Atom::Atom(int Z) : Primitive("Atom"), m_charge(0.0), m_spin(0.0), m_nmr(0.0),
m_smallerHydrogens(true), m_haveNmrShift(false), m_reorderIndex(0),
m_hybridization(0)
{
setAtomicNumber(Z);
if (!s_vibrationColorInitialized) {
setVibrationVectorColor(Preferences::VibrationVectorColor());
}
// We don't allow changes to the valency at the moment as it seems to be unstable
// Need to check the OpenBabel code again.
return;
QActionGroup* hybrids(new QActionGroup(this));
QStringList labels;
labels << "sp" << "sp2" << "sp3" << "Square Planar"
<< "Trigonal Bipyramid" << "Octahedral";
for (int i = 0; i < labels.size() ; ++i) {
QAction* action(newAction(labels[i]));
action->setData(i+1);
action->setCheckable(true);
action->setChecked(false);
hybrids->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(updateHybridization()));
}
}
bool loadFromFile( const std::string& filename )
{
setAtomicNumber("X", -1);
std::ifstream file( filename );
enum EParameterType{
EUnknown,
EMass,
EBonds,
EAngles,
EDihedrals,
EImproper,
ENonBonded
} state;
state = EUnknown;
std::string line;
std::string value;
while( file.good() )
{
std::getline( file , line );
auto it = line.find('!');
if( it != std::string::npos )
line = line.substr( 0 , --it );
std::stringstream ss;
ss << line;
ss >> value;
bool newCategory = true;
// there are different cases
// is the current value a new category?
if( value == "BONDS" )
state = EBonds;
else if( value == "ANGLES" )
state = EAngles;
else if( value == "DIHEDRALS" )
state == EDihedrals;
else if( value == "IMPROPER" )
state = EImproper;
else if( value == "NONBONDED")
state = ENonBonded;
else
newCategory = false;
// ok, if the current line is not the title of a new category,
// then we exect it to contain parameters or a comment
if( !newCategory )
{
switch(state)
{
case EBonds:
{
std::string a1,a2;
double kb,b0;
a1 = value;
ss >> a2 >> kb >> b0;
Eigen::Vector2i v;
v[0] = atomID(a1);
v[1] = atomID(a2);
m_kb[v] = kb;
m_b0[v] = b0;
}
break;
case EAngles:
{
std::string a1,a2,a3;
double k_theta,theta0;
a1 = value;
ss >> a2 >> a3 >> k_theta >> theta0;
Eigen::Vector3i v;
v[0] = atomID(a1);
v[1] = atomID(a2);
v[2] = atomID(a3);
m_k_theta[v] = k_theta;
m_theta0[v] = theta0;
}
break;
case EDihedrals:
{
std::string a1,a2,a3,a4;
double k_chi,delta;
int n;
a1 = value;
ss >> a2 >> a3 >> a4 >> k_chi >> n >> delta;
Eigen::Vector4i v;
v[0] = atomID(a1);
v[1] = atomID(a2);
v[2] = atomID(a3);
v[3] = atomID(a4);
m_k_chi[v] = k_chi;
m_n[v] = n;
m_delta[v] = delta;
}
break;
case EImproper:
{
std::string a1,a2,a3,a4;
double k_psi,psi0;
a1 = value;
ss >> a2 >> a3 >> a4 >> k_psi >> psi0;
Eigen::Vector4i v;
v[0] = atomID(a1);
v[1] = atomID(a2);
v[2] = atomID(a3);
v[3] = atomID(a4);
m_k_psi[v] = k_psi;
m_psi0[v] = psi0;
}
break;
case ENonBonded:
{
std::string a1;
double epsilon,r_min_half;
a1 = value;
ss >> epsilon >> r_min_half;
int v = atomID(a1);
m_epsilon[v] = epsilon;
m_r_min_half[v] = r_min_half;
}
break;
case EMass:
{
std::string a1;
double mass;
a1 = value;
ss >> mass;
int v = atomID(a1);
m_mass[v] = mass;
}
break;
default: // do nothing
break;
}
}
}
return true;
}
