Tutorial:Selecting subsets of atoms - Revision history

Dwkulp: /* Background */

2010-03-23T22:02:26Z

‎Background

Dwkulp at 22:02, 23 March 2010

2010-03-23T22:02:16Z

Dwkulp: /* Program description */

2010-03-23T22:01:26Z

‎Program description

Dwkulp: /* Program description */

2010-03-23T21:24:04Z

‎Program description

Dwkulp: /* Program description */

2010-03-23T21:22:11Z

‎Program description

Dwkulp at 20:53, 23 March 2010

2010-03-23T20:53:22Z

Dwkulp: /* Selection By Name: */

2010-03-23T20:52:39Z

‎Selection By Name:

Dwkulp at 20:51, 23 March 2010

2010-03-23T20:51:48Z

Dwkulp at 20:47, 23 March 2010

2010-03-23T20:47:01Z

Dwkulp: Created page with 'NOTE: TUTORIAL WRITING IN PROGRESS DO NOT FOLLOW THIS This is an example on how to select atoms and residues with MSL, following the example program ex…'

2010-03-23T20:16:40Z

Created page with '<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 ex…'

New page

<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 ===

=== 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 ===
* Read a PDB file.
<source lang="cpp">
60 System container;
61 if (!container.readPdb(file)) {
// reading failed, error handling code here
68 }
</source>

* Print the sequence. This PDB happens to have 3 chains.
<source lang="cpp">
73 cout << container << endl;
</source>
which outputs:
<source lang="text">
A: {1}GLY LYS LYS MET VAL VAL ALA {8}LEU
B: {1}ASP LYS ASP PHE ALA SER GLU LYS LEU ALA GLU LEU {13}VAL
C: {1}ASP ALA LEU VAL ILE LEU {7}THR
</source>

* In each object of the molecular hierarchy, the () operator returns elements of the next step down by index ''i'' (as a reference). The following lines demonstrate that.
<source lang="cpp">
92 Chain & chn = container(0); // get the first chain in the System (chain "A") by reference
93 Position & pos = chn(0); // get the first position in the Chain (1) by reference
94 Residue & res = pos(0); // get the first identity in the Position (ASP) by reference
95 Atom & atm = res(0); // get the first atom in the Residue (N) by reference
</source>
* The molecular objects can all be printed using the << operator.
<source lang="cpp">
97 cout << "First chain of System: " << chn << endl;
98 cout << "First position of the Chain: " << pos << endl;
99 cout << "First identity of the Position: " << res << endl;
100 cout << "First atom of the Residue: " << atm << endl;
</source>
which outputs:
<source lang="text">
First chain of System: A: {1}GLY LYS LYS MET VAL VAL ALA {8}LEU

First position of the Chain: A,1 [GLY]
First identity of the Position: A,1,GLY
First atom of the Residue: N GLY 1 A [ 23.784 49.695 6.481] (conf 1/ 1) +
</source>
* Let's now loop over the entire hierarchy. The ''size()'' function tells us how many elements there are
<source lang="cpp">
109 cout << "The System has " << container.size() << " chains" << endl;
110 // loop over each chain and get the number of positions
111 for (unsigned int i=0; i<container.size(); i++) {
112 cout << " Chain " << i << " (id: " << container(i).getChainId() << ") has " << container(i).size() << " positions" << endl;
113
114 // loop over each position and get the number of identities
115 for (unsigned int j=0; j<container(i).size(); j++) {
116 cout << " Position " << j << " (id: " << container(i)(j).getPositionId() << ") has " << container(i)(j).size() << " identity" << endl;
117
118 // loop over each identity and print the name
119 for (unsigned int k=0; k<container(i)(j).size(); k++) {
120 cout << " Identity " << k << " (id: " << container(i)(j)(k).getIdentityId() << ") is a " << container(i)(j)(k).getResidueName() << endl;
121
122 // loop over each atom and print the name
123 for (unsigned int l=0; l<container(i)(j)(k).size(); l++) {
124 cout << " Atom " << l << " (id: " << container(i)(j)(k)(l).getAtomOfIdentityId() << ") is a " << container(i)(j)(k)(l).getName() << endl;
125 }
126 }
127 }
128 }
</source>

which outputs:
<source lang="text">
The System has 3 chains
Chain 0 (id: A) has 8 positions
Position 0 (id: A,1) has 1 identity
Identity 0 (id: A,1,GLY) is a GLY
Atom 0 (id: A,1,GLY,N) is a N
Atom 1 (id: A,1,GLY,CA) is a CA
Atom 2 (id: A,1,GLY,C) is a C
Atom 3 (id: A,1,GLY,O) is a O
Position 1 (id: A,2) has 1 identity
Identity 0 (id: A,2,LYS) is a LYS
Atom 0 (id: A,2,LYS,N) is a N
Atom 1 (id: A,2,LYS,CA) is a CA
...
</source>

* The hierarchy is '''System'''>'''Chain'''>'''Position'''>'''Residue'''>'''Atom'''. However, in most cases each Position contains just one residue type, unless design or mutagenesis is involved. The above loop can be rewritten to skip the identities and go from Position to Atom. To do so we use the [] operator in Position. In all objects [] returns an atom (by reference).

<source lang="cpp">
138 Atom & aSys = container[0]; // get the first atom (N) of tye system by reference
139 Atom & aChn = chn[0]; // get the first atom (N) of the chain by reference
140 Atom & aPos = pos[0]; // get the first atom (N) of the position by reference
141 Atom & aRes = res[0]; // get the first atom (N) of the identity by reference
</source>

* The total number of atoms is given by the function ''atomSize()'', which is used by the Position in the loop System>Chain>Position>Atom
<source lang="cpp">
157 cout << "The System has " << container.size() << " chains" << endl;
158 // loop over each chain and get the number of positions
159 for (unsigned int i=0; i<container.size(); i++) {
160 cout << " Chain " << i << " (id: " << container(i).getChainId() << ") has " << container(i).size() << " positions" << endl;
161
162 // loop over each position and get the number of atoms
163 for (unsigned int j=0; j<container(i).size(); j++) {
164 cout << " Position " << j << " (id: " << container(i)(j).getPositionId() << ") is a " << container(i)(j).getResidueName() << " and has " << container(i)(j).atomSize() << " atoms" << endl;
165
166 // loop over each atom and print the name, note using atomSize instead of size
167 for (unsigned int k=0; k<container(i)(j).atomSize(); k++) {
168 // note using the [] operator
169 cout << " Atom " << k << " (id: " << container(i)(j)[k].getAtomId() << ") is a " << container(i)(j)[k].getName() << endl;
170 }
171 }
172 }
</source>

which outputs:
<source lang="text">
The System has 3 chains
Chain 0 (id: A) has 8 positions
Position 0 (id: A,1) is a GLY and has 4 atoms
Atom 0 (id: A,1,N) is a N
Atom 1 (id: A,1,CA) is a CA
Atom 2 (id: A,1,C) is a C
</source>

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

[[Category:Tutorial]]

@@ Line 14: / Line 14: @@
 <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.
@@ Line 27: / Line 28: @@
 <font color="blue">Selection By Property</font>
 Using '''[[MSL Objects:AtomSelection|AtomSelection]]''' Object, to select all atoms of chain A:
   <source lang="cpp">

@@ Line 13: / Line 13: @@
-====Selection By Name:====
+<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.
@@ Line 26: / Line 26: @@
 </source>
-====Selection By Property====
+<font color="blue">Selection By Property</font>
 Using '''[[MSL Objects:AtomSelection|AtomSelection]]''' Object, to select all atoms of chain A:
   <source lang="cpp">

@@ Line 75: / Line 75: @@
-	// Selections using names from previous selections
-	cout << "Create a selection using the name of a previous selection.."<<endl;
+* Selections using names from previous selections
-	cout << "    AtomPointerVector test = sel.select(\"new, bb AND name O\");"<<endl;
+<source lang="cpp">
 	AtomPointerVector test = sel.select("new, bb AND name O");
-	for (uint i = 0; i < test.size();i++){
+</source>
-	  cout << *test[i]<<endl;
+* Selections using NOT operator
 	AtomPointerVector notBB = sel.select("notBB, not name CA+C+O+N");
-	// Selections using range "-" operator.
+</source>
-	cout << "Create a selection using the '-' operator.."<<endl;
-	cout <<"      AtomPointerVector res26 = sel.select(\"res26, resi 2-6\")"<<endl;
+* Selections using range "-" operator.
-	cout << " Hit any character and enter to execute test"<<endl;
+<source lang="cpp">
 	AtomPointerVector res26 = sel.select("res26, resi 2-6");
-	for (uint i = 0; i < res26.size();i++){
+</source>
-	// Selection using distances to a sub-selection
+* Selection using distances to a sub-selection
-	cout << "Create an atom selection named 'oxygensHbondSer', based on a distance from another selection 'name OG'\n";
+<source lang="cpp">
 	AtomPointerVector oxygensHbondSer = sel.select("oxygensHbondSer, name O WITHIN 3.5 OF name OG");
-	for (uint i = 0; i < oxygensHbondSer.size();i++){
+</source>
 ----

@@ Line 54: / Line 54: @@
 <source lang="cpp">
 	AtomPointerVector allAts = sel.select("all");
-<source>
+</source>
@@ Line 65: / Line 65: @@
-	// Expanding the selection logic
+* Expanding the selection logic , first a long-hand selection string is used. second a short-hand version of the same selection is used.
-	cout << "Select backbone atoms using selection logic"<<endl;
+<source lang="cpp">
 	AtomPointerVector backbone    = sel.select("bb, (((name CA OR name N) OR name C) OR name O)");
-	for (uint i = 0; i < backbone.size();i++){
 	AtomPointerVector bbShortHand = sel.select("bb2, name CA+N+C+O");
-	for (uint i = 0; i < bbShortHand.size();i++){
-	  cout << *bbShortHand[i]<<endl;
+</source>
-−
 	// Selections using names from previous selections

@@ Line 17: / Line 17: @@
 You can create selection flags for atoms by:
 * Using  '''[[MSL Objects:Atom|Atom]]''' object:
      a.setSelectionFlag("foobar")
 * Using  '''[[MSL Objects:AtomSelection|AtomSelection]]''' object:
      as.select("foobar, chain A")
 ====Selection By Property====
-Using '''[[MSL Objects:AtomSelection|AtomSelection]]''' Object, to select all atoms of chain A:     as.select("chain A")
+Using '''[[MSL Objects:AtomSelection|AtomSelection]]''' Object, to select all atoms of chain A:
 === To compile ===

@@ Line 44: / Line 44: @@
 === Program description ===
-* Read a PDB file.
+*  Creating an AtomSelection object
 <source lang="cpp">
-	System container;
-	if (!container.readPdb(file)) {
+	AtomSelection sel(sys.getAtomPointers());
-		// reading failed, error handling code here
-	}
+</source>
 </source>

@@ Line 9: / Line 9: @@
 === Background ===
-MSL objects can be selected if they inherit the "Selectable" object.
+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
-             Selection By Name:
+====Selection By Name:====
-	         Can select based on selection flags that are inside each Atom.
+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:
+You can create selection flags for atoms by:
-. Using Atom object:             a.setSelectionFlag("foobar")
+* Using  '''[[MSL Objects:Atom|Atom]]''' object:                      a.setSelectionFlag("foobar")
-. Using AtomSelection object:    as.select("foobar, chain A")
+* Using  '''[[MSL Objects:AtomSelection|AtomSelection]]''' object:    as.select("foobar, chain A")
-	     Selection By Property:
+====Selection By Property====
-	           Chain A:     as.select("chain A")
+Using '''[[MSL Objects:AtomSelection|AtomSelection]]''' Object, to select all atoms of chain A:     as.select("chain A")
 === To compile ===
 <source lang="text">