Python Molecular-structures Resources

Best Data Science Resources Hey, Data Enthusiasts out there! Finally, after lots of requests from the community I finally came up with the best free D

ML-ProjectKart 📌 Repository This kart showcases the finest collection of all projects based on machine learning, deep learning, computer vision, natu

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

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

WIE-WoC IEEE-WIE presents WIE Week of Code (WIEWoC), a 3-days long open-source contribution event starting from 1st March, highlighting different pyth

GVP Transformer (wip) Implementation of the GVP-Transformer, which was used in the paper Learning inverse folding from millions of predicted structure

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

Data Structures and Algorithms All the essential resources and template code nee

Cormen Lib Sample Problems Description This repository contnains sample problems with test cases using Cormen-Lib. These problems were made for the pu

TorchMD-net TorchMD-Net provides state-of-the-art graph neural networks and equivariant transformer neural networks potentials for learning molecular

Python red-black trees A Python implementation of red-black trees. This code was originally copied from programiz.com, but I have made a few tweaks to

Direct Molecular Conformation Generation This repository contains the code for Direct Molecular Conformation Generation (DMCG). Dataset Download rdkit

A stack-based systems language that supports structures, functions, expressions, and user-defined operator behaviour. Currently compiles to URCL with plans to add additional formats in the future.

This script is responsible for the operation of the program, it is responsible for both creating the GUI and the process of processing images from dicom files. The program is based on the use of the PyQt5 library, on the basis of which the entire interface containing the appropriate buttons and functions was created.

chem: collection of mostly python code for molecular visualization, QM/MM, FEP,

scrapy-folder-tree This is a scrapy pipeline that provides an easy way to store files and images using various folder structures. Supported folder str

A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories.

Boltzmann visualization - Visualize the Boltzmann distribution for simple quantum models of molecular motion

TUPÃ: Electric field analyses for molecular simulations What is TUPÃ? TUPÃ (pronounced as tu-pan) is a python algorithm that employs MDAnalysis engine

The Cormen-lib module is an insular data structures and algorithms library based on the Thomas H. Cormen's Introduction to Algorithms Third Edition. This library was made specifically for administering and grading assignments related to data structure and algorithms in computer science.

nextPARS, a novel Illumina-based implementation of in-vitro parallel probing of RNA structures. Here you will find the scripts necessary to produce th

100 Days of Code Learning program to keep a habit of coding daily and learn things at your own pace with help from our remote community.

Introduction This repository contains the code for Instance-wise Ordered Transformer (IOT), which is introduced in the ICLR2021 paper IOT: Instance-wi

PyElastica PyElastica is the python implementation of Elastica: an open-source project for simulating assemblies of slender, one-dimensional structure

Riemannian Geometry for Molecular Surface Approximation (RGMolSA) Introduction Ligand-based virtual screening aims to reduce the cost and duration of

Supporting information (calculation outputs, structures)

Understand-conversation-AI This repository structures data in title, summary, tags, sentiment given a fragment of a conversation How to install: pip i

bidict The bidirectional mapping library for Python. Status bidict: has been used for many years by several teams at Google, Venmo, CERN, Bank of Amer

Data Structures and Algorithms: This is a collection of data structures and algorithms that I write while learning the subject Stack: stack.py A stack

Hands-on Algorithmic Problem Solving A one-stop coding interview prep book! About this book In short, this is a middle-to-high level algorithm book de

Data Structures and Algorithms Clean example implementations of data structures and algorithms written in different languages. List of implementations

Coursera Assignments This repository is aimed to help Coursera learners who have difficulties in their learning process. The quiz and programming home

wikidot-forum-dump Script is partially based on 2stacks by bluesoul: https://github.com/scuttle/2stacks To dump a Wiki's forum, edit config.py and put

CSG: Chemical Structure Generator A simple Chemical Structure Generator. Requirements Python 3 (= v3.8) PyQt5 (optional; = v5.15.0 required for grap

pymbar Python implementation of the multistate Bennett acceptance ratio (MBAR) method for estimating expectations and free energy differences from equ

unit-converter-albert-ext Extension for converting units of length, mass, speed, temperature, time, current, luminosity, printing measurements, molecu

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

HyFactor Graph-based architectures are becoming increasingly popular as a tool for structure generation. Here, we introduce a novel open-source archit

naniar naniar provides principled, tidy ways to summarise, visualise, and manipulate missing data with minimal deviations from the workflows in ggplot

AtlasNet V2 - Learning Elementary Structures This work was build upon Thibault Groueix's AtlasNet and 3D-CODED projects. (you might want to have a loo

👀 mols2grid mols2grid is an interactive chemical viewer for 2D structures of small molecules, based on RDKit. ➡️ Try the demo notebook on Google Cola

Selenium job to automate queries to check last posts of Module Data Structures & Algorithms Web-testing for course Data Structures & Algorithms Struct

Pyrsistent Pyrsistent is a number of persistent collections (by some referred to as functional data structures). Persistent in the sense that they are

Welcome to fastcore Python goodies to make your coding faster, easier, and more maintainable Python is a powerful, dynamic language. Rather than bake

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

gridthings Python library for doing things with Grid-like structures Development This project uses poetry for dependency management, pre-commit for li

No non-sense and no BS repo for how data structure code should be in Python - simple and elegant.

GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles This repository contains a method to generate 3D conformer ensembles direct

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

Junction Tree Variational Autoencoder for Molecular Graph Generation Official implementation of our Junction Tree Variational Autoencoder https://arxi

Ultra-Fast Force Fields (UF3) S. R. Xie, M. Rupp, and R. G. Hennig, "Ultra-fast interpretable machine-learning potentials", preprint arXiv:2110.00624

Contribute in this repository and help other students with their assignment by adding python scripts for various management system programs.

Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures Code for the Multiplex Molecular Graph Neural Network (M

GDSC UIET KUK 📍 , welcomes you all to this amazing event where you will be introduced to the world of coding 💻 .

Knowledge-enhanced Contrastive Learning (KCL) Molecular Contrastive Learning with Chemical Element Knowledge Graph [ AAAI 2022 ]. We construct a Chemi

My notes on DS and Algo Table of Contents Arrays LinkedList Trees Types of trees: Tree/Graph Traversal Algorithms Heap Priorty Queue Trie Graphs Graph

bitlist Minimal Python library for working with bit vectors natively. Purpose This library allows programmers to work with a native representation of

Algorithm and Data Structures Interview Questions HackerRank | Practice, Tutorials & Interview Preparation Solutions This repository consists of solut

ReacNetGenerator An automatic reaction network generator for reactive molecular dynamics simulation. ReacNetGenerator: an automatic reaction network g

structural-probes Codebase for testing whether hidden states of neural networks encode discrete structures. Based on the paper A Structural Probe for

MoT - Molecular Transformer Large-scale Pretraining for Molecular Property Prediction Samsung AI Challenge for Scientific Discovery This repository is

DeepGeneAnnotator: A tool to annotate the gene in the genome The master thesis of the "Using deep learning to predict gene structures of the coding ge

SfM disambiguation with COLMAP About Structure-from-Motion generally fails when the scene exhibits symmetries and duplicated structures. In this repos

Description Small wrapper around 3dmol.js and html2canvas for creating self-contained HTML files that display a 3D molecular representation. Double cl

Molecular Sets (MOSES): A benchmarking platform for molecular generation models Deep generative models are rapidly becoming popular for the discovery

BlenderCreateFolderStructure Simple Add-on to create a folder structure in Blender. Installation Download BlenderCreateFolderStructure.py Open Blender

Code for "Semantic Role Labeling as Dependency Parsing: Exploring Latent Tree Structures Inside Arguments".

PandasVault ⁠— Advanced Pandas Functions and Code Snippets The only Pandas utility package you would ever need. It has no exotic external dependencies

PandaPy "I came across PandaPy last week and have already used it in my current project. It is a fascinating Python library with a lot of potential to

Problems and it's solutions. Problem solving, a great Speed comes with a good Accuracy. The more Accurate you can write code, the more Speed you will

Geomstats Code Continuous Integration Code coverage (numpy) Code coverage (autograd, tensorflow, pytorch) Documentation Community NEWS: Geomstats is r

Music Trees Supplementary code for the experiments described in the 2021 ISMIR submission: Leveraging Hierarchical Structures for Few Shot Musical Ins

AptaMAT Purpose AptaMat is a simple script which aims to measure differences between DNA or RNA secondary structures. The method is based on the compa

High Performance Molecular Dynamics Logging into CINECA's computer systems To logon to the M100 system use the following command from an SSH client ss

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

Code for generating alloy / disordered structures through the special quasirandom structure (SQS) algorithm

Efficient electromagnetic solver based on rigorous coupled-wave analysis for 3D and 2D multi-layered structures with in-plane periodicity, such as gratings, photonic-crystal slabs, metasurfaces, surface-emitting lasers, nano-antennas, and more.

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.

Svector Svector (pronounced Swag-tor) provides extension methods to pyrsistent data structures. Easily chain your methods confidently with tons of add

README: GromacsWrapper A primitive Python wrapper around the Gromacs tools. The library is tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, and 2021

duality Data science, Data manipulation and Machine learning package. Use permitted according to the terms of use and conditions set by the attached l

Sample-specific Bayesian Networks A framework for estimating the structures and parameters of Bayesian networks (DAGs) at per-sample or per-patient re

MIRCO PyTorch implementation for paper: Latent Structures Mining with Contrastive Modality Fusion for Multimedia Recommendation Dependencies Python 3.

Molecular Orbital Transitions (MOT) Animate molecular orbital transitions using Psi4 and Blender Author: Maximilian Paradiz Dominguez, University of A

Molecular Sets (MOSES): A benchmarking platform for molecular generation models Deep generative models are rapidly becoming popular for the discovery

Data Structure and Algorithm : Want to learn data strutrues and algorithms ??? Then Stop thinking more and start to learn today. This repo will help y

CodingSimplified_GK This repository is aimed at creating a One stop Destination of codes of all Data structures and Algorithms along with basic explai

Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations This directory contains the model architectures and experimental

Documentation Simple and Easy Package --This is package for enabling basic linear and non-linear data structures and algos-- Data Structures Array Sta

Python Rapid Artificial Intelligence Ab Initio Molecular Dynamics

DBSegment This tool generates 30 deep brain structures segmentation, as well as a brain mask from T1-Weighted MRI. The whole procedure should take ~1

The leading use-case for the staircase package is for the creation and analysis of step functions. Pretty exciting huh. But don't hit the close button

A framework for building (and incrementally growing) graph-based data structures used in hierarchical or DAG-structured clustering and nearest neighbor search

Python Repositori ini berisi kumpulan dari berbagai macam contoh struktur data, algoritma dan komputasi matematika yang diimplementasikan dengan mengg

3D-Transformer: Molecular Representation with Transformer in 3D Space

ON-LSTM This repository contains the code used for word-level language model and unsupervised parsing experiments in Ordered Neurons: Integrating Tree

DSA-Code-Snippet This repository is for adding codes of data structures and algorithms, leetCode, hackerrank etc solutions in different languages Cont

Python DSA 🐍 This repository is a compilation of important Data Structures and Algorithms based on Python. Please make seperate folders for different

Wiki and tutorials | Documentation | Getting Started | Algorithms | Design | FAQ Distiller is an open-source Python package for neural network compres

CodeForces This repository is dedicated to my Python solutions for CodeForces problems. Feel free to copy, contribute and/or comment. If you find any