Projects in Awesome Lists tagged with pymol

https://github.com/rdk/p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

binding-sites bioinformatics drug-discovery groovy java ligand machine-learning mmcif molecular-structures p2rank pdb protein-ligand-docking protein-ligand-interactions protein-structure protein-surface proteins pymol random-forest structural-bioinformatics virtual-screening

Last synced: 16 Dec 2024

https://github.com/mooerslab/pymolshortcuts

The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent functions that make work in PyMOL more productive..

agile-programming agile-pymol aliases biomolecular-artwork efficient-programming ergonomic-keyword-use figure-making image-making molecular-artwork molecular-graphics pdb pml protein-structure-analysis pymol pymol-plugin pymol-python scripting shortcuts startup-script structural-bioinformatics

Last synced: 14 Dec 2024

https://github.com/mooerslab/pymolsnips

Pymolsnips is a library of PyMOL scripting language code fragments for several popular text editors.

atom autocompletion code-fragments cudatext gedit molecular-artwork pml pymol pymol-code-fragments pymol-macro-language pymol-snippet-library pymol-snippets snippet-library snippets st3 sublime-text-3 tab-triggers text-editors textmate vsc

Last synced: 14 Dec 2024

https://github.com/cgohlke/pymol-open-source-wheels

Pymol-open-source wheels for Python on Windows

pymol pymol-python python wheels windows

Last synced: 11 Nov 2024

https://github.com/smutao/PyVibMS

A PyMOL plugin for visualizing vibrations in molecules and solids

computational-chemistry computational-physics pymol pymol-plugin quantum-chemistry theoretical-chemistry vibrational-spectroscopy

Last synced: 20 Nov 2024

https://github.com/liyigerry/gmx

molecular dynamics simulation and analysis. 分子动力学模拟和分析。

gromacs md plumed pymol

Last synced: 12 Oct 2024

https://github.com/patonlab/wsterimol

Generate Boltzmann-weighted Sterimol Steric Parameters for Conformationally-Flexible Substituents

conformational-analysis organic-chemistry pymol pymol-plugin qsar steric-parameters sterics sterimol sterimol-parameters

Last synced: 23 Oct 2024

https://github.com/insilichem/esigen

:memo::sparkles: Generate supporting information documents for your computational chemistry manuscripts - Documentation: https://esigen.readthedocs.io

computational-chemistry flask molecular-graphics publication pymol webgl

Last synced: 10 Nov 2024

https://github.com/zachcp/ferritin

protein utilities in Rust

proteins pymol rust

Last synced: 21 Dec 2024

https://github.com/mooerslab/easypymol

Script to facilitate the making of horizontal scripts

ambient-occulsion biomolecular-structures black-and-white-cartoons coordinate-covalent-bonds horizontal-scripts metal-coordination molecular-artwork molecular-graphics molecular-structures molecular-visuallization pml protein-structure pymol pymol-macro-language rna-structure roundview scripting startup-aliases structural-bioinformatics tutorial-videos

Last synced: 14 Dec 2024

https://github.com/filipspl/cadd-pw

Computer Aided Drug Design / Komputerowe Wsparcie Projektowania Leków

cadd drug-design drug-discovery knime leki marvin pymol

Last synced: 12 Nov 2024

https://github.com/mooerslab/orgpymolpysnips

Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.

emacs emacs-jupyter literate-programming mmcif molecular-graphics org-babel org-mode pdb protein pymol

Last synced: 14 Dec 2024

https://github.com/zmactep/pymol-gpt

Fast and dirty GPT injection into PyMOL

gpt plugin pymol

Last synced: 17 Dec 2024

https://github.com/thibaudcolas/moulinette

Bioinformatics (biochemistry) data processing scripts for NMR, and protein data analysis (PyMOL)

biochemistry perl pymol python

Last synced: 18 Dec 2024

https://github.com/mooerslab/colabpymolpysnips

Library of PyMOL Python snippets for Google Colab.

biomolecular-structure ca-trace code-fragments code-snippets colab colab-notebook drug-molecules grayscale ligand-binding-sites literate-programming molecular molecular-graphics molecular-surface notebook protein protein-structure pymol python ribbon-diagrams

Last synced: 14 Dec 2024

https://github.com/mooerslab/mooerslab

Landing page for MooersLab repository

cctbx colab crystallographic-computing emacs jupyter literate-programming neovim pymol saxs scientific-writing speech-to-text sst supercomputing time-management vim voice-computing writing writing-aids writing-tools

Last synced: 14 Dec 2024

https://github.com/mooerslab/pymolwallhangings

Protocol for making large scale images to be framed or for background images of posters.

large-scale-image molecular-graphics poster-sized-image pymol wall-hanging

Last synced: 14 Dec 2024

https://github.com/mooerslab/rstudiopymolpysnips

PyMOL snippet library is written in Python for use in RStudio via the R reticulate package and the PyMOL Python API.

dna-structure literate-programming molecular-artwork molecular-graphics molecular-structure molecular-visualization pdb protein-structure pymol pymolpysnips r-programming reticulate rmarkdown rna-structure rstudio

Last synced: 14 Dec 2024

https://github.com/mooerslab/pymolrc

Blaine's pymolrc file, the configuration file for the molecular graphics program.

molecular molecular-graphics pymol pymolrc

Last synced: 14 Dec 2024

https://github.com/zachcp/pseutils

Make pymol session files vieweable on the web

molstar pymol rust

Last synced: 13 Nov 2024

https://github.com/mooerslab/taggedpymolpysnips

PyMOL Python Script Writing with Code Templates in Jupyter notebooks with JupyterLab using the Elyra extension

elyra jupyter-notebook jupyterlab literate-programming pymol tagged-snippets

Last synced: 14 Dec 2024

https://github.com/mooerslab/aca2022

Slideshow to talk in August 2022 at 72nd Annual Meeting of the American Crystallographic Association

aca cloud-computing colab-notebook emacs ghosttext literate-programming molecular-graphics pdb-database protein-structure pymol python sublime-text vim vsc

Last synced: 14 Dec 2024

https://github.com/mooerslab/colabopensourcepymolpysnips

Code snippets for colab-notebooks running open-source PyMOL

google-colab literate-programming molecular-graphics open-source-pymol pymol

Last synced: 14 Dec 2024

https://github.com/mooerslab/pymolpysnips

The pymolsnips rewritten in Python. This Python enables direct interaction with the pymol api from other Python environments like electronic notebooks (e.g. Jupyter Notebooks), IDEs, and literate programming documents (e.g., Rmarkdown, org-mode ).

installing-snippets jupyter-notebook pymol snippet-files snippet-libraries

Last synced: 14 Dec 2024

https://github.com/tushar98644/ribo-replicator

Generation and visualization of 3d protein sequences

3dmol acertinityui dashboard dna-sequences enery-minimization enthalpy gromacs nextjs pdb pymol ramachandran-plot rib ribosome shadcn-ui tailwindcss

Last synced: 08 Dec 2024

https://github.com/giatraskon/algorithms-in-structural-bioinformatics-assignments

Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.

alphafold2 bioinformatics biopython chimerax computational-biology conformational-analysis crude-energy-minimization jupyter-notebook protein-structure-analysis pymol python rmsd rna-folding root-mean-square-deviation sars-cov-2 secondary-structure-elements serotonin structural-bioinformatics structural-biology structure-visualization

Last synced: 13 Dec 2024