The BiRetroSys includes 1.Preprocess, 2.Single-Step Template-Free Prediction, 3.Beam Search, and 4.Multi-Step Retrosynthesis Search modules. Specifically, the single-step model is a dual-task SeqAGraph(https://github.com/AILBC/SeqAGraph) trained on USPTO-full, and the multi-step search is a custom Retro*(https://github.com/binghong-ml/retro_star) with a dynamic molecule filter set, a lower-bound beam search score, and a consistency checking mechanism based on forward synthesis.

The Single-Step autoregressive model is fully implemented by ONNX and ONNXRuntime(ORT), which means it will have a noticeable speed-up compared with naive PyTorch implementation in CPU (about 1 sec. per molecule per step).

• numpy
• onnxruntime
• rdkit
• graphviz

1. Make a copy of the source code, and download the molecule set, encoder ONNX file, and decoder ONNX file from the link below, then put them into the /Models/(for molecule set) and /Models/full/(for ONNX models). https://drive.google.com/drive/folders/1R5I4Yb1Ss8hBpgg7H4jLzpM1g719doJE?usp=drive_link
2. RunsearchModel.py, your target molecule is "example_smi".
3. Find your results and the corresponding GraphViz file in /MultiStepSearch/SearchResults.

• CMake $\geq 3.21$, C++17, PkgConfig(for graphviz libraries)
• Eigen3
• RDKit Libraries
• onnxruntime
• graphviz

1. Make a copy of the source code, and download the molecule set, encoder ONNX file, and decoder ONNX file from the link below, then put them into the /Models/(for molecule set) and /Models/full/(for ONNX models). https://drive.google.com/drive/folders/1R5I4Yb1Ss8hBpgg7H4jLzpM1g719doJE?usp=drive_link
2. Check your PkgConfig directory, and copy this directory to the CMakeLists.txt set(ENV{PKG_CONFIG_PATH} ${DIR})
3. In the main BiRetroSys-cpp directory, use mkdir ${DIRNAME} at the terminal to create the cmake directory, then use cd ${DIRNAME}, cmake .. to create the cmake builder, finally, use make to build the executable program BiRetroSys.exe
4. Run BiRetroSys.exe, then input the NAME and SMILES to generate the corresponding Search Tree and Routes.

1. C++ test in CUDA execution.
2. A simple interface of BiRetroSys.
3. An installation channel, maybe pip or homebrew?