jewettaij

moltemplate

A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies

superpose3d

register 3D point clouds using rotation, translation, and scale transformations.

superpose3d_cpp

header-only C++ library for registering 3D point clouds using rotation, translation, and scale transformations

jacobi_pd

a short, simple public-domain header-only C++ library for calculating eigenvalues and eigenvectors of real symmetric matrices

ndmansfield

generate random lattice Hamiltonian paths

visfd

volumetric image toolkit for simple feature detection (segment tomograms)

dlpdb

collect statistics from the entire PDB library

lammps_mca_examples

Molecular Cellular Automata examples in LAMMPS

sabl_mpl

A hacky spline drawing program for measuring features in EM images

cellpack2moltemplate

A tool to run simulations of molecular assemblies created by CellPACK using moltemplate and LAMMPS

emoltemplate

A general cross-platform text-based molecule builder for ESPResSo similar to moltemplate

find_hairpins

a small utility to find hairpins in polymer conformations

lammps

Public development project of the LAMMPS MD software package

moltemplate-DREIDING

The DREIDING force field recreated in Moltemplate

adjacency_ubin

find all nearby points in an nd point cloud with uniform binning

calc_writhe

calculate the writhe of a closed curve

colvars

Collective variables module for molecular simulation and analysis programs

lambda-lanczos

C++ adaptive and header-only Lanczos algorithm library

minrms

A bioinformatics algorithm for generating sequence alignments from 3D structures

mrc_spectra_example

ndautocrr

a simple program to calculate autocorrelation functions used in the moltemplate examples

networkx

Official NetworkX source code repository.

PoissonRecon

Poisson Surface Reconstruction for VISFD users (low memory version)

relion

Image-processing software for cryo-electron microscopy

visfd_tutorials

tutorials for the VISFD tools (in rough draft form)