Visualize a molecule and its conformations in Jupyter notebooks/lab using py3dmol

Overview

Mol Viewer

This is a simple package wrapping py3dmol for a single command visualization of a RDKit molecule and its conformations (embed as Conformer objects in the Molecule)

Installation

pip install molconfviewer

Usage

from molconfviewer import MolConfViewer
mol_conf_viewer = MolConfViewer() 
mol_conf_viewer.view(mol=mol) # where mol is a rdkit mol

See the MolConfViewer object code to customize the visualization. For more possibilities, please check py3dmol and 3dmol.js.

Owner
Benoît BAILLIF
PhD student in computational chemistry in Cambridge UK
Benoît BAILLIF
A collection of infrastructure and tools for research in neural network interpretability.

Lucid Lucid is a collection of infrastructure and tools for research in neural network interpretability. We're not currently supporting tensorflow 2!

4.5k Jan 07, 2023
Code for "High-Precision Model-Agnostic Explanations" paper

Anchor This repository has code for the paper High-Precision Model-Agnostic Explanations. An anchor explanation is a rule that sufficiently “anchors”

Marco Tulio Correia Ribeiro 735 Jan 05, 2023
Auralisation of learned features in CNN (for audio)

AuralisationCNN This repo is for an example of auralisastion of CNNs that is demonstrated on ISMIR 2015. Files auralise.py: includes all required func

Keunwoo Choi 39 Nov 19, 2022
Visualizer for neural network, deep learning, and machine learning models

Netron is a viewer for neural network, deep learning and machine learning models. Netron supports ONNX, TensorFlow Lite, Keras, Caffe, Darknet, ncnn,

Lutz Roeder 20.9k Dec 28, 2022
PyTorch implementation of DeepDream algorithm

neural-dream This is a PyTorch implementation of DeepDream. The code is based on neural-style-pt. Here we DeepDream a photograph of the Golden Gate Br

121 Nov 05, 2022
pytorch implementation of "Distilling a Neural Network Into a Soft Decision Tree"

Soft-Decision-Tree Soft-Decision-Tree is the pytorch implementation of Distilling a Neural Network Into a Soft Decision Tree, paper recently published

Kim Heecheol 262 Dec 04, 2022
A library that implements fairness-aware machine learning algorithms

Themis ML themis-ml is a Python library built on top of pandas and sklearnthat implements fairness-aware machine learning algorithms. Fairness-aware M

Niels Bantilan 105 Dec 30, 2022
ModelChimp is an experiment tracker for Deep Learning and Machine Learning experiments.

ModelChimp What is ModelChimp? ModelChimp is an experiment tracker for Deep Learning and Machine Learning experiments. ModelChimp provides the followi

ModelChimp 124 Dec 21, 2022
Contrastive Explanation (Foil Trees), developed at TNO/Utrecht University

Contrastive Explanation (Foil Trees) Contrastive and counterfactual explanations for machine learning (ML) Marcel Robeer (2018-2020), TNO/Utrecht Univ

M.J. Robeer 41 Aug 29, 2022
Python implementation of R package breakDown

pyBreakDown Python implementation of breakDown package (https://github.com/pbiecek/breakDown). Docs: https://pybreakdown.readthedocs.io. Requirements

MI^2 DataLab 41 Mar 17, 2022
FairML - is a python toolbox auditing the machine learning models for bias.

======== FairML: Auditing Black-Box Predictive Models FairML is a python toolbox auditing the machine learning models for bias. Description Predictive

Julius Adebayo 338 Nov 09, 2022
🎆 A visualization of the CapsNet layers to better understand how it works

CapsNet-Visualization For more information on capsule networks check out my Medium articles here and here. Setup Use pip to install the required pytho

Nick Bourdakos 387 Dec 06, 2022
⬛ Python Individual Conditional Expectation Plot Toolbox

⬛ PyCEbox Python Individual Conditional Expectation Plot Toolbox A Python implementation of individual conditional expecation plots inspired by R's IC

Austin Rochford 140 Dec 30, 2022
Using / reproducing ACD from the paper "Hierarchical interpretations for neural network predictions" 🧠 (ICLR 2019)

Hierarchical neural-net interpretations (ACD) 🧠 Produces hierarchical interpretations for a single prediction made by a pytorch neural network. Offic

Chandan Singh 111 Jan 03, 2023
👋🦊 Xplique is a Python toolkit dedicated to explainability, currently based on Tensorflow.

👋🦊 Xplique is a Python toolkit dedicated to explainability, currently based on Tensorflow.

DEEL 343 Jan 02, 2023
Logging MXNet data for visualization in TensorBoard.

Logging MXNet Data for Visualization in TensorBoard Overview MXBoard provides a set of APIs for logging MXNet data for visualization in TensorBoard. T

Amazon Web Services - Labs 327 Dec 05, 2022
Visualization toolkit for neural networks in PyTorch! Demo -->

FlashTorch A Python visualization toolkit, built with PyTorch, for neural networks in PyTorch. Neural networks are often described as "black box". The

Misa Ogura 692 Dec 29, 2022
Interactive convnet features visualization for Keras

Quiver Interactive convnet features visualization for Keras The quiver workflow Video Demo Build your model in keras model = Model(...) Launch the vis

Keplr 1.7k Dec 21, 2022
Model analysis tools for TensorFlow

TensorFlow Model Analysis TensorFlow Model Analysis (TFMA) is a library for evaluating TensorFlow models. It allows users to evaluate their models on

1.2k Dec 26, 2022
Pytorch Feature Map Extractor

MapExtrackt Convolutional Neural Networks Are Beautiful We all take our eyes for granted, we glance at an object for an instant and our brains can ide

Lewis Morris 40 Dec 07, 2022