View source for Tutorial:Selecting subsets of atoms

<font color="red">NOTE: TUTORIAL WRITING IN PROGRESS DO NOT FOLLOW THIS</font>


This is an example on how to select atoms and residues with MSL, following the example program example_selecting_atoms_and_residues.cpp in the examples/ subdirectory.

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_selecting_atoms_and_residues.cpp?view=markup Complete source of example_selecting_atoms_and_residues]


=== Background ===
	
MSL objects can be selected if they inherit the  '''[[MSL Objects:Selectable|Selectable]]''' object.  So far, Atoms and Residues are Selectable.  The requirement for being selectable is to implement the
virtual "addSelectableFunctions", which define what properties of the object can be selected upon.
   
	 
<font color="blue">Selection By Name</font>
Can select based on selection flags that are inside each Atom.   By default every atom has an "all" selection flag set.
	       
You can create selection flags for atoms by:
* Using  '''[[MSL Objects:Atom|Atom]]''' object:      
<source lang="cpp">    
    a.setSelectionFlag("foobar")
</source>
* Using  '''[[MSL Objects:AtomSelection|AtomSelection]]''' object:    
<source lang="cpp">
    as.select("foobar, chain A")
</source>

<font color="blue">Selection By Property</font>
Using '''[[MSL Objects:AtomSelection|AtomSelection]]''' Object, to select all atoms of chain A:
 <source lang="cpp">
    as.select("chain A")
</source>

=== To compile ===
<source lang="text">
% make bin/example_selecting_atoms_and_residues
</source>

=== To run the program ===
Go to the main directory and run the command ('''note''', the location of the exampleFiles subdirectory needs to be provided as an argument)
<source lang="text">
% bin/example_selecting_atoms_and_residues exampleFiles
</source>

=== Program description ===
*  Creating an AtomSelection object
<source lang="cpp">
	
	AtomSelection sel(sys.getAtomPointers());

</source>

* Basic selection 'all'
<source lang="cpp">
	AtomPointerVector allAts = sel.select("all");
</source>

	
* Select chain A atoms and store as "chA" for easy retrieval
<source lang="cpp">

	AtomPointerVector chainAAts = sel.select("chA, chain A");

</source>

	
* Expanding the selection logic , first a long-hand selection string is used. second a short-hand version of the same selection is used.
<source lang="cpp">

	AtomPointerVector backbone    = sel.select("bb, (((name CA OR name N) OR name C) OR name O)");

	AtomPointerVector bbShortHand = sel.select("bb2, name CA+N+C+O");

</source>



* Selections using names from previous selections
<source lang="cpp">
	AtomPointerVector test = sel.select("new, bb AND name O");
</source>

* Selections using NOT operator
<source lang="cpp">

	AtomPointerVector notBB = sel.select("notBB, not name CA+C+O+N");

</source>

* Selections using range "-" operator.
<source lang="cpp">
	AtomPointerVector res26 = sel.select("res26, resi 2-6");
</source>

* Selection using distances to a sub-selection
<source lang="cpp">
	AtomPointerVector oxygensHbondSer = sel.select("oxygensHbondSer, name O WITHIN 3.5 OF name OG");
</source>



----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]