Merge branch 'openbabel:master' into master

.github/workflows/lint_python.yml

@@ -4,9 +4,12 @@ jobs:
   lint_python:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
       - run: pip install --upgrade pip wheel
+      - run: pip install --upgrade setuptools
       - run: pip install bandit black codespell flake8 flake8-bugbear
                          flake8-comprehensions isort mypy pytest pyupgrade safety
       - run: bandit --recursive  --skip B101,B314,B404,B405,B602,B603,B607 .

src/confsearch.cpp

@@ -131,7 +131,7 @@ namespace OpenBabel
 
     const double arr[] = {3.0, 2.0, 1.5, 1.0, 0.5, 0.25};
     std::vector<double> vec (arr, arr + sizeof(arr) / sizeof(arr[0]) );
-    vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less<double>(), (cutoff + 0.1) )), vec.end());
+    vec.erase(std::remove_if(vec.begin(), vec.end(), [=](double v) { return v < cutoff + 0.1; }), vec.end());
     vec.push_back(cutoff);
 
     levels = vec;
@@ -443,7 +443,7 @@ int OBForceField::DiverseConfGen(double rmsd, unsigned int nconfs, double energy
     UpdateConformersFromTree(&_mol, _energies, &divposes, verbose);
 
     // Add back the energy offset
-    transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(std::plus<double>(), energy_offset));
+    transform(_energies.begin(), _energies.end(), _energies.begin(), [=](double e) { return e + energy_offset; });
 
     // Clean up
     delete [] store_initial;

src/distgeom.cpp

@@ -529,10 +529,10 @@ namespace OpenBabel {
 
               float lBounds = _d->GetLowerBounds(a->GetIdx() - 1, d->GetIdx() - 1) + DIST14_TOL;
               float uBounds = _d->GetUpperBounds(a->GetIdx() - 1, d->GetIdx() - 1) - DIST14_TOL;
-              if (ct->IsTrans(a, d)) {
+              if (ct->IsTrans(a->GetId(), d->GetId())) {
                 // lower bounds should be trans (current upper bounds)
                 _d->SetLowerBounds(a->GetIdx() - 1, d->GetIdx() - 1, uBounds - DIST14_TOL);
-              } else if (ct->IsCis(a, d)) {
+              } else if (ct->IsCis(a->GetId(), d->GetId())) {
                 // upper bounds should be cis (current lower bounds)
                 _d->SetUpperBounds(a->GetIdx() - 1, d->GetIdx() - 1, lBounds + DIST14_TOL);
               }

src/formats/cifformat.cpp

@@ -83,6 +83,7 @@ namespace OpenBabel
         "  B  Use bonds listed in CIF file from _geom_bond_etc records (overrides option b)\n\n"
 
         "Write Options e.g. -xg:\n"
+        "  w  Wrap atomic coordinates to unit cell (default = off)\n"
         "  g  Write bonds using _geom_bond_etc fields \n\n";
     }
 
@@ -1565,6 +1566,9 @@ namespace OpenBabel
       return false;
     ostream &ofs = *pConv->GetOutStream();
 
+    // default is false - leave coordinates as they are
+    bool wrapFractional = pConv->IsOption("w", OBConversion::OUTOPTIONS);
+
     char buffer[BUFF_SIZE];
 
     ofs <<"# CIF file generated by openbabel "<<BABEL_VERSION<<", see https://openbabel.org"<<endl;
@@ -1621,7 +1625,8 @@ namespace OpenBabel
          vector3 v = atom->GetVector();
          if (pUC != nullptr) {
            v = pUC->CartesianToFractional(v);
-           v = pUC->WrapFractionalCoordinate(v);
+           if (wrapFractional)
+            v = pUC->WrapFractionalCoordinate(v);
          }
          X = v.x();
          Y = v.y();

src/formats/fchkformat.cpp

@@ -665,16 +665,16 @@ namespace OpenBabel
            no atom numbers < 0 or > Natoms */
         if (NBond.end() != find_if(NBond.begin(),
                                    NBond.end(),
-                                   bind2nd(less_equal<int>(), 0)) ||
+                                   [](int i) { return i <= 0; }) ||
             NBond.end() != find_if(NBond.begin(),
                                    NBond.end(),
-                                   bind2nd(greater<int>(), MxBond)) ||
+                                   [=](int i) { return i > MxBond; }) ||
             IBond.end() != find_if(IBond.begin(),
                                    IBond.end(),
-                                   bind2nd(less<int>(), 0)) ||
+                                   [](int i) { return i < 0; }) ||
             IBond.end() != find_if(IBond.begin(),
                                    IBond.end(),
-                                   bind2nd(greater<int>(), Natoms)))
+                                   [=](int i) { return i > Natoms; }))
           {
             error_msg << "Invalid connectivity : check the \"NBond\" and/or"
                       << " \"IBond\" section(s).";

src/formats/groformat.cpp

@@ -168,7 +168,7 @@ bool GROFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
   string tempstr = "";
   long int residx = 0;
   OBAtom* atom;
-  OBResidue* res;
+  OBResidue* res = nullptr;
   OBVectorData* velocity;
 
   if (!ifs || ifs.peek() == EOF) {
@@ -275,6 +275,11 @@ bool GROFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
 
     if (resid == residx) {
       // Add atom to an existing residue
+      if (res == nullptr) {
+        res = pmol->NewResidue();
+        res->SetName(resname);
+        res->SetNum(resid);
+      }
       res->AddAtom(atom);
     } else {
       // Create new residue and use that

src/formats/json/chemicaljsonformat.cpp

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

src/formats/json/pubchemjsonformat.cpp

@@ -760,7 +760,7 @@ class PubChemJSONFormat : public OBMoleculeFormat
       // Coordinates
       // TODO: An option to round coordinates to n decimal places?
       xcoords.PushBack(rapidjson::Value(patom->GetX()).Move(), al);
-      ycoords.PushBack(rapidjson::Value(patom->GetX()).Move(), al);
+      ycoords.PushBack(rapidjson::Value(patom->GetY()).Move(), al);
       if (pmol->GetDimension() == 3) {
         zcoords.PushBack(rapidjson::Value(patom->GetZ()).Move(), al);
       }

src/formats/pdbqtformat.cpp

@@ -403,7 +403,7 @@ namespace OpenBabel
     }
 
     double charge = atom->GetPartialCharge();
-    snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d%c   %8.3f%8.3f%8.3f  0.00  0.00    %+5.3f %.2s",
+    snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d%c   %8.3f%8.3f%8.3f  0.00  0.00  %+8.3f %-2.2s",
       het?"HETATM":"ATOM  ",
       index,
       type_name,