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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: tutorial1.C,v 1.7 2005/12/23 17:03:21 amoll Exp $
// tutorial example 1
// ------------------
// build two water molecules and write them to a file
// needed for cout
#include <iostream>
// the BALL kernel classes
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/molecule.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/PTE.h>
// reading and writing of HyperChem files
#include <BALL/FORMAT/HINFile.h>
// the TranslationProcessor
#include <BALL/STRUCTURE/geometricTransformations.h>
// we use the BALL namespace and the std namespace (for cout and endl)
using namespace BALL;
using namespace std;
int main()
{
// we create a new atom caleld oxygen
// and set its element to oxygen (PTE[Element::O])
Atom* oxygen = new Atom;
oxygen->setElement(PTE[Element::O]);
// now we create two hydrogen atoms...
Atom* hydrogen1 = new Atom;
Atom* hydrogen2 = new Atom;
hydrogen1->setElement(PTE[Element::H]);
hydrogen2->setElement(PTE[Element::H]);
// ...and move them to approximately correct positions
hydrogen1->setPosition(Vector3(-0.95, 0.00, 0.0));
hydrogen2->setPosition(Vector3( 0.25, 0.87, 0.0));
// We create our water molecule...
Molecule* water = new Molecule;
// ...and insert the three atoms into the molecule.
water->insert(*oxygen);
water->insert(*hydrogen1);
water->insert(*hydrogen2);
// Then we build the two O-H bonds
oxygen->createBond(*hydrogen1);
oxygen->createBond(*hydrogen2);
// Some statics: Molecule::countAtoms() writes the number of
// atoms, Atom::countBonds() the number of bonds the atom shares
cout << "# of atoms in water: " << water->countAtoms() << endl;
cout << "# of bonds in O: " << oxygen->countBonds() << endl;
cout << "# of atoms in H1: " << hydrogen1->countBonds() << endl;
cout << "# of atoms in H2: " << hydrogen2->countBonds() << endl;
// compute the bond length
float distance = oxygen->getDistance(*hydrogen1);
cout << "bond length: " << distance << endl;
// Now we copy our molecule using a copy constructor.
Molecule* water2 = new Molecule(*water);
// A translation processor moves the second molecule
// 5 Angstrom along the x axis
TranslationProcessor translation(Vector3(5, 0, 0));
water2->apply(translation);
// We insert our two molecules into a system
System* S = new System;
S->insert(*water);
S->insert(*water2);
// and write this system to a HyperChem file
HINFile outfile("water.hin", File::MODE_OUT);
outfile << *S;
outfile.close();
// We delete the system. This also deletes the molecules
// and the atoms therein
delete S;
}
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