Protocols

Python dependencies

Pytorch

Pytorch was chosen as our main deep learning library for its enormous power and efficiency. Numerous deep learning models were created with Pytorch to explore options for Peplib Generator in the early stage.

Img2mol

Pytorch was chosen as our main deep learning library for its enormous power and efficiency. Numerous deep learning models were created with Pytorch to explore options for Peplib Generator in the early stage.Img2Mol is able to correctly translate up to 88% of the molecular depictions into their SMILES representation. A pretrained version of Img2Mol is made publicly available on GitHub for non-commercial users.

Multiwfn

Multiwfn is an extremely powerful program for realizing electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods.

Argparse

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python that we use it mainly for changing the molecular conformations to RGB pixels.

Rdkit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python that we use it mainly for changing the molecular conformations to RGB pixels.

Numpy

NumPy offers comprehensive mathematical functions, random number generators, linear algebra routines, Fourier transforms, and more.

Pillow

The Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, an efficient internal representation, and fairly powerful image processing capabilities. The core image library is designed for fast access to data stored in a few basic pixel formats. It should provide a solid foundation for a general image processing tool.

Pandas

pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language.

Pennylane

A cross-platform Python library for differentiable programming of quantum computers. Train a quantum computer the same way as a neural network.