine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of piperdine rings | source code
fr_piperzine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of piperzine rings | source code
fr_priamide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of primary amides | source code
fr_prisulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of primary sulfonamides | source code
fr_pyridine(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of pyridine rings | source code
fr_quatN(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of quarternary nitrogens | source code
fr_sulfide(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of thioether | source code
fr_sulfonamd(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of sulfonamides | source code
fr_sulfone(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of sulfone groups | source code
fr_term_acetylene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of terminal acetylenes | source code
fr_tetrazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of tetrazole rings | source code
fr_thiazole(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of thiazole rings | source code
fr_thiocyan(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of thiocyanates | source code
fr_thiophene(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) Number of thiophene rings | source code
fr_unbrch_alkane(mol, countUnique=True, pattern=<rdkit.Chem.rdchem.Mol object>) 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>) Number of urea groups | source code

Variables | [hide private]
| defaultPatternFileName = ``'``/scratch/RDKit_git/Data/FragmentDesc``...``
| fns = ``[``(``'``fr_C_O``'``,` <__builtin__.function object>`)``,` `(``'``fr_C_O_noC``...``
| 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>) | 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:
      [('fr_C_O', <__builtin__.function object>),
       ('fr_C_O_noCOO', <__builtin__.function object>),
       ('fr_Al_OH', <__builtin__.function object>),
       ('fr_Ar_OH', <__builtin__.function object>),
       ('fr_methoxy', <__builtin__.function object>),
       ('fr_oxime', <__builtin__.function object>),
       ('fr_ester', <__builtin__.function object>),
       ('fr_Al_COO', <__builtin__.function object>),
      ...