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atom.cpp
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atom.cpp
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#include "atom.h"
Atom::Atom () :
_name(""), _residue(""), _ID(-1), _molid(-1),
_pmolecule((Molecule *)NULL),
_mass(0.0), _charge(0.0), _element(NO_ELEMENT)
{ }
Atom::Atom (const std::string& name, const VecR& position, const VecR& force) :
_name(name), _residue(""), _ID(-1), _molid(-1),
_pmolecule((Molecule *)NULL),
_mass(0.0), _charge(0.0),
_position(position), _force(force)
{ this->SetAtomProperties (); }
Atom::Atom (const std::string& name, const VecR& position) :
_name(name),
_residue(""),
_ID(-1),
_molid(-1),
_pmolecule((Molecule *)NULL),
_mass(0.0),
_charge(0.0),
_position(position)
{ this->SetAtomProperties (); }
// copy constructor will pull over all the member values, and copy over the vector values
Atom::Atom (const Atom& oldAtom) :
_name(oldAtom._name), _residue(oldAtom._residue), _ID(oldAtom._ID), _molid(oldAtom._molid),
_pmolecule(oldAtom._pmolecule),
_mass(oldAtom._mass), _charge(oldAtom._charge),
_position(oldAtom._position), _force(oldAtom._force)
{ this->SetAtomProperties (); }
Atom::Atom (const VecR& position) :
_name(""), _residue(""), _ID(-1), _molid(-1),
_pmolecule((Molecule *)NULL),
_mass(0.0), _charge(0.0),
_position(position)
{ }
Atom::~Atom () {
}
void Atom::Position (const VecR& position) {
_position = position;
}
void Atom::Position (const double X, const double Y, const double Z) {
_position.Set(X, Y, Z);
}
void Atom::Position (coord const axis, double const value) {
_position.Set (axis, value);
}
double Atom::operator[] (const coord index) const {
double pos = -1.0;
switch (index) {
case x: pos = _position.x();
case y: pos = _position.y();
case z: pos = _position.z();
}
return pos;
}
double Atom::operator- (const Atom& input) const {
return (_position - input.Position()).Magnitude();
}
bool Atom::operator< (const AtomPtr& rhs) const {
return this->_ID < rhs->ID();
}
bool Atom::operator< (const Atom& rhs) const {
return this->_ID < rhs.ID();
}
void Atom::Print () const {
printf ("%5s (ID:%6d nuc:%4d)\t%4s (molID:%5d)\t% f\t% f\t% f\n", _name.c_str(), _ID, _element, _residue.c_str(), _molid, _position.x(), _position.y(), _position.z());
}
void Atom::SetAtomProperties () {
//const double AMU2KG = 1.6762158e-27; // conversion for amu -> kg
if (_name.find("DW") != std::string::npos) {
_mass = 0.0;
_charge = 0.0;
_element = DW;
}
else if (_name.find("SW") != std::string::npos) {
_mass = 0.0;
_charge = 0.0;
_element = SW;
}
else if (_name.find("Cl") != std::string::npos) {
_mass = 35.453;
_charge = 7.0;
_element = Cl;
}
else if (_name.find("H") != std::string::npos) {
_mass = 1.0078250321;
_charge = 1.0;
_element = H;
}
else if (_name.find("O") != std::string::npos) {
_mass = 15.9949146221;
_charge = 6.0;
_element = O;
}
else if (_name.find("N") != std::string::npos) {
_mass = 14.0030740052;
_charge = 5.0;
_element = N;
}
else if (_name.find("D") != std::string::npos) {
_mass = 2.0156500641;
_charge = 1.0;
_element = D;
}
else if (_name.find("C") != std::string::npos) {
_mass = 12.0000000;
_charge = 4.0;
_element = C;
}
else if (_name.find("Si") != std::string::npos) {
_mass = 28.0855;
_charge = 4.0;
_element = Si;
}
else if (_name.find("S") != std::string::npos) {
_mass = 32.065;
_charge = 6.0;
_element = S;
}
else if (_name.find("F") != std::string::npos) {
_mass = 18.9984;
_charge = 7.0;
_element = F;
}
return;
}
Atom::Element_t Atom::String2Element (const std::string& name) {
AtomPtr atom = new Atom(name, VecR());
Atom::Element_t elmt = atom->Element();
delete atom;
return elmt;
}
std::string Atom::Element2String (Atom::Element_t elmt) {
std::string name;
switch (elmt) {
case(0) : name = "NO_ELEMENT"; break;
case(1) : name = "H"; break;
case(2) : name = "He"; break;
case(5) : name = "B"; break;
case(6) : name = "C"; break;
case(7) : name = "N"; break;
case(8) : name = "O"; break;
case(9) : name = "F"; break;
case(10) : name = "Ne"; break;
case(11) : name = "Na"; break;
case(12) : name = "Mg"; break;
case(13) : name = "Al"; break;
case(14) : name = "Si"; break;
case(15) : name = "P"; break;
case(16) : name = "S"; break;
case(17) : name = "Cl"; break;
case(18) : name = "Ar"; break;
case(19) : name = "L"; break;
case(20) : name = "Ca"; break;
case(53) : name = "I"; break;
case(55) : name = "Cs"; break;
case(56) : name = "Ba"; break;
default : name = "NO_ELEMENT_DEFAULT"; break;
}
return name;
}