Difference between revisions of "Tutorial"

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* [[Tutorial:Gettting started|Getting started]]
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=== NOTE: the tutorial is under construction ===
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* [[Tutorial:Molecular Object Getters| Checking for existance of Atoms, Residues, Chains and getting them]]
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The tutorial is a collection of articles that illustrate specific features of MSL.  Each article explains example programs found in the [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/ examples/] subdirectory.  Previous knowledge of C++ is assumed.
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* '''Getting started'''
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** ''Getting MSL''
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*** [[Tutorial:Getting started: Downloading MSL|Getting started: Downloading MSL]]
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** ''Compiling''
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*** [[Tutorial:Getting started: Compiling MSL with external libraries|Getting started: Compiling MSL with external libraries]]
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*** [[Tutorial:Getting started: Compiling MSL|Getting started: Compiling MSL without external libraries]]
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*** [[Tutorial:Getting started: Compiling your own programs in MSL|Getting started: Compiling your own programs in MSL]]
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** ''Developers - Checking In''
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*** [[Tutorial:Check in procedure]]
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* '''Download topology/parameter files'''
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** [[Tutorial: Download CHARMM topology and parameter files]]
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* '''Molecular objects: atoms, residues, chains...'''
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** ''Read and write coordinates to/from files''
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*** [[Tutorial:Reading a PDB file with the simpler molecular object: the AtomContainer | Reading a PDB file with the simpler molecular object: the AtomContainer]]
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*** [[Tutorial:Reading a PDB file with the complex molecular object: the System | Reading a PDB file with the complex molecular object: the System]]
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** ''Interacting and manipulating molecular objects''
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*** [[Tutorial:Looping over Chains, Residues, Atoms in the System| Looping over Chains, Residues, Atoms in the System]]
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*** Getting Chains, Residues, Atoms by id
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<!-- *** [[Tutorial:Molecular Object Getters | Checking for existance of Atoms, Residues, Chains and getting them]] -->
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*** [[Tutorial:Passing atoms between objects: the AtomPointerVector | Passing atoms between objects: the AtomPointerVector]]
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*** [[Tutorial:Selecting subsets of atoms|Selecting subsets of atoms]]
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*** [[Tutorial:Using regular expression:  Selecting sequence motifs of a Chain|Using regular expression:  Getting parts of a structure that match a sequence motif ]]
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* '''Molecular Modifications, Movements and Computing Geometries'''
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** [[Tutorial:Measuring distances, angles, dihedrals| Measuring distances, angles, dihedrals]]
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** Applying translations and rotations
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** Changing conformation
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** [[Tutorial:Molecular alignments| Molecular (Structural) Alignments]]
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** [[Tutorial::CoiledCoils_Bundles| Generating Coiled-coils and Symmetric Bundles]]
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** Generating Fusion Proteins
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** [[Tutorial::Mutating Residues|Mutating residues and adding additional conformations]]
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* '''Calculating Molecular Properties and Energies'''
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** Calculating Solvent Exposed Surface Area
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** Calculating CHARMM Energies
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** Using Statistical Potentials in MSL
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* '''Using MSL Supporting Classes'''
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** [[Tutorial:OptionParser|Parse command line options]]
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* '''Interfacing with PyMOL'''
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** Using the  '''[[MSL Objects:PyMolVisualization|PyMolVisualization object]]''' to write out PyMOL script files
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** Using  the '''[[MSL Objects:PythonMSL|PythonMSL object]]''' to call MSL from within PyMOL
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* '''Interfacing with R'''
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** Calling R from within MSL (including passing data back and forth)
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* '''Cartesian Minimization'''
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** Minimization of a simple System of atoms

Latest revision as of 21:30, 22 September 2013

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.

  • Calculating Molecular Properties and Energies
    • Calculating Solvent Exposed Surface Area
    • Calculating CHARMM Energies
    • Using Statistical Potentials in MSL




  • Interfacing with R
    • Calling R from within MSL (including passing data back and forth)
  • Cartesian Minimization
    • Minimization of a simple System of atoms
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