Add hydrogen was broken; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@38 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/Scripts/formula.rb b/Scripts/formula.rb
index fa6010a..c65b8a8 100755 (executable)
--- a/Scripts/formula.rb
+++ b/Scripts/formula.rb
@@ -568,11 +568,11 @@ class Molecule
   #  "td": tetrahedral, "tr": trigonal, "py": pyramidal (like amine nitrogen), "li": linear
   def add_hydrogen(idx, atype, bond = 1.07, anum = 1)
     nc = atoms[idx].connects.length
-       p = atoms[idx].cr
+       p = atoms[idx].r
        if nc == 0
          vx = Vector3D[1, 0, 0]
        else
-         v = atoms[idx].connects.map { |i| (atoms[i].cr - p).normalize }
+         v = atoms[idx].connects.map { |i| (atoms[i].r - p).normalize }
          vx = Vector3D[0, 0, 0]
          v.each { |v0| vx += v0 }
          if nc == 3
@@ -606,7 +606,7 @@ class Molecule
                  j = atoms[i].connects.sort_by { |n| (n == i ? 0 : atoms[n].connects.length) }
                  vy = nil
                  j.each { |j0|
-                   vy = vx.cross(atoms[j0].cr - atoms[i].cr)
+                   vy = vx.cross(atoms[j0].r - atoms[i].r)
                    if vy.length > 1e-3
                          #  The atoms j[0]-i-idx are not linear
                      vz = vx.cross(vy).normalize
@@ -653,8 +653,8 @@ class Molecule
            vn << -vx
          else
            vn << vx if nc == 0
-               vn << vx * 0.5 + vy * 0.86603
-               vn << vx * 0.5 - vy * 0.86603
+               vn << vx * (-0.5) + vy * 0.86603
+               vn << vx * (-0.5) - vy * 0.86603
          end
          type = "ha" if anum == 1
        elsif atype == "py"