fix PrincipalAxes

src/mol-math/linear-algebra/matrix/matrix.ts

@@ -52,9 +52,13 @@ namespace Matrix {
     }
 
     export function transpose<N extends number, M extends number>(out: Matrix<M, N>, mat: Matrix<N, M>): Matrix<M, N> {
+        if (out.cols !== mat.rows || out.rows !== mat.cols) {
+            throw new Error('transpose: matrix dimensions incompatible')
+        }
+        if (out.data === mat.data) {
+            throw new Error('transpose: matrices share memory')
+        }
         const nrows = mat.rows, ncols = mat.cols
-        // TODO add in-place transpose
-        if (out as any === mat) mat = clone(mat)
         const md = mat.data, mtd = out.data
         for (let i = 0, mi = 0, mti = 0; i < nrows; mti += 1, mi += ncols, ++i) {
             let ri = mti

src/mol-math/linear-algebra/matrix/principal-axes.ts

@@ -45,7 +45,7 @@ namespace PrincipalAxes {
         // calculate
         const mean = Matrix.meanRows(points)
         const pointsM = Matrix.subRows(Matrix.clone(points), mean)
-        const pointsT = Matrix.transpose(pointsM as Matrix<number, 3>, pointsM)
+        const pointsT = Matrix.transpose(Matrix.create(n, 3), pointsM)
         Matrix.multiplyABt(A, pointsT, pointsT)
         svd(A, W, U, V)