Re: [Rdkit-discuss] Descriptor3d not exposed in python

[Greg L. <gre...@gm...>]

Ah, right,
I forgot to bring it over into rdkit.Chem.Descriptors. The functions are in
rdkit.Chem.rdMolDescriptors:

In [4]: from rdkit.Chem import rdMolDescriptors
In [5]: rdMolDescriptors.CalcRadiusOfGyration?
Docstring:
CalcRadiusOfGyration( (Mol)mol [, (int)confId=-1 [,
(bool)useAtomicMasses=True]]) -> float :

    C++ signature :
        double CalcRadiusOfGyration(RDKit::ROMol [,int=-1 [,bool=True]])
Type:      function

I'll fix rdkit.Chem.Descriptors too.



On Tue, Oct 11, 2016 at 8:37 PM, Guillaume GODIN <
Gui...@fi...> wrote:

> Maybe I made a wrong request:
>
>
> from rdkit import Chem
> from rdkit.Chem import Descriptors
>
> from rdkit import rdBase
>
>
> print rdBase.rdkitVersion
>
> print rdBase.boostVersion
>
> m = Chem.MolFromSmiles('c1ccccc1C(=O)O')
>
>
> print dir(Descriptors)
>
> print Descriptors.CalcRadiusOfGyration(m)
>
>
> output is:
>
> 2016.09.1.dev1
>
> 1_61
>
> ['BalabanJ', 'BertzCT', 'Chem', 'Chi0', 'Chi0n', 'Chi0v', 'Chi1', 'Chi1n',
> 'Chi1v', 'Chi2n', 'Chi2v', 'Chi3n', 'Chi3v', 'Chi4n', 'Chi4v',
> 'EState_VSA1', 'EState_VSA10', 'EState_VSA11', 'EState_VSA2',
> 'EState_VSA3', 'EState_VSA4', 'EState_VSA5', 'EState_VSA6', 'EState_VSA7',
> 'EState_VSA8', 'EState_VSA9', 'ExactMolWt', 'FractionCSP3',
> 'HallKierAlpha', 'HeavyAtomCount', 'HeavyAtomMolWt', 'Ipc', 'Kappa1',
> 'Kappa2', 'Kappa3', 'LabuteASA', 'MaxAbsEStateIndex',
> 'MaxAbsPartialCharge', 'MaxEStateIndex', 'MaxPartialCharge',
> 'MinAbsEStateIndex', 'MinAbsPartialCharge', 'MinEStateIndex',
> 'MinPartialCharge', 'MolLogP', 'MolMR', 'MolWt', 'NHOHCount', 'NOCount',
> 'NumAliphaticCarbocycles', 'NumAliphaticHeterocycles', 'NumAliphaticRings',
> 'NumAromaticCarbocycles', 'NumAromaticHeterocycles', 'NumAromaticRings',
> 'NumHAcceptors', 'NumHDonors', 'NumHeteroatoms', 'NumRadicalElectrons',
> 'NumRotatableBonds', 'NumSaturatedCarbocycles', 'NumSaturatedHeterocycles',
> 'NumSaturatedRings', 'NumValenceElectrons', 'PEOE_VSA1', 'PEOE_VSA10',
> 'PEOE_VSA11', 'PEOE_VSA12', 'PEOE_VSA13', 'PEOE_VSA14', 'PEOE_VSA2',
> 'PEOE_VSA3', 'PEOE_VSA4', 'PEOE_VSA5', 'PEOE_VSA6', 'PEOE_VSA7',
> 'PEOE_VSA8', 'PEOE_VSA9', 'PropertyFunctor', 'RingCount', 'SMR_VSA1',
> 'SMR_VSA10', 'SMR_VSA2', 'SMR_VSA3', 'SMR_VSA4', 'SMR_VSA5', 'SMR_VSA6',
> 'SMR_VSA7', 'SMR_VSA8', 'SMR_VSA9', 'SlogP_VSA1', 'SlogP_VSA10',
> 'SlogP_VSA11', 'SlogP_VSA12', 'SlogP_VSA2', 'SlogP_VSA3', 'SlogP_VSA4',
> 'SlogP_VSA5', 'SlogP_VSA6', 'SlogP_VSA7', 'SlogP_VSA8', 'SlogP_VSA9',
> 'TPSA', 'VSA_EState1', 'VSA_EState10', 'VSA_EState2', 'VSA_EState3',
> 'VSA_EState4', 'VSA_EState5', 'VSA_EState6', 'VSA_EState7', 'VSA_EState8',
> 'VSA_EState9', '_ChargeDescriptors', '__builtins__', '__doc__', '__file__',
> '__name__', '__package__', '_descList', '_isCallable', '_rdMolDescriptors',
> '_setupDescriptors', '_test', 'collections', 'descList', 'fr_Al_COO',
> 'fr_Al_OH', 'fr_Al_OH_noTert', 'fr_ArN', 'fr_Ar_COO', 'fr_Ar_N',
> 'fr_Ar_NH', 'fr_Ar_OH', 'fr_COO', 'fr_COO2', 'fr_C_O', 'fr_C_O_noCOO',
> 'fr_C_S', 'fr_HOCCN', 'fr_Imine', 'fr_NH0', 'fr_NH1', 'fr_NH2', 'fr_N_O',
> 'fr_Ndealkylation1', 'fr_Ndealkylation2', 'fr_Nhpyrrole', 'fr_SH',
> 'fr_aldehyde', 'fr_alkyl_carbamate', 'fr_alkyl_halide', 'fr_allylic_oxid',
> 'fr_amide', 'fr_amidine', 'fr_aniline', 'fr_aryl_methyl', 'fr_azide',
> 'fr_azo', 'fr_barbitur', 'fr_benzene', 'fr_benzodiazepine', 'fr_bicyclic',
> 'fr_diazo', 'fr_dihydropyridine', 'fr_epoxide', 'fr_ester', 'fr_ether',
> 'fr_furan', 'fr_guanido', 'fr_halogen', 'fr_hdrzine', 'fr_hdrzone',
> 'fr_imidazole', 'fr_imide', 'fr_isocyan', 'fr_isothiocyan', 'fr_ketone',
> 'fr_ketone_Topliss', 'fr_lactam', 'fr_lactone', 'fr_methoxy',
> 'fr_morpholine', 'fr_nitrile', 'fr_nitro', 'fr_nitro_arom',
> 'fr_nitro_arom_nonortho', 'fr_nitroso', 'fr_oxazole', 'fr_oxime',
> 'fr_para_hydroxylation', 'fr_phenol', 'fr_phenol_noOrthoHbond',
> 'fr_phos_acid', 'fr_phos_ester', 'fr_piperdine', 'fr_piperzine',
> 'fr_priamide', 'fr_prisulfonamd', 'fr_pyridine', 'fr_quatN', 'fr_sulfide',
> 'fr_sulfonamd', 'fr_sulfone', 'fr_term_acetylene', 'fr_tetrazole',
> 'fr_thiazole', 'fr_thiocyan', 'fr_thiophene', 'fr_unbrch_alkane',
> 'fr_urea', 'rdMolDescriptors', 'rdPartialCharges']
>
> Traceback (most recent call last):
>
>   File "newdesc.py", line 16, in <module>
>
>     print Descriptors.CalcRadiusOfGyration(m)
>
>
>
> AttributeError: 'module' object has no attribute 'CalcRadiusOfGyration'​
>
>
>
>
> *Dr. Guillaume GODIN*
> Principal Scientist
> Chemoinformatic & Datamining
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645
> MOBILE          +41 (0)79 536 1039
>         Firmenich SA
>         RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
> ------------------------------
> *De :* Greg Landrum <gre...@gm...>
> *Envoyé :* mardi 11 octobre 2016 18:39
> *À :* Guillaume GODIN
> *Cc :* rdk...@li...
> *Objet :* Re: [Rdkit-discuss] Descriptor3d not exposed in python
>
> Guillaume,
>
> Are you sure that the 3D descriptors built? If you don't have the eigen
> library installed ("conda install -c conda-forge eigen" if you are using
> anaconda python), the 3D descriptor build will be automatically disabled.
> If eigen is not present, when you run cmake, you will see a message like
> this:
>
> -- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
> (Required is at least version "2.91.0")
> Eigen3 not found, disabling the Descriptors3D build.
>
> as part of the output of cmake.
>
> -greg
>
>
>
> On Tue, Oct 11, 2016 at 6:00 PM, Guillaume GODIN <
> Gui...@fi...> wrote:
>
>> Dear all,
>>
>> I'm trying to use 3D descriptors in Python after compiling without issue,
>> there is no new descriptors available in Python, is it normal?
>> Best regards,
>>
>> Guillaume
>>
>> Envoyé de mon iPhone
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