clang-tidy-7 pass (#2408)

Code/Numerics/Alignment/AlignPoints.h

@@ -20,7 +20,7 @@ namespace RDNumeric {
 namespace Alignments {
 
 //! \brief Compute an optimal alignment (minimum sum of squared distance)
-//between
+// between
 //! two sets of points in 3D
 /*!
   \param refPoints      A vector of pointers to the reference points
@@ -38,11 +38,12 @@ namespace Alignments {
   This function returns the sum of squared distance (SSR) not the RMSD
   RMSD = sqrt(SSR/numPoints)
 */
-double RDKIT_ALIGNMENT_EXPORT AlignPoints(const RDGeom::Point3DConstPtrVect &refPoints,
-                   const RDGeom::Point3DConstPtrVect &probePoints,
-                   RDGeom::Transform3D &trans, const DoubleVector *weights = 0,
-                   bool reflect = false, unsigned int maxIterations = 50);
-}
-}
+double RDKIT_ALIGNMENT_EXPORT
+AlignPoints(const RDGeom::Point3DConstPtrVect &refPoints,
+            const RDGeom::Point3DConstPtrVect &probePoints,
+            RDGeom::Transform3D &trans, const DoubleVector *weights = 0,
+            bool reflect = false, unsigned int maxIterations = 50);
+}  // namespace Alignments
+}  // namespace RDNumeric
 
 #endif

Code/Numerics/EigenSolvers/PowerEigenSolver.h

@@ -19,7 +19,7 @@
 namespace RDNumeric {
 namespace EigenSolvers {
 //! Compute the \c numEig largest eigenvalues and, optionally,  the
-//corresponding
+// corresponding
 //! eigenvectors.
 /*!
 
@@ -53,16 +53,18 @@ We use the iterative power method, which works like this:
 
 
 */
-bool RDKIT_EIGENSOLVERS_EXPORT powerEigenSolver(unsigned int numEig, DoubleSymmMatrix &mat,
-                      DoubleVector &eigenValues, DoubleMatrix *eigenVectors = 0,
-                      int seed = -1);
+bool RDKIT_EIGENSOLVERS_EXPORT powerEigenSolver(unsigned int numEig,
+                                                DoubleSymmMatrix &mat,
+                                                DoubleVector &eigenValues,
+                                                DoubleMatrix *eigenVectors = 0,
+                                                int seed = -1);
 //! \overload
 static inline bool powerEigenSolver(unsigned int numEig, DoubleSymmMatrix &mat,
                                     DoubleVector &eigenValues,
                                     DoubleMatrix &eigenVectors, int seed = -1) {
   return powerEigenSolver(numEig, mat, eigenValues, &eigenVectors, seed);
 }
-};
-};
+};  // namespace EigenSolvers
+};  // namespace RDNumeric
 
 #endif

Code/Numerics/Matrix.h

@@ -324,7 +324,7 @@ Vector<TYPE> &multiply(const Matrix<TYPE> &A, const Vector<TYPE> &x,
 };
 
 typedef Matrix<double> DoubleMatrix;
-};
+};  // namespace RDNumeric
 
 //! ostream operator for Matrix's
 template <class TYPE>

Code/Numerics/Optimizer/BFGSOpt.h

@@ -175,9 +175,9 @@ void linearSearch(unsigned int dim, double *oldPt, double oldVal, double *grad,
                            will be stored after as many steps as indicated
                            through this parameter; defaults to 0 (no
                            snapshots stored)
-   \param snapshotVect     pointer to a std::vector<Snapshot> object that will receive
-                           the coordinates and energies every snapshotFreq steps;
-                           defaults to NULL (no snapshots stored)
+   \param snapshotVect     pointer to a std::vector<Snapshot> object that will
+   receive the coordinates and energies every snapshotFreq steps; defaults to
+   NULL (no snapshots stored)
 
    \return a flag indicating success (or type of failure). Possible values are:
     -  0: success
@@ -382,8 +382,8 @@ int minimize(unsigned int dim, double *pos, double gradTol,
              unsigned int &numIters, double &funcVal, EnergyFunctor func,
              GradientFunctor gradFunc, double funcTol = TOLX,
              unsigned int maxIts = MAXITS) {
-  return minimize(dim, pos, gradTol, numIters, funcVal, func,
-             gradFunc, 0, NULL, funcTol, maxIts);
+  return minimize(dim, pos, gradTol, numIters, funcVal, func, gradFunc, 0, NULL,
+                  funcTol, maxIts);
 }
 
-}
+}  // namespace BFGSOpt

Code/Numerics/SquareMatrix.h

@@ -84,6 +84,6 @@ class SquareMatrix : public Matrix<TYPE> {
   }
 };
 typedef SquareMatrix<double> DoubleSquareMatrix;
-}
+}  // namespace RDNumeric
 
 #endif

Code/Numerics/SymmMatrix.h

@@ -339,7 +339,7 @@ Vector<TYPE> &multiply(const SymmMatrix<TYPE> &A, const Vector<TYPE> &x,
 typedef SymmMatrix<double> DoubleSymmMatrix;
 typedef SymmMatrix<int> IntSymmMatrix;
 typedef SymmMatrix<unsigned int> UintSymmMatrix;
-}
+}  // namespace RDNumeric
 
 //! ostream operator for Matrix's
 template <class TYPE>