RDKit2D: Failed to initialize: unable to find specified properties

[nizamibilal]

Hi,

I started to see the issue recently while using Reinvent4 within a conda environment (RDkit is installed properly). It did worked fine in the past. Here are the details of the issue.

The error message:

Unable to make new descriptors, descriptor generator requirements not properly installed
Traceback (most recent call last):
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/descriptastorus/DescriptaStore.py", line 42, in
from .descriptors import MakeGenerator
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/descriptastorus/descriptors/init.py", line 2, in
from .rdDescriptors import *
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/descriptastorus/descriptors/rdDescriptors.py", line 371, in
RDKit2D()
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/descriptastorus/descriptors/rdDescriptors.py", line 362, in init
raise ValueError("%s: Failed to initialize: unable to find specified properties:\n\t%s"%(
ValueError: RDKit2D: Failed to initialize: unable to find specified properties:
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
Unable to find specified property fr_Al_COO
Unable to find specified property fr_Al_OH
Unable to find specified property fr_Al_OH_noTert
Unable to find specified property fr_ArN
Unable to find specified property fr_Ar_COO
Unable to find specified property fr_Ar_N
Unable to find specified property fr_Ar_NH
Unable to find specified property fr_Ar_OH
Unable to find specified property fr_COO
Unable to find specified property fr_COO2
Unable to find specified property fr_C_O
Unable to find specified property fr_C_O_noCOO
Unable to find specified property fr_C_S
Unable to find specified property fr_HOCCN
Unable to find specified property fr_Imine
Unable to find specified property fr_NH0
Unable to find specified property fr_NH1
Unable to find specified property fr_NH2
Unable to find specified property fr_N_O
Unable to find specified property fr_Ndealkylation1
Unable to find specified property fr_Ndealkylation2
Unable to find specified property fr_Nhpyrrole
Unable to find specified property fr_SH
Unable to find specified property fr_aldehyde
Unable to find specified property fr_alkyl_carbamate
Unable to find specified property fr_alkyl_halide
Unable to find specified property fr_allylic_oxid
Unable to find specified property fr_amide
Unable to find specified property fr_amidine
Unable to find specified property fr_aniline
Unable to find specified property fr_aryl_methyl
Unable to find specified property fr_azide
Unable to find specified property fr_azo
Unable to find specified property fr_barbitur
Unable to find specified property fr_benzene
Unable to find specified property fr_benzodiazepine
Unable to find specified property fr_bicyclic
Unable to find specified property fr_diazo
Unable to find specified property fr_dihydropyridine
Unable to find specified property fr_epoxide
Unable to find specified property fr_ester
Unable to find specified property fr_ether
Unable to find specified property fr_furan
Unable to find specified property fr_guanido
Unable to find specified property fr_halogen
Unable to find specified property fr_hdrzine
Unable to find specified property fr_hdrzone
Unable to find specified property fr_imidazole
Unable to find specified property fr_imide
Unable to find specified property fr_isocyan
Unable to find specified property fr_isothiocyan
Unable to find specified property fr_ketone
Unable to find specified property fr_ketone_Topliss
Unable to find specified property fr_lactam
Unable to find specified property fr_lactone
Unable to find specified property fr_methoxy
Unable to find specified property fr_morpholine
Unable to find specified property fr_nitrile
Unable to find specified property fr_nitro
Unable to find specified property fr_nitro_arom
Unable to find specified property fr_nitro_arom_nonortho
Unable to find specified property fr_nitroso
Unable to find specified property fr_oxazole
Unable to find specified property fr_oxime
Unable to find specified property fr_para_hydroxylation
Unable to find specified property fr_phenol
Unable to find specified property fr_phenol_noOrthoHbond
Unable to find specified property fr_phos_acid
Unable to find specified property fr_phos_ester
Unable to find specified property fr_piperdine
Unable to find specified property fr_piperzine
Unable to find specified property fr_priamide
Unable to find specified property fr_prisulfonamd
Unable to find specified property fr_pyridine
Unable to find specified property fr_quatN
Unable to find specified property fr_sulfide
Unable to find specified property fr_sulfonamd
Unable to find specified property fr_sulfone
Unable to find specified property fr_term_acetylene
Unable to find specified property fr_tetrazole
Unable to find specified property fr_thiazole
Unable to find specified property fr_thiocyan
Unable to find specified property fr_thiophene
Unable to find specified property fr_unbrch_alkane
Unable to find specified property fr_urea
Traceback (most recent call last):
File "/home/user/anaconda3/envs/reinvent4_2/bin/reinvent", line 8, in
sys.exit(main_script())
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent/Reinvent.py", line 195, in main_script
main(args)
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent/Reinvent.py", line 164, in main
runner(
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent/runmodes/RL/run_staged_learning.py", line 296, in run_staged_learning
packages = create_packages(reward_strategy, stages, rdkit_smiles_flags2)
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent/runmodes/RL/run_staged_learning.py", line 157, in create_packages
scoring_function = Scorer(stage.scoring)
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent/scoring/scorer.py", line 80, in init
self.components = get_components(config.component)
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent/scoring/config.py", line 43, in get_components
component_registry = get_registry()
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent/scoring/importer.py", line 36, in get_registry
module = importlib.import_module(name)
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1050, in _gcd_import
File "", line 1027, in _find_and_load
File "", line 1006, in _find_and_load_unlocked
File "", line 688, in _load_unlocked
File "", line 883, in exec_module
File "", line 241, in _call_with_frames_removed
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/reinvent_plugins/components/comp_chemprop.py", line 27, in
import chemprop
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/chemprop/init.py", line 1, in
import chemprop.data
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/chemprop/data/init.py", line 1, in
from .data import cache_graph, cache_mol, MoleculeDatapoint, MoleculeDataset, MoleculeDataLoader,
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/chemprop/data/data.py", line 11, in
from chemprop.features import get_features_generator
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/chemprop/features/init.py", line 1, in
from .features_generators import get_available_features_generators, get_features_generator,
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/chemprop/features/features_generators.py", line 93, in
from descriptastorus.descriptors import rdDescriptors, rdNormalizedDescriptors
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/descriptastorus/descriptors/init.py", line 2, in
from .rdDescriptors import *
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/descriptastorus/descriptors/rdDescriptors.py", line 371, in
RDKit2D()
File "/home/user/anaconda3/envs/reinvent4_2/lib/python3.10/site-packages/descriptastorus/descriptors/rdDescriptors.py", line 362, in init
raise ValueError("%s: Failed to initialize: unable to find specified properties:\n\t%s"%(
ValueError: RDKit2D: Failed to initialize: unable to find specified properties:
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

I did try to pinpoint the issue by creating a fresh conda env with Rdkit and descriptastorus, but the same issue comes up.
Additionally I tried the following from within jupyter-notebook/python prompt without any issue.

1.

from descriptastorus.descriptors.DescriptorGenerator import MakeGenerator

generator = MakeGenerator(("RDKit2D",))  # Instead of "RDKit2D"
generator

output: <descriptastorus.descriptors.rdDescriptors.RDKit2D at 0x7f239e55eaa0>

2

from rdkit import Chem
from rdkit.Chem import rdMolDescriptors

print(dir(rdMolDescriptors))

output: ['AtomPairsParameters', 'BCUT2D', '.....]

However the following lines lead to the issue.

from descriptastorus.descriptors import rdDescriptors
print(rdDescriptors) 

Any idea how to resolve this?