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
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RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
________________________________
De : Greg Landrum <[email protected]>
Envoyé : mardi 11 octobre 2016 18:39
À : Guillaume GODIN
Cc : [email protected]
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
<[email protected]<mailto:[email protected]>> 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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