const MmffBondStrechParameters* MmffParameters::empiricalBondStrechParameters(int atomicNumberA, int atomicNumberB) const
{
CHEMKIT_UNUSED(atomicNumberA);
CHEMKIT_UNUSED(atomicNumberB);
return 0;
}
/// Write the contents of \p file to \p output.
bool PolymerFileFormat::write(const PolymerFile *file, std::ostream &output)
{
CHEMKIT_UNUSED(file);
CHEMKIT_UNUSED(output);
setErrorString((boost::format("'%1' writing not supported.") % name()).str());
return false;
}
// --- Input and Output ---------------------------------------------------- //
/// Read the data from \p input into \p file.
bool PolymerFileFormat::read(std::istream &input, PolymerFile *file)
{
CHEMKIT_UNUSED(input);
CHEMKIT_UNUSED(file);
setErrorString((boost::format("'%1' reading not supported.") % name()).str());
return false;
}
bool XyzFileFormat::read(std::istream &input, chemkit::MoleculeFile *file)
{
// atom count line
int atomCount = 0;
input >> atomCount;
input.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
// comment line (unused)
std::string commentLine;
std::getline(input, commentLine);
CHEMKIT_UNUSED(commentLine);
// create molecule
boost::shared_ptr<chemkit::Molecule> molecule(new chemkit::Molecule);
// read atoms and coordinates
for(int i = 0; i < atomCount; i++){
std::string symbol;
double x = 0;
double y = 0;
double z = 0;
input >> symbol >> x >> y >> z;
if(input.fail()){
input.clear();
}
// add atom from symbol or atomic number
chemkit::Atom *atom = 0;
if(symbol.empty()){
continue;
}
else if(isdigit(symbol.at(0))){
int atomicNumber = boost::lexical_cast<int>(symbol);
atom = molecule->addAtom(atomicNumber);
}
else{
atom = molecule->addAtom(symbol);
}
// set atom position
if(atom){
atom->setPosition(x, y, z);
}
}
// add molecule to file
file->addMolecule(molecule);
return true;
}
bool MdlFileFormat::readPropertyBlock(QIODevice *iodev, chemkit::Molecule *molecule)
{
CHEMKIT_UNUSED(molecule);
while(!iodev->atEnd()){
QString line = iodev->readLine();
if(line.startsWith("M END")){
return true;
}
}
return false;
}
bool MmffElectrostaticCalculation::setup(const MmffParameters *parameters)
{
CHEMKIT_UNUSED(parameters);
const MmffAtom *a = atom(0);
const MmffAtom *b = atom(1);
chemkit::Real oneFourScaling;
if(a->isOneFour(b)){
oneFourScaling = 0.75;
}
else{
oneFourScaling = 1.0;
}
setParameter(0, a->charge());
setParameter(1, b->charge());
setParameter(2, oneFourScaling);
return true;
}
// --- Descriptor ---------------------------------------------------------- //
/// Calculates the value of the descriptor for \p molecule.
Variant MolecularDescriptor::value(const Molecule *molecule) const
{
CHEMKIT_UNUSED(molecule);
return Variant();
}
