From d4fe209980d00ce119aeff68e36508a81b9851d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicklas=20=C3=96sterbacka?= Date: Wed, 3 Dec 2025 12:01:10 +0100 Subject: [PATCH 1/2] Replaced RDKit.six instances with six --- .../GCPN/gym-molecule/gym_molecule/envs/sascorer.py | 4 ++-- .../docking_generation/MARS/estimator/scorer/sa_scorer.py | 2 +- tdc/chem_utils/oracle/oracle.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/generation/docking_generation/GCPN/gym-molecule/gym_molecule/envs/sascorer.py b/examples/generation/docking_generation/GCPN/gym-molecule/gym_molecule/envs/sascorer.py index 492f2ff3..28f6a581 100644 --- a/examples/generation/docking_generation/GCPN/gym-molecule/gym_molecule/envs/sascorer.py +++ b/examples/generation/docking_generation/GCPN/gym-molecule/gym_molecule/envs/sascorer.py @@ -19,8 +19,8 @@ from rdkit import Chem from rdkit.Chem import rdMolDescriptors -from rdkit.six.moves import cPickle -from rdkit.six import iteritems +from six.moves import cPickle +from six import iteritems import math from collections import defaultdict diff --git a/examples/generation/docking_generation/MARS/estimator/scorer/sa_scorer.py b/examples/generation/docking_generation/MARS/estimator/scorer/sa_scorer.py index 0e293064..7e5f4586 100644 --- a/examples/generation/docking_generation/MARS/estimator/scorer/sa_scorer.py +++ b/examples/generation/docking_generation/MARS/estimator/scorer/sa_scorer.py @@ -24,7 +24,7 @@ from rdkit import Chem from rdkit.Chem import rdMolDescriptors -from rdkit.six import iteritems +from six import iteritems _fscores = None diff --git a/tdc/chem_utils/oracle/oracle.py b/tdc/chem_utils/oracle/oracle.py index faa6d705..6341a16b 100644 --- a/tdc/chem_utils/oracle/oracle.py +++ b/tdc/chem_utils/oracle/oracle.py @@ -21,7 +21,7 @@ rdBase.DisableLog("rdApp.error") from rdkit.Chem import rdMolDescriptors - from rdkit.six import iteritems + from six import iteritems except: raise ImportError( "Please install rdkit by 'conda install -c conda-forge rdkit'! ") From 1c0567a2f2b876464e6ae9ce86d9c66ad755aa51 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicklas=20=C3=96sterbacka?= Date: Wed, 3 Dec 2025 12:57:35 +0100 Subject: [PATCH 2/2] Added six as a dependency --- environment.yml | 1 + requirements.txt | 1 + 2 files changed, 2 insertions(+) diff --git a/environment.yml b/environment.yml index 5f7135e1..135a4e09 100644 --- a/environment.yml +++ b/environment.yml @@ -41,6 +41,7 @@ dependencies: - torchvision==0.16.1 - transformers==4.43.4 - yapf==0.40.2 + - six==1.17.0 variables: KMP_DUPLICATE_LIB_OK: "TRUE" diff --git a/requirements.txt b/requirements.txt index b0001814..8b139d24 100644 --- a/requirements.txt +++ b/requirements.txt @@ -17,3 +17,4 @@ gget>=0.28.4,<1.0.0 pydantic>=2.6.3,<3.0.0 rdkit>=2023.9.5,<2024.3.1 tiledbsoma>=1.7.2,<2.0.0 +six==1.17.0