balazsfabian

platonic-solids

Models, code, and images of the platonic solids in 3D.

curved-diffusion

Tools to calculate MSD on meshed surfaces from molecular dynamics

asyncmd

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

aimmd

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

Pymol-script-repo

Collected scripts for Pymol

propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

PyMol-syntax

PyMol syntax

python-ternary

:small_red_triangle: Ternary plotting library for python with matplotlib

GMRES

A c++ implementation of the GMRES method for approximating the solution to a linear system.

cunumeric

An Aspiring Drop-In Replacement for NumPy at Scale

dssp

The DSSP building software

vermouth-martinize

Describe and apply transformation on molecular structures and topologies

membrane-curvature

MDAnalysis tool to calculate membrane curvature.

Gradient-Free-Optimizers

Simple and reliable optimization with local, global, population-based and sequential techniques in numerical discrete search spaces.

PyLipID

A python toolkit for analysing membrane protein-lipid interactions.

PhosphoinositideParameters

The Melo Lab's development repository for Martini coarse-grain phosphoinositide parameters

Algorithms

A collection of algorithms and data structures

rich

Rich is a Python library for rich text and beautiful formatting in the terminal.

pyacvd

Python implementation of surface mesh resampling algorithm ACVD

bsort

Extremely fast inplace radix sort

VTP_source_code

An implementation of our paper: Fast and Exact Discrete Geodesic Computation Based on Triangle-Oriented Wavefront Propagation

splocs

Sparse Localized Deformation Components

tvb-gdist

Geodesic Library (adaptation by TVB Team)

webdis

A Redis HTTP interface with JSON output

st

simple statistics from the command line

maestrowf

A tool to easily orchestrate general computational workflows both locally and on supercomputers

merlin

Machine Learning for HPC Workflows