Difference between revisions of "Tutorial"

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(NOTE: the tutorial is under construction)
 
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*** [[Tutorial:Getting started: Downloading MSL|Getting started: Downloading MSL]]
 
*** [[Tutorial:Getting started: Downloading MSL|Getting started: Downloading MSL]]
 
** ''Compiling''
 
** ''Compiling''
*** [[Tutorial:Getting started: Compiling MSL|Getting started: Compiling MSL]]
 
 
*** [[Tutorial:Getting started: Compiling MSL with external libraries|Getting started: Compiling MSL with external libraries]]
 
*** [[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]]
 
*** [[Tutorial:Getting started: Compiling your own programs in MSL|Getting started: Compiling your own programs in MSL]]
 
*** [[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]]
 
* '''Molecular objects: atoms, residues, chains...'''
 
* '''Molecular objects: atoms, residues, chains...'''
 
** ''Read and write coordinates to/from files''
 
** ''Read and write coordinates to/from files''
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*** [[Tutorial:Passing atoms between objects: the AtomPointerVector | Passing atoms between objects: the AtomPointerVector]]
 
*** [[Tutorial:Passing atoms between objects: the AtomPointerVector | Passing atoms between objects: the AtomPointerVector]]
 
*** [[Tutorial:Selecting subsets of atoms|Selecting subsets of atoms]]
 
*** [[Tutorial:Selecting subsets of atoms|Selecting subsets of atoms]]
** Measuring distances, angles, dihedrals
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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]]
 
** Applying translations and rotations
 
** Applying translations and rotations
 
** Changing conformation
 
** Changing conformation
** Molecular alignments
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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'''
 
** Calculating Solvent Exposed Surface Area
 
** 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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 +
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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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 +
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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