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cp2k-1

Quantum chemistry and solid state physics software package

cp2k-input-tools

Fully validating pure-python CP2K input file tools including preprocessing capabilities

cp2k-output-tools

Python tools to handle CP2K output files

cyclic-graph-to-spanning-tree

In this python script, you can create an undirected graph then convert it to a acyclic graph

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

dgraphdta

a novel DTA predition method using graph neural network

diffusiongls

Estimate the self-diffusion coefficient of a trajectory with a Generalized Least Squares (GLS) optimization procedure.

dionysus

Library for computing persistent homology

dioscuri-tda

dipole-acf

A Python (version 2.7) script for calculating the IR spectrum based on the Fast Fourier Transform (FFT) of the Auto-Correlation Function of the total dipole moment data (Dipole-ACF, or DACF). The total dipole moment data were generated from the CP2K ab initio molecular dynamics (AIMD) simulations.

dippol

Program calculating dipole moments and polarizabilities based on atomic positions

dips

Database of Interacting Protein Structures (DIPS)

do_x3dna

To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.

easy-tensorflow

Simple and comprehensive tutorials in TensorFlow

euroscipy-networkx

https://github.com/MridulS/pydata-networkx

examples

Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Clone or download" button, or follow the "...releases" link below.

factory

install the factory to get started with BioPhysCode

fatslim

Main code repository for FATSLiM

fbm

Exact methods for simulating fractional Brownian motion and fractional Gaussian noise in python

flyinggaussiantutorial

Flying Gaussian Tutorial

fresnel-examples

Example notebooks for fresnel

freud

Powerful, efficient particle trajectory analysis in scientific Python.

freud-examples

Examples for the freud library.

gcicenet

graph convolutional network for classification of ice phases

genewa

📓Notebook of Climente-González et al. (2020), Combining network-guided GWAS to discover susceptibility mechanisms for breast cancer.

gnuplot-palettes

Color palettes for gnuplot

grade

GRADE: A code to determine clathrate hydrate structures. GRADE analyzes atomic positions of water molecules to compute the number of 5(12), 6(2)5(12) and 6(4)5(12) cages and account for their three-dimensional structures. The output of GRADE can be used for visualization of clathrate hydrate evolution in trajectories using software such as VMD (Visual Molecular Dynamics). Four-body order parameter (F4) can also be calculated for trajectories.

graph-theory

Julia and Python complex system applications in ecology, epidemiology, sociology, economics & finance; network science models including Bianconi-Barabási, Barabási-Albert, Watts-Strogatz & Erdős-Rényi; graph theory algorithms involving Gillespie, Bron Kerbosch, Bellman Ford, A*, Kruskal, Borůvka, Prim, Dijkstra, Topological Sort, DFS, BFS

graphein

Protein Graph Library

gro2lam

Gromacs to Lammps simulation converter