Molecular Design Toolkit 0.7.3

The Molecular Design Toolkit offers access to a large and still-growing set of computational modeling methods with a science-focused Python API. When you call MDT functions from a Jupyter notebook, you’ll also get inline 2D and 3D visualization, ready-to-plot data structures, and interactive user interfaces. MDT is free, open source, and built for scientific collaboration.

Try a live demo now.

Getting started

• 1. Quickstart
  • 1.1. Install with pip
  • 1.2. Get started
  • 1.3. Explore the API
  • 1.4. Get help
• 2. Molecular Design Toolkit Features
  • 2.1. Molecular Mechanics
  • 2.2. Quantum Chemistry
  • 2.3. Interactive visualization
  • 2.4. Data analysis
  • 2.5. Interfaces
  • 2.6. Tools
• 3. Installing MDT
  • 3.1. Basic installation
  • 3.2. Optional python installs
  • 3.3. Changing where your jobs run
  • 3.4. System-specific installation

Recipes

• 1. Reading and building molecules
  • 1.1. From names and IDs
  • 1.2. From files
  • 1.3. From strings
  • 1.4. From other molecules
  • 1.5. From other python packages
• 2. Molecular structure
  • 2.1. Atoms
  • 2.2. Bonds
  • 2.3. Molecules
  • 2.4. Molecular properties
  • 2.5. Electronic structure
• 3. Biomolecular structure
  • 3.1. Residues
  • 3.2. Chains
  • 3.3. Biomolecular assemblies
• 4. Geometry tools
  • 4.1. Atomic positions
  • 4.2. Internal coordinates
  • 4.3. Manipulating coordinates
  • 4.4. Monitor coordinates
  • 4.5. Groups of atoms
  • 4.6. Analyze dynamics
  • 4.7. Constrain geometry
• 5. Property calculations
  • 5.1. Optimize a geometry
• 6. Molecular dynamics
  • 6.1. Protein MD
  • 6.2. Small molecule MD
  • 6.3. Quantum chemical potentials
• 7. Visualization
  • 7.1. Visualize molecular orbitals
  • 7.2. Maniuplate a 3D visualization

Physical object API

• 1. Molecular data model
  • 1.1. UML Diagram
  • 1.2. Object ownership
  • 1.3. Lists of molecular components
  • 1.4. Building a molecule from scratch
  • 1.5. Editing molecules
• 2. Molecule API
  • 2.1. Molecules
  • 2.2. Atoms
• 3. Biopolymer API
  • 3.1. Residues
  • 3.2. Chains
• 4. Electronic wavefunction API
  • 4.1. Electronic Wavefunctions
  • 4.2. Molecular Orbital Sets
  • 4.3. Electronic Orbitals

Simulation and tools API

• 1. Geometry API
• 2. Widgets API
• 3. Tools API
• 4. Energy models API
• 5. Integrators API
• 6. Data API

• Alphabetical index
• Search