conda create -n Geom3D python=3.7 conda activate Geom3D conda install -y -c rdkit rdkit conda install -y numpy networkx scikit-learn conda install -y -c conda-forge -c pytorch pytorch=1.9.1 conda install -y -c pyg -c conda-forge pyg=2.0.2 pip install ogb==1.2.1 pip install ...
.sdf containing all mol blocks with descriptors as entries.The order of the descriptors for each atom per molecule must match the ordering of atoms in the RDKit molecule object. Further information on supplying atomic descriptors can be found here.Users...
rdkit 2020.03.3.0 scikit_learn 0.22.1 torch 1.7.0 By using npvae_env.yml in the env folder, you can build an anaconda environment exactly the same as this research. conda env create -f npvae_env.yml conda activate npvae_env Compound Datasets The datasets used in this study is in th...
cd $RDBASE/lib for i in $(ls -1 *.so.1.2017.03.1); do name=`basename $i .so.1.2017.03.1`; namef=`echo $name | sed 's/RDKit//g'`; ln -s $i ${namef}.so.1; ln -s ${namef}.so.1 ${namef}.so; done Continue with gnina compilation We need to set the variable fo...
We use RDKiT1to generate a 3D conformation for each molecule if the molecules do not have a conformation. Here is the code snippet to generate the 3D conformation: Click here for the code! defgenerate_3d_comformer(smiles,sdf_save_path,mmffVariant="MMFF94",randomSeed=0,maxIters=5000,incr...