Pinned Repositories
100-Days-Of-ML-Code
100 Days of ML Coding
advanced-data-mining-project
Community Detection on Higher-Order Networks: Identifying Patterns in US Air Traffic
Advanced-Density-Peaks
analysis
Trajectory analysis tool for Tinker & Gromacs & Amber
anncolvar
Collective variables by artificial neural networks
ASPH-Code
data and code to reduplicate paper: Topological representations of crystalline compounds for the machine-learning prediction of materials properties
awesome-community-detection
A curated list of community detection techniques.
GROMACS
Tools, tutorials, and wiki for GROMACS
MD-TASK
Tool suite for analysing molecular dynamics trajectories using network analysis and PRS
surf
calculates instantaneous liquid interfaces according to Willard, AP; Chandler, D; J. Phys. Chem. B, 2010, 114 (5), pp 1954–1958
NKM-ML's Repositories
NKM-ML/advanced-data-mining-project
Community Detection on Higher-Order Networks: Identifying Patterns in US Air Traffic
NKM-ML/CHM579
This is the course GitHub page for CHM 579 at Purdue University
NKM-ML/ClusterSAM
Fast estimation of ion-pairing for screening battery electrolytes
NKM-ML/CodeEntropy
NKM-ML/covid-19-community
Community effort to build a Neo4j Knowledge Graph (KG) that links heterogeneous data about COVID-19
NKM-ML/cp2k_2_deepmdkit
cp2k-2-deepmdkit (c2d): A comprehensive tool for converting cp2k output to DeepMD-kit input
NKM-ML/cytoscape-tutorials
Collection of modular Cytoscape tutorials for online presentation using reveal.js
NKM-ML/dioscuri-tda
NKM-ML/freud
Powerful, efficient particle trajectory analysis in scientific Python.
NKM-ML/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.
NKM-ML/graphein
Protein Graph Library
NKM-ML/InfleCS-free-energy-clustering-tutorial
Python tutorial for estimating and clustering free energy landscapes with InfleCS.
NKM-ML/introduction_graph_tool
Introduction to Python's Graph-Tool
NKM-ML/IULM_Social_Network_Analysis_2021
NKM-ML/lammps-input-files
LAMMPS inputs and data files
NKM-ML/leidenalg
Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
NKM-ML/memtools
A python package for the extraction of memory kernels from time series
NKM-ML/mosdef-workflows
Sample molecular simulation workflows using a MoSDeF and community tools
NKM-ML/node2vec
Implementation of the node2vec algorithm.
NKM-ML/notebooks-1
Examples and IPython Notebooks about NetworkX
NKM-ML/papers
Material from papers from KULL centre
NKM-ML/partycls
Unsupervised learning of structure in systems of interacting particles.
NKM-ML/persistent_homology_image_analysis
NKM-ML/POT
POT : Python Optimal Transport
NKM-ML/pygsp
Graph Signal Processing in Python
NKM-ML/python-for-lammps
Python scripts for dealing with molecular dynamics script for LAMMPS
NKM-ML/python-louvain
Louvain Community Detection
NKM-ML/RASPA2
Classical molecular simulation code
NKM-ML/viamd
Visual Interactive Analysis of Molecular Dynamics
NKM-ML/X-Entropy
This package is meant to calculate the dihedral entropy of a biomolecule. However, it can also calculate the entropy of any binnable data or simply the KDE of that data.