Welcome to the tentative AquaLab’s documentation!

The whole project AquaLab is public available at https://github.com/dprada/Aqua.git . There is not stable version yet, for this reason the use of these libraries it is under your responsability. Find more info here, but be aware, somesections are under construction.

Overview, license and future references.

Introduction

• What’s Aqua?
  • Molecular Systems
  • Kinetic Lab
  • Conformational Space Networks
• Getting Started
  • The testing version
  • Installing
  • Being updated

Molecular Systems

• Introduction
  • A quick view
    • Example
  • Units
  • Periodic Box and Cell
• Molecular system
  • System
  • Atom
  • Residue
  • Chain
  • Water
• Trajectories
  • Trajectory
  • Frame
  • Box and Cell
• Functions
  • Topology
    • Loading
    • Top_Par defined by user
    • Selection
    • Donors and Acceptors
    • Info
    • Writting pdb files
  • Trajectories
    • Load Trajectory
    • Info Trajectories
    • Delete Trajectory
    • Load Frames
    • Info Frames
    • Delete Frames
    • Writting dcd files
  • Analysis
    • Distances
    • Ramachandran Map
    • Covalent chains
    • Dihedral Angles
• Tutorials
  • Loading/Writting the topology
    • Loading
    • Navigating
    • Writting
  • Loading/Writting a MD trajectory
    • Loading
    • Converting a trajectory into other format
  • How to make atoms selections
  • Distances
    • Computing distances
    • Neighbors and Ranked contacts
  • Contact Maps
  • Dihedral Angles
    • Ramachandran Map
    • Computing any dihedral angle
  • Radial Distribution Funcions

Kinetic Lab

• Kinetic Analysis
  • 1D trajectories
• Tutorial Kinetic Analysis
  • 1D Trajectories
    • Loading a trajectory
    • First order kinetic model
    • Life time distribution
    • First Passage Time distribution
    • First Committed Passage Time distribution
    • Trip Time distribution
    • Committed Trip Time distribution
    • Accurate kinetic decomposition
• Berezovska2012
  • Getting Aqua
  • Loading Aqua
  • Loading a trajectory
  • Analysis
    • Kinetic Model and Flux between clusters
    • Kinetic observables

Conformational Space Networks

• Introduction
  • A quick view
    • Example
• Networks
  • Network
    • Node
    • Cluster
    • Component
• Functions
  • Topology
    • Loading network
    • Loading labels
    • Adding node
    • Adding link
    • Info
    • Merging network
    • Extracting network
    • Writting network
    • Writting labels
  • Clustering
    • MCL
    • Gradient Clusters
• Tutorials
  • Networks
    • A network from scratch
    • Loading networks from files
    • Writting networks
    • Merging networks
  • Kinetic Networks
    • Examples
    • Symmetrize Network (detailed balance)
    • cFEPs
    • Dijkstra
    • MFPT
    • MCL
    • Components
    • Extracting subnetwork
    • Weight-core
    • K-core
  • Water
    • The second solvation shell
    • The Kinetic network
  • Encoding a trajectory into a Kinetic Network

FAQs

• Molecular Systems
  • The topology of my molecular system is not recognized by AquaLab.
• Kinetic Lab
• Conformational Space Network

Indices and tables

• Index
• Module Index
• Search Page