Tutorial:Reading a PDB file with the simpler molecular object: the AtomContainer

An example on how to read and write atoms from/to a PDB file into using an AtomContainer can be found in the example program example_AtomContainer_usage.cpp in the examples/ subdirectory.

Complete source of example_AtomContainer_usage.cpp

To compile

make bin/example_AtomContainer_usage

To run the program

Go to the main directory and run the command

% bin/example_AtomContainer_usage exampleFiles/

Program description

• First the container is created. The PDB is read using the readPdb function, which takes the file name (string object).

60	AtomContainer container;
61	if (!container.readPdb(file)) {
		// reading failed, error handling code here
68	}

• All atoms can be printed out using the << operator.

73	cout << container << endl;

which produces a list of the atoms

N    ALA    1  A [     2.143      1.328      0.000] (conf   1/  1) +
CA   ALA    1  A [     1.539      0.000      0.000] (conf   1/  1) +
CB   ALA    1  A [     2.095     -0.791      1.207] (conf   1/  1) +
...

• Atoms can also printed (or otherwise accessed) one by one using the [] operator, like if the container was an atom array

79	for (unsigned int i=0; i<container.size(); 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) +
...

• 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 () operator

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	}