Difference between revisions of "Tutorial:Reading a PDB file with the complex molecular object: the System"
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− | An example on how to read and write atoms from/to a PDB file into using an '''[[MSL Objects:System|System]]''' can be found in the example program example_System_usage.cpp in the examples/ subdirectory. | + | An example on how to read and write atoms from/to a PDB file into using an '''[[MSL Objects:System|System]]''' – the more complex molecular container in MSL – can be found in the example program example_System_usage.cpp in the examples/ subdirectory. |
[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_read_write_PDBs_with_the_System.cpp?view=markup Complete source of example_read_write_PDBs_with_the_System.cpp] | [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_read_write_PDBs_with_the_System.cpp?view=markup Complete source of example_read_write_PDBs_with_the_System.cpp] | ||
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=== Program description === | === Program description === | ||
+ | {| border="0" cellpadding="2" style="background:#FFFF99" | ||
+ | | | ||
+ | '''NOTE:''' the programs is very similar to the example_read_write_PDBs_with_the_AtomContainer example program illustrated in the [[Tutorial:Reading a PDB file with the simpler molecular object: the AtomContainer | previous tutorial]]. Where the two differ it is highlighted with a note. | ||
+ | |} | ||
+ | |||
+ | |||
* First the container is created. The PDB is read using the ''readPdb'' function, which takes the file name (string object). | * First the container is created. The PDB is read using the ''readPdb'' function, which takes the file name (string object). | ||
<source lang="cpp"> | <source lang="cpp"> | ||
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A: {1}ALA ILE {3}ALA | A: {1}ALA ILE {3}ALA | ||
</source> | </source> | ||
− | + | {| border="0" cellpadding="2" style="background:#FFFF99" | |
+ | | | ||
+ | '''NOTE:''' here the System behave differently from the AtomContainer, which would print all atoms. | ||
+ | |} | ||
+ | |||
* Atoms can also printed (or otherwise accessed) one by one using the [] operator, as if the container was an atom array. | * Atoms can also printed (or otherwise accessed) one by one using the [] operator, as if the container was an atom array. | ||
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... | ... | ||
</source> | </source> | ||
+ | {| border="0" cellpadding="2" style="background:#FFFF99" | ||
+ | | | ||
'''NOTE:''' unlike in the AtomContainer, the [] and () operators are NOT redundant in the System. The () operator would returns Chain objects instead of Atom objects). | '''NOTE:''' unlike in the AtomContainer, the [] and () operators are NOT redundant in the System. The () operator would returns Chain objects instead of Atom objects). | ||
+ | |} | ||
+ | {| border="0" cellpadding="2" style="background:#FFFF99" | ||
+ | | | ||
+ | '''NOTE 2:''' unlike the AtomContainer, the number of atoms in the System is given by the function ''atomSize''. The ''size'' function returns the number of chains. | ||
+ | |} | ||
− | |||
* Atoms can be accessed by ''id'' ("chain,resnum,name", for example "A,2,CD1") with the ''getAtom'' function | * Atoms can be accessed by ''id'' ("chain,resnum,name", for example "A,2,CD1") with the ''getAtom'' function |
Revision as of 00:41, 17 March 2010
An example on how to read and write atoms from/to a PDB file into using an System – the more complex molecular container in MSL – can be found in the example program example_System_usage.cpp in the examples/ subdirectory.
Complete source of example_read_write_PDBs_with_the_System.cpp
To compile
% make bin/example_read_write_PDBs_with_the_System
To run the program
Go to the main directory and run the command
% bin/example_read_write_PDBs_with_the_System exampleFiles/
Program description
NOTE: the programs is very similar to the example_read_write_PDBs_with_the_AtomContainer example program illustrated in the previous tutorial. Where the two differ it is highlighted with a note. |
- First the container is created. The PDB is read using the readPdb function, which takes the file name (string object).
60 System container;
61 if (!container.readPdb(file)) {
// reading failed, error handling code here
68 }
- The sequence be printed out using the << operator
73 cout << container << endl;
which produces
A: {1}ALA ILE {3}ALA
NOTE: here the System behave differently from the AtomContainer, which would print all atoms. |
- Atoms can also printed (or otherwise accessed) one by one using the [] operator, as if the container was an atom array.
79 for (unsigned int i=0; i<container.atomSize(); i++) {
80 cout << "Atom " << i << " is " << container[i] << endl;
81 }
which produces
Atom 0 is N ALA 1 A [ 2.143 1.328 0.000] (conf 1/ 1) +
Atom 1 is CA ALA 1 A [ 1.539 0.000 0.000] (conf 1/ 1) +
Atom 2 is CB ALA 1 A [ 2.095 -0.791 1.207] (conf 1/ 1) +
...
NOTE: unlike in the AtomContainer, the [] and () operators are NOT redundant in the System. The () operator would returns Chain objects instead of Atom objects). |
NOTE 2: unlike the AtomContainer, the number of atoms in the System is given by the function atomSize. The size function returns the number of chains. |
- Atoms can be accessed by id ("chain,resnum,name", for example "A,2,CD1") with the getAtom function
89 Atom & a = container.getAtom("A,2,CD1");
or using the [] string operator (NOTE: again, the [] and () operators are NOT redundant)
96 Atom & b = container["A,2,CD1"];
- The above functions do not allow for error checking. To check if the atom exists use the atomExists function, followed by the getLastFoundAtom to get the atom without a second lookup.
102 if (container.atomExists("A,2,CD1")) {
103 cout << "Atom A 2 CD1 exists" << endl;
104 // get the atom without a second lookup
105 Atom & c = container.getLastFoundAtom();
106 cout << c << endl;
107 } else {
108 cout << "Atom A 2 CD1 does no exist" << endl;
109 }
- Finally, to write all atoms to a PDB file use the writePdb function
116 if (!container.writePdb("/tmp/example0001_out.pdb")) {
// writing failed, error handling code here
120 }