Automatic angle and dihedral settings in 'Guess UFF Parameters' dialog is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@399 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/Scripts/uff.rb b/Scripts/uff.rb
index 11c01df..e6bbaa0 100644 (file)
--- a/Scripts/uff.rb
+++ b/Scripts/uff.rb
@@ -787,6 +787,8 @@ def guess_uff_parameters
       catch(:exit) {
         #  Atoms
         xatoms.each { |idx|
+                 pref = arena.vdw_par(idx) 
+                 next if pref.source != false   #  Already defined
           ap0 = mol.atoms[idx]
           next if exclude.member?(ap0.atomic_number)
                  next if ap0.anchor_list != nil
@@ -859,6 +861,136 @@ def guess_uff_parameters
                  pref.k = force
                  pref.r0 = len
            }
+               #  Angles
+               xangles.each { |idx|
+                 pref = arena.angle_par(idx)
+                 next if pref.source != false   #  Already defined
+                 a = mol.angles[idx]
+                 is = []
+                 aps = [mol.atoms[a[0]], mol.atoms[a[1]], mol.atoms[a[2]]]
+                 3.times { |i|
+                   if aps[i].anchor_list != nil
+                         is[i] = -1
+                         next
+                       end
+                   uff_type = aps[i].uff_type
+                   UFFParams.each_with_index { |u, j|
+                         if u[0] == uff_type
+                           is[i] = j
+                               break
+                         end
+                       }
+                   if is[i] == nil
+                         error_message_box("The UFF type for atom #{b[i]} (#{aps[i].name}) is not defined.")
+                         throw(:exit)
+                       end
+                 }
+                 bos = [1.0, 1.0]
+                 2.times { |i|
+                   #  Look up the bond and get the bond order
+                       mol.bonds.each_with_index { |b, j|
+                         if (a[i] == b[0] && a[i + 1] == b[1]) || (a[i] == b[1] && a[i + 1] == b[0])
+                           bos[i] = mol.get_bond_order(j)
+                               if bos[i] == nil || bos[i] == 0.0
+                                 bos[i] = 1.0
+                               end
+                         end
+                       }
+                 }
+                 ang = mol.calc_angle(a[0], a[1], a[2])
+                 met = [aps[0].atomic_number, aps[1].atomic_number, aps[2].atomic_number].max
+                 if is[1] == -1 && is[0] != -1 && is[2] != 0
+                   #  Metal-Dummy-C angle
+                       case met
+                       when 0..23
+                         force = 85.0
+                       when 24
+                         force = 93.0
+                       when 25..27
+                         force = 100.0
+                       when 28..36
+                         force = 28.0
+                       when 37..54
+                         force = 125.0
+                       else
+                         force = 130.0
+                       end
+                 elsif is[1] != -1 && is[0] == -1 && is[2] == -1
+                   #  Dummy-Metal-Dummy angle
+                       case met
+                       when 0..23
+                         force = 50.0
+                       when 24
+                         force = 40.0
+                       when 25..27
+                         force = 40.0
+                       when 28..36
+                         force = 40.0
+                       when 37..54
+                         force = 52.0
+                       else
+                         force = 56.0
+                       end
+                 elsif is[0] >= 0 && is[1] >= 0 && is[2] >= 0
+                   force = mol.uff_angle_force(is[0], is[1], is[2], bos[0], bos[1], ang)
+                 else
+                   force = 0.0
+                 end
+                 pref = mol.parameter.lookup(:angle, a, :local, :missing, :create, :nowildcard, :nobasetype)
+                 pref.atom_types = [a[0], a[1], a[2]]
+                 pref.k = force
+                 pref.a0 = ang
+           }
+               xdihedrals.each { |idx|
+                 pref = arena.dihedral_par(idx)
+                 next if pref.source != false   #  Already defined
+                 d = mol.dihedrals[idx]
+                 is = []
+                 aps = [mol.atoms[d[0]], mol.atoms[d[1]], mol.atoms[d[2]], mol.atoms[d[3]]]
+                 4.times { |i|
+                   if aps[i].anchor_list != nil
+                         is[i] = -1
+                         next
+                       end
+                   uff_type = aps[i].uff_type
+                   UFFParams.each_with_index { |u, j|
+                         if u[0] == uff_type
+                           is[i] = j
+                               break
+                         end
+                       }
+                   if is[i] == nil
+                         error_message_box("The UFF type for atom #{b[i]} (#{aps[i].name}) is not defined.")
+                         throw(:exit)
+                       end
+                 }
+                 if is[1] == -1 && is[2] == -1 && is[0] != -1 && is[3] != -1
+                   #  X-##-##-X dihedral
+                       met = (aps[1].connects & aps[2].connects)[0]
+                       if met != nil
+                         case mol.atoms[met].atomic_number
+                         when 0..36
+                           force = 0.36
+                     when 37..54
+                           force = 3.4
+                         else
+                           force = 3.4
+                         end
+                         pref = mol.parameter.lookup(:dihedral, ["X", d[1], d[2], "X"], :local, :missing, :create)
+                         pref.atom_types = ["X", d[1], d[2], "X"]
+                         pref.period = 5
+                         pref.phi0 = 180.0
+                         pref.k = force
+                         arena.prepare(true)
+                       end
+                 else
+                   pref = mol.parameter.lookup(:dihedral, d, :local, :missing, :create, :nowildcard, :nobasetype)
+                       pref.atom_types = d
+                       pref.period = 2
+                       pref.phi0 = 180.0
+                       pref.k = 0.0
+                 end
+           }
       }
          arena.prepare(true)
          item_with_tag("table")[:refresh] = true