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Initial support for total charge and spin through CJSON. #1058

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Jul 27, 2022
Merged

Initial support for total charge and spin through CJSON. #1058

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17 changes: 17 additions & 0 deletions avogadro/core/molecule.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -321,6 +321,23 @@ const Array<signed char>& Molecule::formalCharges() const
return m_formalCharges;
}

signed char Molecule::totalCharge() const
{
signed char charge = 0;

// check the data map first
if (m_data.hasValue("totalCharge")) {
charge = m_data.value("totalCharge").toInt();
}

if (m_formalCharges.size() > 0) {
for (Index i = 0; i < m_formalCharges.size(); ++i)
charge += m_formalCharges[i];
return charge;
}
return charge; // should be zero
}

Array<Vector3ub>& Molecule::colors()
{
return m_colors;
Expand Down
11 changes: 10 additions & 1 deletion avogadro/core/molecule.h
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Expand Up @@ -136,6 +136,15 @@ class AVOGADROCORE_EXPORT Molecule
/** \overload */
const Array<signed char>& formalCharges() const;

/**
* Get the total charge on the molecule.
* The method will first check to see if a total charge has been set. If not,
* it will calculate the total charge from the formal charges (if set).
* If neither has been set, it will assume the total charge is zero.
* @return The total charge of the molecule.
*/
signed char totalCharge() const;

/**
* Get the formal charge for the requested atom.
* @param atomId The index of the atom.
Expand All @@ -159,7 +168,7 @@ class AVOGADROCORE_EXPORT Molecule
*/
bool setFormalCharge(Index atomId, signed char charge);

/** Returns a vector of colors for the atoms in the moleucle. */
/** \returns a vector of colors for the atoms in the moleucle. */
Array<Vector3ub>& colors();

/** \overload */
Expand Down
69 changes: 47 additions & 22 deletions avogadro/io/cjsonformat.cpp
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Expand Up @@ -119,7 +119,7 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
// This represents our minimal spec for a molecule - atoms that have an
// atomic number.
if (isNumericArray(atomicNumbers) && atomicNumbers.size() > 0) {
for (auto & atomicNumber : atomicNumbers)
for (auto& atomicNumber : atomicNumbers)
molecule.addAtom(atomicNumber);
} else {
appendError("Malformed array for in atoms.elements.number");
Expand Down Expand Up @@ -367,21 +367,21 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
json occupations = orbitals["occupations"];
if (isNumericArray(occupations)) {
std::vector<unsigned char> occs;
for (auto & occupation : occupations)
for (auto& occupation : occupations)
occs.push_back(static_cast<unsigned char>(occupation));
basis->setMolecularOrbitalOccupancy(occupations);
}
json energies = orbitals["energies"];
if (isNumericArray(energies)) {
std::vector<double> energyArray;
for (auto & energie : energies)
for (auto& energie : energies)
energyArray.push_back(static_cast<double>(energie));
basis->setMolecularOrbitalEnergy(energyArray);
}
json numbers = orbitals["numbers"];
if (isNumericArray(numbers)) {
std::vector<unsigned int> numArray;
for (auto & number : numbers)
for (auto& number : numbers)
numArray.push_back(static_cast<unsigned int>(number));
basis->setMolecularOrbitalNumber(numArray);
}
Expand All @@ -390,16 +390,16 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
json moCoefficientsB = orbitals["betaCoefficients"];
if (isNumericArray(moCoefficients)) {
std::vector<double> coeffs;
for (auto & moCoefficient : moCoefficients)
for (auto& moCoefficient : moCoefficients)
coeffs.push_back(static_cast<double>(moCoefficient));
basis->setMolecularOrbitals(coeffs);
} else if (isNumericArray(moCoefficientsA) &&
isNumericArray(moCoefficientsB)) {
std::vector<double> coeffsA;
for (auto & i : moCoefficientsA)
for (auto& i : moCoefficientsA)
coeffsA.push_back(static_cast<double>(i));
std::vector<double> coeffsB;
for (auto & i : moCoefficientsB)
for (auto& i : moCoefficientsB)
coeffsB.push_back(static_cast<double>(i));
basis->setMolecularOrbitals(coeffsA, BasisSet::Alpha);
basis->setMolecularOrbitals(coeffsB, BasisSet::Beta);
Expand All @@ -416,16 +416,16 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
moCoefficientsB = orbSets[idx]["betaCoefficients"];
if (isNumericArray(moCoefficients)) {
std::vector<double> coeffs;
for (auto & moCoefficient : moCoefficients)
for (auto& moCoefficient : moCoefficients)
coeffs.push_back(static_cast<double>(moCoefficient));
basis->setMolecularOrbitals(coeffs, BasisSet::Paired, idx);
} else if (isNumericArray(moCoefficientsA) &&
isNumericArray(moCoefficientsB)) {
std::vector<double> coeffsA;
for (auto & i : moCoefficientsA)
for (auto& i : moCoefficientsA)
coeffsA.push_back(static_cast<double>(i));
std::vector<double> coeffsB;
for (auto & i : moCoefficientsB)
for (auto& i : moCoefficientsB)
coeffsB.push_back(static_cast<double>(i));
basis->setMolecularOrbitals(coeffsA, BasisSet::Alpha, idx);
basis->setMolecularOrbitals(coeffsB, BasisSet::Beta, idx);
Expand All @@ -444,23 +444,23 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
json frequencies = vibrations["frequencies"];
if (isNumericArray(frequencies)) {
Array<double> freqs;
for (auto & frequencie : frequencies) {
for (auto& frequencie : frequencies) {
freqs.push_back(static_cast<double>(frequencie));
}
molecule.setVibrationFrequencies(freqs);
}
json intensities = vibrations["intensities"];
if (isNumericArray(intensities)) {
Array<double> intens;
for (auto & intensitie : intensities) {
for (auto& intensitie : intensities) {
intens.push_back(static_cast<double>(intensitie));
}
molecule.setVibrationIRIntensities(intens);
}
json raman = vibrations["ramanIntensities"];
if (isNumericArray(raman)) {
Array<double> intens;
for (auto & i : raman) {
for (auto& i : raman) {
intens.push_back(static_cast<double>(i));
}
molecule.setVibrationRamanIntensities(intens);
Expand All @@ -473,7 +473,7 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
Array<Vector3> mode;
mode.resize(arr.size() / 3);
double* ptr = &mode[0][0];
for (auto & j : arr) {
for (auto& j : arr) {
*(ptr++) = static_cast<double>(j);
}
disps.push_back(mode);
Expand All @@ -483,6 +483,22 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
}
}

// properties
if (jsonRoot.find("properties") != jsonRoot.end()) {
json properties = jsonRoot["properties"];
if (properties.is_object()) {
if (properties.find("totalCharge") != properties.end()) {
molecule.setData("totalCharge",
static_cast<int>(properties["totalCharge"]));
}
if (properties.find("totalSpinMultiplicity") != properties.end()) {
molecule.setData("totalSpinMultiplicity",
static_cast<int>(properties["totalSpinMultiplicity"]));
}
// todo - put everything into the data map
}
}

if (jsonRoot.find("layer") != jsonRoot.end()) {
auto names = LayerManager::getMoleculeInfo(&molecule);
json visible = jsonRoot["layer"]["visible"];
Expand Down Expand Up @@ -537,6 +553,15 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
root["inchi"] = molecule.data("inchi").toString().c_str();
}

json properties;
properties["totalCharge"] = molecule.totalCharge();
if (molecule.data("totalSpinMultiplicity").type() == Variant::Int)
properties["totalSpinMultiplicity"] =
molecule.data("totalSpinMultiplicity").toInt();
else
properties["totalSpinMultiplicity"] = 1; // assume singlet if not specified
root["properties"] = properties;

if (molecule.unitCell()) {
json unitCell;
unitCell["a"] = molecule.unitCell()->a();
Expand Down Expand Up @@ -605,7 +630,7 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)

auto atomIndices = gaussian->atomIndices();
json shellToAtomMap;
for (unsigned int & atomIndice : atomIndices)
for (unsigned int& atomIndice : atomIndices)
shellToAtomMap.push_back(atomIndice);
basis["shellToAtomMap"] = shellToAtomMap;

Expand Down Expand Up @@ -648,22 +673,22 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
auto energies = gaussian->moEnergy();
if (energies.size() > 0) {
json energyData;
for (double & energie : energies) {
for (double& energie : energies) {
energyData.push_back(energie);
}
root["orbitals"]["energies"] = energyData;
}
auto occ = gaussian->moOccupancy();
if (occ.size() > 0) {
json occData;
for (unsigned char & it : occ)
for (unsigned char& it : occ)
occData.push_back(static_cast<int>(it));
root["orbitals"]["occupations"] = occData;
}
auto num = gaussian->moNumber();
if (num.size() > 0) {
json numData;
for (unsigned int & it : num)
for (unsigned int& it : num)
numData.push_back(it);
root["orbitals"]["numbers"] = numData;
}
Expand Down Expand Up @@ -726,7 +751,7 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
if (molecule.atomPositions3d().size() == molecule.atomCount()) {
// everything gets real-space Cartesians
json coords3d;
for (const auto & it : molecule.atomPositions3d()) {
for (const auto& it : molecule.atomPositions3d()) {
coords3d.push_back(it.x());
coords3d.push_back(it.y());
coords3d.push_back(it.z());
Expand All @@ -739,7 +764,7 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
Array<Vector3> fcoords;
CrystalTools::fractionalCoordinates(
*molecule.unitCell(), molecule.atomPositions3d(), fcoords);
for (auto & fcoord : fcoords) {
for (auto& fcoord : fcoords) {
coordsFractional.push_back(fcoord.x());
coordsFractional.push_back(fcoord.y());
coordsFractional.push_back(fcoord.z());
Expand All @@ -751,7 +776,7 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
// 2d positions:
if (molecule.atomPositions2d().size() == molecule.atomCount()) {
json coords2d;
for (const auto & it : molecule.atomPositions2d()) {
for (const auto& it : molecule.atomPositions2d()) {
coords2d.push_back(it.x());
coords2d.push_back(it.y());
}
Expand Down Expand Up @@ -903,4 +928,4 @@ vector<std::string> CjsonFormat::mimeTypes() const
return mime;
}

} // namespace Avogadro
} // namespace Avogadro::Io