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2019-alogorithm-interview

转行研究僧的笔记整理

ase_ani

ANI-1 neural net potential with python interface (ASE)

bernaise

Binary ElectrohydRodyNAmIc SolvEr

best-labs-of-3d-genome

Data and the co-authored network I extracted for lab selection in 3D genome research field

bumpy

Quick tutorial of scientific computing with Python using a real physics application.

cassandra

Cassandra is a Monte Carlo package to conduct atomistic simulations.

cgnet

learning coarse-grained force fields

chemlab

The chemistry library you were waiting for

cp2k-input-tools

Fully validating pure-python CP2K input file tools including preprocessing capabilities

cp2k-output-tools

Python tools to handle CP2K output files

cpp2python

C++ to Python converter

deeplearningbook-chinese

Deep Learning Book Chinese Translation

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

deepmilo

deeptact

DeepTACT: predicting three-dimensional chromatin contacts via bootstrapping deep learning

dft-book

A book on modeling materials using VASP, ase and vasp

differentiable-atomistic-potentials

Automatically differentiable atomistic potentials for molecular simulations

dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data

dipole-acf

A Python (version 2.7) script for calculating the IR spectrum based on the Fast Fourier Transform (FFT) of the Auto-Correlation Function of the total dipole moment data (Dipole-ACF, or DACF). The total dipole moment data were generated from the CP2K ab initio molecular dynamics (AIMD) simulations.

dlacluster

Python code for simple diffusion limited aggregation (DLA) simulation. The code provided creates a .gif for cluster growth and calculates fractal dimensionality of the cluster. User can vary the radius of the cluster.

dna-seq-analysis

DNA sequencing analysis notes from Ming Tang

domaincaller

A Python implementation of the original DI domain caller

dos_and_band_plot

dpgen

The deep potential generator

elba-lammps

Automatically exported from code.google.com/p/elba-lammps

fractaldim_proteininteract

calculate the topological dimension of protein interaction networks (active CI)

gaussian09_tools

gitim

Generalized Identification of Truly Interfacial Molecules

gmx_tutorials_livecoms

LiveCoMS GROMACS Tutorials Paper

gnnpapers

Must-read papers on graph neural networks (GNN)