Python Computational-chemistry Resources

Computational Xmas Tree This repo contains the code for the computational illumination of a Christmas Tree! It is based on the work by Matt Parker fro

Molecular Docking integrated in Jupyter Notebooks Description | Citation | Installation | Examples | Limitations | License Table of content Descriptio

ICLR Computational Geometry & Topology Challenge 2022 Welcome to the ICLR 2022 Computational Geometry & Topology challenge 2022 --- by the ICLR 2022 W

NATURAL-LANGUAGE-PROCESSING-AND-COMPUTATIONAL-LAB-II DLO8012: NLP & CSL804: CL-II [SEMESTER VIII] Syllabus NLP - Reference Books THE WALL MEGA SATISH

GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [OpenReview] [arXiv] [Code] The official implementation of GeoDiff: A Geome

Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology Self-Supervised Vision Transformers Learn Visual Concepts in Histopatholog

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

Table of Contents The general idea How these scripts work? Loading data Needed modules and global variables Parsing the arrays in dataset Extracting a

WikiPron WikiPron is a command-line tool and Python API for mining multilingual pronunciation data from Wiktionary, as well as a database of pronuncia

POTHER: Patch-Voted Deep Learning-based Chest X-ray Bias Analysis for COVID-19 Detection Source code related to the article submitted to the Internati

CSPML (crystal structure prediction with machine learning-based element substitution) CSPML is a unique methodology for the crystal structure predicti

HistoKT: Cross Knowledge Transfer in Computational Pathology Exciting News! HistoKT has been accepted to ICASSP 2022. HistoKT: Cross Knowledge Transfe

asciiMOL A basic molecule viewer written in Python, using curses; Thus, meant for linux terminals. This is an alpha version, featuring: Opening defaul

A310 Computational Neuroscience - Okinawa Institute of Science and Technology, 2022 This repository contains modeling practice materials and homework

TensorDebugger (TDB) is a visual debugger for deep learning. It extends TensorFlow (Google's Deep Learning framework) with breakpoints + real-time visualization of the data flowing through the computational graph.

Computational Optimal Transport for Machine Learning Reading Group Over the last few years, optimal transport (OT) has quickly become a central topic

The best way to use this material is by forking it by click the Fork button at the top, right corner. Then you will get your own copy to play with! Th

Python implementation of 3D facial mesh exaggeration using the techniques described in the paper: Computational Caricaturization of Surfaces.

A computational optimization project towards the goal of gerrymandering the results of a hypothetical election in the UK.

TIA Toolbox Computational Pathology Toolbox developed at the TIA Centre Getting Started All Users This package is for those interested in digital path

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Computational Design and Dynamics of Soft Systems · This is a repository that contains the source code for generating the lecture notes, handouts, exe

DefAP is a program developed to facilitate the exploration of a material's defect chemistry. A large number of features are provided and rapid exploration is supported through the use of autoplotting with carefully considered automatic data labelling and simplification options enabling production of publication quality plots.

MothPruning Scientific Overview Originally inspired by biological nervous systems, deep neural networks (DNNs) are powerful computational tools for mo

PySDM PySDM is a package for simulating the dynamics of population of particles. It is intended to serve as a building block for simulation systems mo

Reaction Mechanism Generator (RMG) Description This repository contains the Python version of Reaction Mechanism Generator (RMG), a tool for automatic

PyCharge PyCharge is an open-source computational electrodynamics Python simulator that can calculate the electromagnetic fields and potentials genera

pyiron pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform: Atomi

NeoDTI NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions (Bioinformatics).

Chemicology Chemical Analysis Calculator, to solve problems efficiently by displaying whole solution. Go to releases for downloading .exe, .dmg, Linux

The neural architecture of language: Integrative modeling converges on predictive processing Code accompanying the paper The neural architecture of la

OctaDist Octahedral distortion calculator: A tool for calculating distortion parameters in coordination complexes. https://octadist.github.io/ Registe

pyscreener A pythonic interface to high-throughput virtual screening software Overview This repository contains the source of pyscreener, both a libra

naqs-for-quantum-chemistry This repository contains the codebase developed for the paper Autoregressive neural-network wavefunctions for ab initio qua

Documentation | External Resources | Datasets | Examples ChemicalX is a deep learning library for drug-drug interaction, polypharmacy side effect and

Computational Methods for Physics & Astronomy Book version at: https://restrepo.github.io/ComputationalMethods by: Sebastian Bustamante 2014/2015 Dieg

Cross-Camera Convolutional Color Constancy, ICCV 2021 (Oral) Mahmoud Afifi1,2, Jonathan T. Barron2, Chloe LeGendre2, Yun-Ta Tsai2, and Francois Bleibe

Illumination_Decomposition Code for TIP 2017 paper --- Illumination Decomposition for Photograph with Multiple Light Sources. This code implements the

Computational modelling of ray propagation through optical elements using the principles of geometric optics (Ray Tracer) Introduction By applying the

Flow Flow is a computational framework for deep RL and control experiments for traffic microsimulation. See our website for more information on the ap

How to apply? Create your config.ini file following the example provided in config.ini Choose one of the options below to run: Run with Python3 pip in

GebPy is a Python-based, open source tool for the generation of geological data of minerals, rocks and complete lithological sequences. The data can be generated randomly or with respect to user-defined constraints, for example a specific element concentration within minerals and rocks or the order of units within a complete lithological profile.

elemenpy Hello! elements.py is a small Python periodic table module that is used for calling certain information about an element. Installation Instal

MDAnalysis Repository README [*] MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale,

Machine Learning for Argument-Based Computational Persuasion This repo contains the source code and a benchmark for predicting user's utilities with M

A toolkit for computational pathology and machine learning. View documentation Please cite our paper Installation There are several ways to install Pa

LitMatter A template for rapid experimentation and scaling deep learning models on molecular and crystal graphs. How to use Clone this repository and

H2G-Net This repository contains the code relevant for the proposed design H2G-Net, which was introduced in the manuscript "Hybrid guiding: A multi-re

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

Few-shot Deep HDR Deghosting This repository contains code and pretrained models for our paper: Self-Gated Memory Recurrent Network for Efficient Scal

"Dataflow variables are spectacularly expressive in concurrent programming" Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum Quick overview Ne

pyradiomics v3.0.1 Build Status Linux macOS Windows Radiomics feature extraction in Python This is an open-source python package for the extraction of

giotto-tda is a high-performance topological machine learning toolbox in Python built on top of scikit-learn and is distributed under the G

Factorisation-based Image Labelling Overview This is a scheme for training and applying the factorisation-based image labelling (FIL) framework. Some

BookNLP BookNLP is a natural language processing pipeline that scales to books and other long documents (in English), including: Part-of-speech taggin

Exposure: A White-Box Photo Post-Processing Framework ACM Transactions on Graphics (presented at SIGGRAPH 2018) Yuanming Hu1,2, Hao He1,2, Chenxi Xu1,

NoCodeSeg: Deep segmentation made easy! This is the official repository for the manuscript "Code-free development and deployment of deep segmentation

StackNet This repository contains StackNet Meta modelling methodology (and software) which is part of my work as a PhD Student in the computer science

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

Rotapy Purpose Generate Gaussian 09 input files for the rotamers of an input compound. Distance to the axis of rotation remains constant throughout th

freud Overview The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics

Polypharmacy - DDI - Synergy Survey The Survey Paper This repository accompanies our survey paper A Unified View of Relational Deep Learning for Polyp

POS-Tagger This repository details the creation of a Part-of-Speech tagger using Trigram Hidden Markov Models to predict word tags in a word sequence.

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

Documentation redrawing Python package provinding tools for artistic interactive applications using AI Created by ReDrawing Campinas team for the Open

Polypharmacy - DDI - Synergy Survey The Survey Paper This repository accompanies our survey paper A Unified View of Relational Deep Learning for Polyp

DQC: Differentiable Quantum Chemistry Differentiable quantum chemistry package. Currently only support differentiable density functional theory (DFT)

feature-set-comp Compares various time-series feature sets on computational performance, within-set structure, and between-set relationships. Reposito

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

pyHype: Computational Fluid Dynamics in Python pyHype is a Python framework for developing parallelized Computational Fluid Dynamics software to solve

MaD GUI Machine Learning and Data Analytics Graphical User Interface MaD GUI is a basis for graphical annotation and computational analysis of time se

MUSCO - Multimodal Descriptions of Social Concepts Automatic Modeling of (Highly Abstract) Social Concepts evoked by Art Images This project aims to i

Chemistry in python Resources Used The following items are not made by me! Click the words to go to the original source Periodic Tab Json - Used in -

Fermi softness calculation for Vienna Ab initio Simulation Package (VASP) Update 1.1.0: Big update: Rewrote the code. Use Bader atomic division instea

CS 506 - Computational Tools for Data Science Code, slides, and notes for Boston University CS506 Fall 2021 The Final Project Repository can be found

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

bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo

nlcc Install pip install nlcc Must have Open-AI Codex key: export OPENAI_API_KEY=your key here then nlcc key bindings ctrl-w copy to clipboard (Note

MolEncoder Molecular AutoEncoder in PyTorch Install $ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder $ python setup.py insta

Contrastive Learning of Object Representations Supervisor: Prof. Dr. Gemma Roig Institutions: Goethe University CVAI - Computational Vision & Artifici

Hello 🤟 #Team-Greider The team of 20 people for HackBio'2021 Virtual Bioinformatics Internship 💝 🖨️ 👨‍💻 HackBio: https://thehackbio.com 💬 Ask us

Evidential Deep Learning for Guided Molecular Property Prediction and Discovery Ava Soleimany*, Alexander Amini*, Samuel Goldman*, Daniela Rus, Sangee

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

JittorVis - Visual understanding of deep learning model.

🧪📈 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.

House-GAN++ Code and instructions for our paper: House-GAN++: Generative Adversarial Layout Refinement Network towards Intelligent Computational Agent

Summit Summit is a set of tools for optimising chemical processes. We’ve started by targeting reactions. What is Summit? Currently, reaction optimisat

PICCL: Philosophical Integrator of Computational and Corpus Libraries PICCL offers a workflow for corpus building and builds on a variety of tools. Th

ReproZip ReproZip is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used comm

Table of contents What is PEM? Overview Installation Usage Executable Library Telegram Bot Try OPEM in Your Browser! MATLAB Issues & Bug Reports Contr

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

cochlea cochlea is a collection of inner ear models. All models are easily accessible as Python functions. They take sound signal as input and return

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

Colibri Core by Maarten van Gompel, [email protected], Radboud University Nijmegen Licensed under GPLv3 (See http://www.gnu.org/licenses/gpl-3.0.html

Ucto for Python This is a Python binding to the tokeniser Ucto. Tokenisation is one of the first step in almost any Natural Language Processing task,