Difference between revisions of "Tutorial"
From MSL-Libraries
Jump to navigationJump to search (→NOTE: the tutorial is under construction) |
|||
| (32 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
=== NOTE: the tutorial is under construction === | === 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 [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/ examples/] subdirectory. Previous knowledge of C++ is assumed. | ||
* '''Getting started''' | * '''Getting started''' | ||
| Line 5: | Line 7: | ||
*** [[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 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]] | ||
| + | *** [[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]] | ||
| + | ** ''Developers - Checking In'' | ||
| + | *** [[Tutorial:Check in procedure]] | ||
| + | * '''Download topology/parameter files''' | ||
| + | ** [[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'' | ||
| Line 14: | Line 20: | ||
** ''Interacting and manipulating molecular objects'' | ** ''Interacting and manipulating molecular objects'' | ||
*** [[Tutorial:Looping over Chains, Residues, Atoms in the System| Looping over Chains, Residues, Atoms in the System]] | *** [[Tutorial:Looping over Chains, Residues, Atoms in the System| Looping over Chains, Residues, Atoms in the System]] | ||
| − | *** [[Tutorial:Molecular Object Getters | Checking for existance of Atoms, Residues, Chains and getting them]] | + | *** Getting Chains, Residues, Atoms by id |
| + | <!-- *** [[Tutorial:Molecular Object Getters | Checking for existance of Atoms, Residues, Chains and getting them]] --> | ||
| + | *** [[Tutorial:Passing atoms between objects: the AtomPointerVector | Passing atoms between objects: the AtomPointerVector]] | ||
| + | *** [[Tutorial:Selecting subsets of atoms|Selecting subsets of atoms]] | ||
| + | *** [[Tutorial:Using regular expression: Selecting sequence motifs of a Chain|Using regular expression: Getting parts of a structure that match a sequence motif ]] | ||
| + | |||
| + | * '''Molecular Modifications, Movements and Computing Geometries''' | ||
| + | ** [[Tutorial:Measuring distances, angles, dihedrals| Measuring distances, angles, dihedrals]] | ||
| + | ** Applying translations and rotations | ||
| + | ** Changing conformation | ||
| + | ** [[Tutorial:Molecular alignments| Molecular (Structural) Alignments]] | ||
| + | ** [[Tutorial::CoiledCoils_Bundles| Generating Coiled-coils and Symmetric Bundles]] | ||
| + | ** Generating Fusion Proteins | ||
| + | ** [[Tutorial::Mutating Residues|Mutating residues and adding additional conformations]] | ||
| + | |||
| + | * '''Calculating Molecular Properties and Energies''' | ||
| + | ** Calculating Solvent Exposed Surface Area | ||
| + | ** Calculating CHARMM Energies | ||
| + | ** Using Statistical Potentials in MSL | ||
| + | |||
| + | |||
| + | * '''Using MSL Supporting Classes''' | ||
| + | ** [[Tutorial:OptionParser|Parse command line options]] | ||
| + | |||
| + | |||
| + | * '''Interfacing with PyMOL''' | ||
| + | ** Using the '''[[MSL Objects:PyMolVisualization|PyMolVisualization object]]''' to write out PyMOL script files | ||
| + | ** Using the '''[[MSL Objects:PythonMSL|PythonMSL object]]''' to call MSL from within PyMOL | ||
| + | |||
| + | |||
| + | * '''Interfacing with R''' | ||
| + | ** Calling R from within MSL (including passing data back and forth) | ||
| + | |||
| + | * '''Cartesian Minimization''' | ||
| + | ** 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.
- Getting started
- Download topology/parameter files
- Molecular objects: atoms, residues, chains...
- Read and write coordinates to/from files
- Interacting and manipulating molecular objects
- Molecular Modifications, Movements and Computing Geometries
- Measuring distances, angles, dihedrals
- Applying translations and rotations
- Changing conformation
- Molecular (Structural) Alignments
- Generating Coiled-coils and Symmetric Bundles
- Generating Fusion Proteins
- Mutating residues and adding additional conformations
- Calculating Molecular Properties and Energies
- Calculating Solvent Exposed Surface Area
- Calculating CHARMM Energies
- Using Statistical Potentials in MSL
- Using MSL Supporting Classes
- Interfacing with PyMOL
- Using the PyMolVisualization object to write out PyMOL script files
- Using the PythonMSL object to call MSL from within PyMOL
- Interfacing with R
- Calling R from within MSL (including passing data back and forth)
- Cartesian Minimization
- Minimization of a simple System of atoms
