Tutorial

NOTE: the tutorial is under construction

The tutorial is a collection of articles that illustrate specific features of MSL. Each article explains example programs found in the examples/ subdirectory. Previous knowledge of C++ is assumed.

• Getting started
  • Getting MSL
    • Getting started: Downloading MSL
  • Compiling
    • Getting started: Compiling MSL
    • Getting started: Compiling MSL with external libraries
    • Getting started: Compiling your own programs in MSL
• Molecular objects: atoms, residues, chains...
  • Read and write coordinates to/from files
    • Reading a PDB file with the simpler molecular object: the AtomContainer
    • Reading a PDB file with the complex molecular object: the System
  • Interacting and manipulating molecular objects
    • Looping over Chains, Residues, Atoms in the System
    • Getting Chains, Residues, Atoms by id
    • Passing atoms between objects: the AtomPointerVector
    • Selecting subsets of atoms
  • Measuring distances, angles, dihedrals
  • Applying translations and rotations
  • Changing conformation
  • Molecular alignments
  • Calculating Solvent Exposed Surface Area
  • Mutating Residues
  • Generating coiled-coils
  • Generating Symmetric Bundles
  • Generating Fusion Proteins
  • Using regular expressions to select sequence motifs of a Chain