Fix codeql warnings

avogadro/core/coordinateblockgenerator.cpp

@@ -64,8 +64,8 @@ std::string CoordinateBlockGenerator::generateCoordinateBlock()
   const Index numAtoms = m_molecule->atomCount();
   Atom atom;
   unsigned char atomicNumber;
-  const char* symbol;
-  const char* name;
+  const char* symbol = "\0";
+  const char* name = "\0";
   Vector3 pos3d;
   Vector3 fpos3d;
   const UnitCell* cell =

avogadro/core/dihedraliterator.cpp

@@ -35,7 +35,7 @@ Dihedral DihedralIterator::begin()
       Index c = bc.second;
 
       // find an a
-      Index a;
+      Index a = 0;
       for (const auto maybeA : graph.neighbors(b)) {
         if (maybeA != c) {
           a = maybeA;

avogadro/core/elements.cpp

@@ -196,7 +196,7 @@ unsigned char Elements::guessAtomicNumber(const std::string& inputStr)
   str[0] = static_cast<char>(toupper(static_cast<int>(str[0])));
 
   int length = str.size();
-  unsigned char atomicNumber;
+  unsigned char atomicNumber = InvalidElement;
   while (length > 0) {
     if (length > 3)
       atomicNumber = atomicNumberFromName(str.substr(0, length));

avogadro/io/gromacsformat.cpp

@@ -54,7 +54,7 @@ bool GromacsFormat::read(std::istream& in, Molecule& molecule)
 {
   string buffer;
   string value;
-  Residue* r;
+  Residue* r = nullptr;
   size_t currentResidueId = 0;
 
   // Title
@@ -138,7 +138,9 @@ bool GromacsFormat::read(std::istream& in, Molecule& molecule)
     // Atom name:
     value = trimmed(buffer.substr(10, 5));
     Atom atom;
-    int atomicNum = r->getAtomicNumber(value);
+    int atomicNum = 0;
+    if (r != nullptr)
+      r->getAtomicNumber(value);
     if (atomicNum) {
       atom = molecule.addAtom(atomicNum);
     } else {

avogadro/io/lammpsformat.cpp

@@ -426,6 +426,7 @@ bool LammpsDataFormat::write(std::ostream& outStream, const Core::Molecule& mol)
 
   std::ostringstream massStream, atomStream, bondStream;
   double xmin, xmax, ymin, ymax, zmin, zmax;
+  xmin = xmax = ymin = ymax = zmin = zmax = 0.0;
 
   size_t numAtoms = mol2.atomCount();
   outStream << to_string(numAtoms) << " atoms\n";

avogadro/io/pdbformat.cpp

@@ -43,7 +43,7 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)
 {
   string buffer;
   std::vector<int> terList;
-  Residue* r;
+  Residue* r = nullptr;
   size_t currentResidueId = 0;
   bool ok(false);
   int coordSet = 0;
@@ -173,7 +173,7 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)
       } else if (coordSet == 0) {
         Atom newAtom = mol.addAtom(atomicNum);
         newAtom.setPosition3d(pos);
-        if (r) {
+        if (r != nullptr) {
           r->addResidueAtom(atomName, newAtom);
         }
         rawToAtomId.push_back(mol.atomCount() - 1);

avogadro/io/turbomoleformat.cpp

@@ -58,6 +58,8 @@ bool TurbomoleFormat::read(std::istream& inStream, Core::Molecule& mol)
 
   // possible lattice constants
   Real a, b, c, alpha, beta, gamma;
+  a = b = c = 100.0;
+  alpha = beta = gamma = 90.0;
   // defaults if periodicity is not 3
   Vector3 v1(100.0, 0.0, 0.0);
   Vector3 v2(0.0, 100.0, 0.0);

avogadro/qtplugins/cp2kinput/cp2kinput.h

@@ -3,8 +3,8 @@
   This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
-#ifndef AVOGADRO_QTPLUGINS_QUANTUMINPUT_H
-#define AVOGADRO_QTPLUGINS_QUANTUMINPUT_H
+#ifndef AVOGADRO_QTPLUGINS_CP2KINPUT_H
+#define AVOGADRO_QTPLUGINS_CP2KINPUT_H
 
 #include <avogadro/qtgui/extensionplugin.h>
 
@@ -63,4 +63,4 @@ private slots:
 } // namespace QtPlugins
 } // namespace Avogadro
 
-#endif // AVOGADRO_QTPLUGINS_QUANTUMINPUT_H
+#endif // AVOGADRO_QTPLUGINS_CP2KINPUT_H

avogadro/qtplugins/focus/focus.h

@@ -3,8 +3,8 @@
   This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
-#ifndef AVOGADRO_QTPLUGINS_RESETVIEW_H
-#define AVOGADRO_QTPLUGINS_RESETVIEW_H
+#ifndef AVOGADRO_QTPLUGINS_FOCUS_H
+#define AVOGADRO_QTPLUGINS_FOCUS_H
 
 #include <Eigen/Geometry>
 #include <avogadro/qtgui/extensionplugin.h>
@@ -14,7 +14,7 @@ namespace Avogadro {
 namespace QtPlugins {
 
 /**
- * @brief The ResetView class is an extension to center the camera in the best
+ * @brief The Focus class is an extension to center the camera in the best
  * fit panel or the default camera position
  */
 class Focus : public Avogadro::QtGui::ExtensionPlugin

avogadro/qtplugins/force/force.h

@@ -3,8 +3,8 @@
   This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
-#ifndef AVOGADRO_QTPLUGINS_WIREFRAME_H
-#define AVOGADRO_QTPLUGINS_WIREFRAME_H
+#ifndef AVOGADRO_QTPLUGINS_FORCE_H
+#define AVOGADRO_QTPLUGINS_FORCE_H
 
 #include <avogadro/qtgui/sceneplugin.h>
 
@@ -45,4 +45,4 @@ class Force : public QtGui::ScenePlugin
 } // end namespace QtPlugins
 } // end namespace Avogadro
 
-#endif // AVOGADRO_QTPLUGINS_WIREFRAME_H
+#endif // AVOGADRO_QTPLUGINS_FORCE_H

avogadro/qtplugins/gamessinput/gamessinput.h

@@ -3,8 +3,8 @@
   This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
-#ifndef AVOGADRO_QTPLUGINS_QUANTUMINPUT_H
-#define AVOGADRO_QTPLUGINS_QUANTUMINPUT_H
+#ifndef AVOGADRO_QTPLUGINS_GAMESSINPUT_H
+#define AVOGADRO_QTPLUGINS_GAMESSINPUT_H
 
 #include <avogadro/qtgui/extensionplugin.h>
 
@@ -65,4 +65,4 @@ private slots:
 }
 }
 
-#endif // AVOGADRO_QTPLUGINS_QUANTUMINPUT_H
+#endif // AVOGADRO_QTPLUGINS_GAMESSINPUT_H

avogadro/qtplugins/templatetool/templatetool.cpp

@@ -370,7 +370,7 @@ void TemplateTool::atomLeftClick(QMouseEvent*)
       return;
 
     // Find dummy atom in template and get all necessary info
-    size_t templateDummyIndex;
+    size_t templateDummyIndex = 0;
     std::vector<size_t> templateLigandIndices;
     std::vector<size_t> templateLigandUIDs;
     for (size_t i = 0; i < templateMolecule.atomCount(); i++) {