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Fix potential crash reading and writing CJSON files (#2612)
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Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
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@ghutchis
ghutchis committed Jul 14, 2023
1 parent fa222a3 commit 6275946
Showing 1 changed file with 79 additions and 67 deletions.
146 changes: 79 additions & 67 deletions src/formats/json/chemicaljsonformat.cpp
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Expand Up @@ -43,6 +43,7 @@ namespace OpenBabel

"Write Options, e.g. -xv\n"
" m minified output formatting, with no line breaks or indents\n"
" s single geometry only, ignoring conformers, etc.\n"
" v verbose output (include default values)\n\n";
};

Expand Down Expand Up @@ -229,7 +230,7 @@ namespace OpenBabel
if (properties.HasMember("totalSpinMultiplicity") &&
properties["totalSpinMultiplicity"].IsInt())
{
pmol->SetTotalSpinMultiplicity(inRoot["totalSpinMultiplicity"].GetInt());
pmol->SetTotalSpinMultiplicity(properties["totalSpinMultiplicity"].GetInt());
}
}

Expand Down Expand Up @@ -303,7 +304,9 @@ namespace OpenBabel
// conformers / multiple coordinates
rapidjson::Value coords(rapidjson::kObjectType);
coords.AddMember("3d", coords3d, al); // default coords
if (pmol->NumConformers() > 1)

// -xs option gives only one geometry
if (pmol->NumConformers() > 1 && !pConv->IsOption("s", pConv->OUTOPTIONS))
{
rapidjson::Value conformers(rapidjson::kArrayType);

Expand Down Expand Up @@ -370,6 +373,7 @@ namespace OpenBabel
if (pmol->HasData(OBGenericDataType::UnitCell))
{
OBUnitCell *uc = (OBUnitCell *)pmol->GetData(OBGenericDataType::UnitCell);
if (uc != nullptr) {
rapidjson::Value unitCell(rapidjson::kObjectType);
unitCell.AddMember("a", uc->GetA(), al);
unitCell.AddMember("b", uc->GetB(), al);
Expand All @@ -390,65 +394,69 @@ namespace OpenBabel
}

doc.AddMember("unitCell", unitCell, al);
}
}

// vibrations
if (pmol->HasData(OBGenericDataType::VibrationData))
{
OBVibrationData *vib =
(OBVibrationData *)pmol->GetData(OBGenericDataType::VibrationData);
rapidjson::Value vibrations(rapidjson::kObjectType);

rapidjson::Value frequencies(rapidjson::kArrayType);
rapidjson::Value modes(rapidjson::kArrayType);
vector<double> wavenumbers = vib->GetFrequencies();
unsigned int mode = 1;
unsigned int modeCount = vib->GetNumberOfFrequencies();
for (unsigned int i = 0; i < modeCount; i++)
if (vib != nullptr)
{
frequencies.PushBack(wavenumbers[i], al);
modes.PushBack(mode++, al);
}
vibrations.AddMember("frequencies", frequencies, al);
vibrations.AddMember("modes", modes, al);
rapidjson::Value vibrations(rapidjson::kObjectType);

rapidjson::Value intensities(rapidjson::kArrayType);
vector<double> intensitiesVec = vib->GetIntensities();
for (unsigned int i = 0; i < modeCount; i++)
{
intensities.PushBack(intensitiesVec[i], al);
}
vibrations.AddMember("intensities", intensities, al);
rapidjson::Value frequencies(rapidjson::kArrayType);
rapidjson::Value modes(rapidjson::kArrayType);
vector<double> wavenumbers = vib->GetFrequencies();
unsigned int mode = 1;
unsigned int modeCount = vib->GetNumberOfFrequencies();
for (unsigned int i = 0; i < modeCount; i++)
{
frequencies.PushBack(wavenumbers[i], al);
modes.PushBack(mode++, al);
}
vibrations.AddMember("frequencies", frequencies, al);
vibrations.AddMember("modes", modes, al);

rapidjson::Value raman(rapidjson::kArrayType);
vector<double> ramanVec = vib->GetRamanActivities();
if (ramanVec.size() > 0)
{
rapidjson::Value intensities(rapidjson::kArrayType);
vector<double> intensitiesVec = vib->GetIntensities();
for (unsigned int i = 0; i < modeCount; i++)
{
raman.PushBack(ramanVec[i], al);
intensities.PushBack(intensitiesVec[i], al);
}
vibrations.AddMember("ramanIntensities", raman, al);
}
vibrations.AddMember("intensities", intensities, al);

rapidjson::Value displacements(rapidjson::kArrayType);
auto lx = vib->GetLx();
for (unsigned int i = 0; i < modeCount; i++)
{
rapidjson::Value displacement(rapidjson::kArrayType);
auto obDisp = lx[i]; // this is a vector<vector3>
for (auto j = obDisp.begin(); j != obDisp.end(); ++j)
rapidjson::Value raman(rapidjson::kArrayType);
vector<double> ramanVec = vib->GetRamanActivities();
if (ramanVec.size() > 0)
{
displacement.PushBack(j->x(), al);
displacement.PushBack(j->y(), al);
displacement.PushBack(j->z(), al);
for (unsigned int i = 0; i < modeCount; i++)
{
raman.PushBack(ramanVec[i], al);
}
vibrations.AddMember("ramanIntensities", raman, al);
}

displacements.PushBack(displacement, al);
}
vibrations.AddMember("eigenVectors", displacements, al);
rapidjson::Value displacements(rapidjson::kArrayType);
auto lx = vib->GetLx();
for (unsigned int i = 0; i < modeCount; i++)
{
rapidjson::Value displacement(rapidjson::kArrayType);
auto obDisp = lx[i]; // this is a vector<vector3>
for (auto j = obDisp.begin(); j != obDisp.end(); ++j)
{
displacement.PushBack(j->x(), al);
displacement.PushBack(j->y(), al);
displacement.PushBack(j->z(), al);
}

doc.AddMember("vibrations", vibrations, al);
displacements.PushBack(displacement, al);
}
vibrations.AddMember("eigenVectors", displacements, al);

doc.AddMember("vibrations", vibrations, al);
}
}

// check for electronic spectra (UV/Vis, CD)
Expand All @@ -457,35 +465,39 @@ namespace OpenBabel
OBElectronicTransitionData *edata =
(OBElectronicTransitionData *)pmol->GetData(
OBGenericDataType::ElectronicTransitionData);
rapidjson::Value electronic(rapidjson::kObjectType);
rapidjson::Value energies(rapidjson::kArrayType);
rapidjson::Value intensities(rapidjson::kArrayType);
// get the energies and intensities
std::vector<double> wavelengths = edata->GetWavelengths();
std::vector<double> forces = edata->GetForces();

// we need to convert the wavelengths to eV
const double hc = 1239.841984332; // in eV*nm
for (unsigned int i = 0; i < wavelengths.size(); i++)
{
energies.PushBack(hc / wavelengths[i], al);
intensities.PushBack(forces[i], al);
}
electronic.AddMember("energies", energies, al);
electronic.AddMember("intensities", intensities, al);

std::vector<double> rotatoryStrengthsVec =
edata->GetRotatoryStrengthsLength();
if (rotatoryStrengthsVec.size() > 0)
if (edata != nullptr)
{
rapidjson::Value rotatoryStrengths(rapidjson::kArrayType);
for (unsigned int i = 0; i < rotatoryStrengthsVec.size(); i++)
rapidjson::Value electronic(rapidjson::kObjectType);
rapidjson::Value energies(rapidjson::kArrayType);
rapidjson::Value intensities(rapidjson::kArrayType);
// get the energies and intensities
std::vector<double> wavelengths = edata->GetWavelengths();
std::vector<double> forces = edata->GetForces();

// we need to convert the wavelengths to eV
const double hc = 1239.841984332; // in eV*nm
for (unsigned int i = 0; i < wavelengths.size(); i++)
{
rotatoryStrengths.PushBack(rotatoryStrengthsVec[i], al);
energies.PushBack(hc / wavelengths[i], al);
intensities.PushBack(forces[i], al);
}
electronic.AddMember("energies", energies, al);
electronic.AddMember("intensities", intensities, al);

std::vector<double> rotatoryStrengthsVec =
edata->GetRotatoryStrengthsLength();
if (rotatoryStrengthsVec.size() > 0)
{
rapidjson::Value rotatoryStrengths(rapidjson::kArrayType);
for (unsigned int i = 0; i < rotatoryStrengthsVec.size(); i++)
{
rotatoryStrengths.PushBack(rotatoryStrengthsVec[i], al);
}
electronic.AddMember("rotation", rotatoryStrengths, al);
}
electronic.AddMember("rotation", rotatoryStrengths, al);
spectra.AddMember("electronic", electronic, al);
}
spectra.AddMember("electronic", electronic, al);
}

if (spectra.MemberCount() > 0)
Expand Down

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