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| Line 8: |
Line 8: |
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| | === Background === | | === Background === |
| − | | + | |
| | + | MSL objects can be selected if they inherit the "Selectable" object. |
| | + | |
| | + | Selection By Name: |
| | + | 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: |
| | + | 1. Using Atom object: a.setSelectionFlag("foobar") |
| | + | 2. Using AtomSelection object: as.select("foobar, chain A") |
| | + | |
| | + | |
| | + | Selection By Property: |
| | + | Chain A: as.select("chain A") |
| | === To compile === | | === To compile === |
| | <source lang="text"> | | <source lang="text"> |
| Line 27: |
Line 40: |
| | // reading failed, error handling code here | | // reading failed, error handling code here |
| | 68 } | | 68 } |
| − | </source>
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| − |
| |
| − | * Print the sequence. This PDB happens to have 3 chains.
| |
| − | <source lang="cpp">
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| − | 73 cout << container << endl;
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| − | </source>
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| − | which outputs:
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| − | <source lang="text">
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| − | A: {1}GLY LYS LYS MET VAL VAL ALA {8}LEU
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| − | B: {1}ASP LYS ASP PHE ALA SER GLU LYS LEU ALA GLU LEU {13}VAL
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| − | C: {1}ASP ALA LEU VAL ILE LEU {7}THR
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| − | </source>
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| − |
| |
| − | * 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.
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| − | <source lang="cpp">
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| − | 92 Chain & chn = container(0); // get the first chain in the System (chain "A") by reference
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| − | 93 Position & pos = chn(0); // get the first position in the Chain (1) by reference
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| − | 94 Residue & res = pos(0); // get the first identity in the Position (ASP) by reference
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| − | 95 Atom & atm = res(0); // get the first atom in the Residue (N) by reference
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| − | </source>
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| − | * The molecular objects can all be printed using the << operator.
| |
| − | <source lang="cpp">
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| − | 97 cout << "First chain of System: " << chn << endl;
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| − | 98 cout << "First position of the Chain: " << pos << endl;
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| − | 99 cout << "First identity of the Position: " << res << endl;
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| − | 100 cout << "First atom of the Residue: " << atm << endl;
| |
| − | </source>
| |
| − | which outputs:
| |
| − | <source lang="text">
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| − | First chain of System: A: {1}GLY LYS LYS MET VAL VAL ALA {8}LEU
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| − |
| |
| − | First position of the Chain: A,1 [GLY]
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| − | First identity of the Position: A,1,GLY
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| − | 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
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| − | <source lang="cpp">
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| − | 109 cout << "The System has " << container.size() << " chains" << endl;
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| − | 110 // loop over each chain and get the number of positions
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| − | 111 for (unsigned int i=0; i<container.size(); i++) {
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| − | 112 cout << " Chain " << i << " (id: " << container(i).getChainId() << ") has " << container(i).size() << " positions" << endl;
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| − | 113
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| − | 114 // loop over each position and get the number of identities
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| − | 115 for (unsigned int j=0; j<container(i).size(); j++) {
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| − | 116 cout << " Position " << j << " (id: " << container(i)(j).getPositionId() << ") has " << container(i)(j).size() << " identity" << endl;
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| − | 117
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| − | 118 // loop over each identity and print the name
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| − | 119 for (unsigned int k=0; k<container(i)(j).size(); k++) {
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| − | 120 cout << " Identity " << k << " (id: " << container(i)(j)(k).getIdentityId() << ") is a " << container(i)(j)(k).getResidueName() << endl;
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| − | 121
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| − | 122 // loop over each atom and print the name
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| − | 123 for (unsigned int l=0; l<container(i)(j)(k).size(); l++) {
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| − | 124 cout << " Atom " << l << " (id: " << container(i)(j)(k)(l).getAtomOfIdentityId() << ") is a " << container(i)(j)(k)(l).getName() << endl;
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| − | 125 }
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| − | 126 }
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| − | 127 }
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| − | 128 }
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| − | </source>
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| − |
| |
| − | which outputs:
| |
| − | <source lang="text">
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| − | The System has 3 chains
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| − | Chain 0 (id: A) has 8 positions
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| − | Position 0 (id: A,1) has 1 identity
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| − | Identity 0 (id: A,1,GLY) is a GLY
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| − | Atom 0 (id: A,1,GLY,N) is a N
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| − | Atom 1 (id: A,1,GLY,CA) is a CA
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| − | Atom 2 (id: A,1,GLY,C) is a C
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| − | Atom 3 (id: A,1,GLY,O) is a O
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| − | Position 1 (id: A,2) has 1 identity
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| − | Identity 0 (id: A,2,LYS) is a LYS
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| − | Atom 0 (id: A,2,LYS,N) is a N
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| − | Atom 1 (id: A,2,LYS,CA) is a CA
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| − | ...
| |
| − | </source>
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| − |
| |
| − | * 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">
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| − | 138 Atom & aSys = container[0]; // get the first atom (N) of tye system by reference
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| − | 139 Atom & aChn = chn[0]; // get the first atom (N) of the chain by reference
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| − | 140 Atom & aPos = pos[0]; // get the first atom (N) of the position by reference
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| − | 141 Atom & aRes = res[0]; // get the first atom (N) of the identity by reference
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| − | </source>
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| − |
| |
| − | * 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">
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| − | 157 cout << "The System has " << container.size() << " chains" << endl;
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| − | 158 // loop over each chain and get the number of positions
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| − | 159 for (unsigned int i=0; i<container.size(); i++) {
| |
| − | 160 cout << " Chain " << i << " (id: " << container(i).getChainId() << ") has " << container(i).size() << " positions" << endl;
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| − | 161
| |
| − | 162 // loop over each position and get the number of atoms
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| − | 163 for (unsigned int j=0; j<container(i).size(); j++) {
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| − | 164 cout << " Position " << j << " (id: " << container(i)(j).getPositionId() << ") is a " << container(i)(j).getResidueName() << " and has " << container(i)(j).atomSize() << " atoms" << endl;
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| − | 165
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| − | 166 // loop over each atom and print the name, note using atomSize instead of size
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| − | 167 for (unsigned int k=0; k<container(i)(j).atomSize(); k++) {
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| − | 168 // note using the [] operator
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| − | 169 cout << " Atom " << k << " (id: " << container(i)(j)[k].getAtomId() << ") is a " << container(i)(j)[k].getName() << endl;
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| − | 170 }
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| − | 171 }
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| − | 172 }
| |
| − | </source>
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| − |
| |
| − | which outputs:
| |
| − | <source lang="text">
| |
| − | The System has 3 chains
| |
| − | Chain 0 (id: A) has 8 positions
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| − | Position 0 (id: A,1) is a GLY and has 4 atoms
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| − | Atom 0 (id: A,1,N) is a N
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| − | Atom 1 (id: A,1,CA) is a CA
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| − | Atom 2 (id: A,1,C) is a C
| |
| | </source> | | </source> |
| | | | |
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 example_selecting_atoms_and_residues.cpp in the examples/ subdirectory.
Complete source of example_selecting_atoms_and_residues
Background
MSL objects can be selected if they inherit the "Selectable" object.
Selection By Name:
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:
1. Using Atom object: a.setSelectionFlag("foobar")
2. Using AtomSelection object: as.select("foobar, chain A")
Selection By Property:
Chain A: as.select("chain A")
To compile
% make bin/example_selecting_atoms_and_residues
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)
% bin/example_selecting_atoms_and_residues exampleFiles
Program description
60 System container;
61 if (!container.readPdb(file)) {
// reading failed, error handling code here
68 }
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