/tools

Stspeckmol is a Streamlit component designed for creating and visualizing Speck molecular structures within a web application. It allows users to easily integrate molecular visualization into their Streamlit apps, making it a useful tool for bioinformatics and molecular biology applications.

Trident Chemwidgets is a set of Jupyter widgets that enhance data visibility in cheminformatics and molecular machine learning. It allows users to interact with molecular datasets through various visualization tools, including histograms and scatter plots, as well as an interactive molecule viewer.

ChemInformatics Model Explorer (CIME) is a web application that enables users to explore chemical compounds through interactive visualizations. It supports the analysis of molecular properties and allows users to upload and visualize datasets, making it a valuable tool for cheminformatics.

PyMOL-MCP connects PyMOL with Claude AI, enabling users to control molecular visualization and perform structural analyses through natural language commands. This integration facilitates interactive exploration of molecular structures and enhances the usability of PyMOL for structural biology applications.

MolOrbDraw is a visualization tool that allows users to interactively view molecular orbitals from Gaussian cube files. It provides advanced molecular structure analysis capabilities, including bond detection and topology analysis.

This repository provides a simple X11 molecular viewer that allows users to visualize molecular structures and vibrations. It supports multiple file formats and offers various command-line options for displaying molecular properties.

fpocketR is a command-line tool designed to analyze RNA structures and visualize drug-like RNA-ligand binding pockets. It provides functionalities for characterizing these pockets and supports various analysis workflows for RNA-ligand interactions.

PySSA is a Python client designed for visual protein sequence to structure analysis, enabling users to predict and analyze 3D protein structures. It integrates with PyMOL and ColabFold, making protein structure prediction accessible for research and educational purposes.

DashMD provides real-time monitoring and visualization of Amber molecular dynamics simulations. It allows users to track various simulation parameters and visualize molecular structures and trajectories interactively.

RNAvigate is a toolset designed for exploring and comparing chemical probing data and structure models of RNA. It offers an easy-to-use interface, particularly effective in Jupyter Notebooks, for documenting and sharing analyses related to RNA structures.

QuickSES is a tool designed to compute molecular Solvent Excluded Surface meshes using GPU acceleration with CUDA. It allows users to generate high-quality surface representations of molecules from PDB files, facilitating molecular visualization and analysis.

AlphaFold Analyser is a command line tool designed for rapid visualization of predictions made by AlphaFold2 and AlphaFold3. It generates publication-quality plots for predicted aligned error (PAE) and pLDDT scores, as well as creating PyMol sessions for structural analysis.

xyz2svg is a lightweight Python script designed to create vector images of molecules from XYZ file formats. It offers various customization options for visual representation, making it a valuable tool for molecular visualization in computational chemistry.

RDKit Heatmaps is a Python package that allows users to draw custom heatmaps on molecular depictions, enhancing the visualization of molecular properties. It utilizes RDKit functionalities to map values to atoms and bonds, providing a visual representation that can aid in understanding molecular characteristics.

MolBokeh is a Python package designed for interactive visualization of molecular structures using Bokeh. It allows users to display molecular data alongside other metrics, enhancing the analysis and understanding of molecular properties.

dash_ngl is a customized Dash component designed for visualizing molecular structures, particularly proteins and DNA. It allows users to select proteins via a dropdown and supports .pdb and .cif file formats, making it a useful tool for molecular representation.

marimo_chem_utils is a collection of utility functions designed for cheminformatics applications within marimo notebooks. It facilitates the analysis and visualization of molecular data, including generating molecular fingerprints and interactive plots.

The `altmol` repository enhances Altair visualizations by integrating interactive 2D molecular structures using RDKit. It allows users to create interactive plots that visualize molecular properties, making it a useful tool for cheminformatics applications.

Lasso-Highlight is a Python tool that allows users to highlight specific substructures within molecules drawn using RDKit. It facilitates the visualization of molecular features by enabling the delineation of substructures, which can be useful in various molecular analysis tasks.

The viewer3d tool enables the visualization of PackedPose and Pose objects, as well as PDB files, within Jupyter notebooks and Google Colab. It supports dynamic updates and various visualization modules, making it useful for analyzing macromolecular structures.

Tinker-FFE is a Java-based graphical user interface designed for molecular engineering and modeling. It allows users to launch and control Tinker calculations and supports downloading molecular structures from various databases.

PyFock-GUI is an interactive web application that enables users to perform density functional theory (DFT) calculations on molecules. It supports various exchange-correlation functionals and basis sets, allowing for the prediction of molecular properties and visualization of molecular orbitals in real-time.

Bokehmol is a library that offers custom extensions for plotting molecules interactively using the Bokeh framework. It allows users to render molecular depictions on-the-fly from SMILES representations, facilitating easier visualization in web applications.

This repository contains a Python script that generates helical wheel visualizations based on input peptide sequences. It is useful for visualizing the arrangement of amino acids in alpha-helices, aiding in protein design and analysis.