Bond/Angle with Sigma dialog is overhauled (now working).

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@420 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/Documents/src/molby_rb/AtomRef.html b/Documents/src/molby_rb/AtomRef.html
index 48f1677..c24924f 100644 (file)
--- a/Documents/src/molby_rb/AtomRef.html
+++ b/Documents/src/molby_rb/AtomRef.html
@@ -416,6 +416,20 @@ Get/set the flag whether to exclude this atom from MM/MD calculation. The atom i
 </div>
 </div>
 
+<div id="method-atom_type" class="method-detail">
+<a name="molecule"></a>
+<div class="method-heading">
+<span class="method-name">
+molecule       &rarr; <a href="Molecule.html">Molecule</a><br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Get the parent molecule object.
+</p>
+</div>
+</div>
+
 <div id="method-name" class="method-detail">
 <a name="name"></a>
 <div class="method-heading">

diff --git a/Documents/src/molby_rb/Molecule.html b/Documents/src/molby_rb/Molecule.html
index d571290..f1b7b30 100644 (file)
--- a/Documents/src/molby_rb/Molecule.html
+++ b/Documents/src/molby_rb/Molecule.html
@@ -574,6 +574,20 @@ representing the array of atoms.
 </div>
 </div>
 
+<div id="bond_exist" class="method-detail">
+<a name="bond_exist"></a>
+<div class="method-heading">
+  <span class="method-name">bond_exist?(idx1, idx2)  &rarr; bool<br />
+  </span>
+</div>
+<div class="method-description">
+<p>
+Returns true if bond exists between atoms idx1 and idx2, otherwise returns false.
+Imaginary bonds between a pi-anchor and member atoms are not considered.
+</p>
+</div>
+</div>
+
 <div id="method-M000212" class="method-detail">
 <a name="M000212"></a>
 <div class="method-heading">

diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c
index 84936f1..ed71a68 100644 (file)
--- a/MolLib/Ruby_bind/ruby_bind.c
+++ b/MolLib/Ruby_bind/ruby_bind.c
@@ -6720,6 +6720,34 @@ s_Molecule_GetBondOrder(VALUE self, VALUE idxval)
 
 /*
  *  call-seq:
+ *     bond_exist?(idx1, idx2) -> bool
+ *
+ *  Returns true if bond exists between atoms idx1 and idx2, otherwise returns false.
+ *  Imaginary bonds between a pi-anchor and member atoms are not considered.
+ */
+static VALUE
+s_Molecule_BondExist(VALUE self, VALUE ival1, VALUE ival2)
+{
+       Molecule *mol;
+       Int idx1, idx2, i;
+       Atom *ap;
+       Int *cp;
+    Data_Get_Struct(self, Molecule, mol);
+       idx1 = NUM2INT(rb_Integer(ival1));
+       idx2 = NUM2INT(rb_Integer(ival2));
+       if (idx1 < 0 || idx1 >= mol->natoms || idx2 < 0 || idx2 >= mol->natoms)
+               rb_raise(rb_eMolbyError, "Atom index (%d or %d) out of range", idx1, idx2);
+       ap = ATOM_AT_INDEX(mol->atoms, idx1);
+       cp = AtomConnectData(&ap->connect);
+       for (i = 0; i < ap->connect.count; i++) {
+               if (cp[i] == idx2)
+                       return Qtrue;
+       }
+       return Qfalse;
+}
+
+/*
+ *  call-seq:
  *     add_angle(n1, n2, n3)       -> Molecule
  *
  *  Add angle n1-n2-n3. Returns self. Usually, angles are automatically added
@@ -10416,6 +10444,7 @@ Init_Molby(void)
        rb_define_alias(rb_cMolecule, "assign_bond_orders", "assign_bond_order");
        rb_define_method(rb_cMolecule, "get_bond_order", s_Molecule_GetBondOrder, 1);
        rb_define_alias(rb_cMolecule, "get_bond_orders", "get_bond_order");
+       rb_define_method(rb_cMolecule, "bond_exist?", s_Molecule_BondExist, 2);
        rb_define_method(rb_cMolecule, "add_angle", s_Molecule_AddAngle, 3);
        rb_define_method(rb_cMolecule, "remove_angle", s_Molecule_RemoveAngle, 3);
        rb_define_method(rb_cMolecule, "add_dihedral", s_Molecule_AddDihedral, 4);

diff --git a/Scripts/crystal.rb b/Scripts/crystal.rb
index a184f24..2f39a17 100755 (executable)
--- a/Scripts/crystal.rb
+++ b/Scripts/crystal.rb
@@ -703,6 +703,9 @@ def bond_angle_with_sigma(*args)
 
   #  Unit cell parameter
   cell = self.cell
+  if cell.length == 6
+    cell.push(0.0, 0.0, 0.0, 0.0, 0.0, 0.0)  #  No sigma information
+  end
   # $a, $b, $c, $alpha, $beta, $gamma, $sig_a, $sig_b, $sig_c, $sig_alpha, $sig_beta, $sig_gamma = self.cell
   cos_a = cos(cell[3] * PI / 180.0)
   cos_b = cos(cell[4] * PI / 180.0)
@@ -826,26 +829,6 @@ def bond_angle_with_sigma(*args)
     6.times { |n|
       sig += (p[4 + n] * cell[6 + n]) ** 2
     }
-    #  Test
-    if nil
-      ncell = cell.dup
-      d0 = calc_bond(i, j)
-      dd = [0, 0, 0, 0, 0, 0]
-      6.times { |n|
-        ncell[n] += 0.0001
-        set_cell(ncell, true)
-        amend_by_symmetry(p[10])
-        d1 = calc_bond(i, j)
-        dd[n] = (d1 - d0) / 0.0001
-        ncell[n] = cell[n]
-      }
-      set_cell(ncell, true)
-      amend_by_symmetry(p[10])
-      printf " dr/d{a,b,c} cal %10.5g %10.5g %10.5g\n", p[4], p[5], p[6]
-      printf " dr/d{a,b,c} est %10.5g %10.5g %10.5g\n", dd[0], dd[1], dd[2]
-      printf " dr/d{alpha,beta,gamma} cal %10.5g %10.5g %10.5g\n", p[7], p[8], p[9]
-      printf " dr/d{alpha,beta,gamma} est %10.5g %10.5g %10.5g\n", dd[3], dd[4], dd[5]
-    end
     sig = sqrt(sig)
     results.push([[i, j], notate_with_sigma.call(p[0], sig), symcode[i], symcode[j], nil])
   }
@@ -861,9 +844,6 @@ def bond_angle_with_sigma(*args)
     t123 = acos_safe((p0[0] ** 2 + p1[0] ** 2 - p2[0] ** 2) / (2 * p0[0] * p1[0]))
     t124 = acos_safe((p0[0] ** 2 + p3[0] ** 2 - p2[0] ** 2 * 0.25) / (2 * p0[0] * p3[0]))
     t324 = acos_safe((p1[0] ** 2 + p3[0] ** 2 - p2[0] ** 2 * 0.25) / (2 * p1[0] * p3[0]))
-    if nil
-      printf "t123 = %.2f t124+t324 = %.2f t124 = %.2f t324 = %.2f\n", t123*180/PI, (t124+t324)*180/PI, t124*180/PI, t324*180/PI
-    end
     dtdr12 = -(p0[0] ** 2 - p3[0] ** 2 + p2[0] ** 2 * 0.25) / (2 * p3[0] * (p0[0] ** 2) * sin(t124))
     dtdr23 = -(p1[0] ** 2 - p3[0] ** 2 + p2[0] ** 2 * 0.25) / (2 * p3[0] * (p1[0] ** 2) * sin(t324))
     dtdr13 = p2[0] / (sin(t124) * 4 * p0[0] * p3[0]) + p2[0] / (sin(t324) * 4 * p1[0] * p3[0])
@@ -878,25 +858,6 @@ def bond_angle_with_sigma(*args)
       c += diff_by_rn.call(p1, n, false) * (dtdr23 * 180.0 / PI)
       c += diff_by_rn.call(p2, n, false) * (dtdr13 * 180.0 / PI)
       c += diff_by_rn.call(p3, n, true) * (dtdr24 * 180.0 / PI)
-      #  Test
-      if nil
-        apn = atoms[n]
-        r = apn.fract_r
-        t0 = calc_angle(i, j, k)
-        apn.fract_r = r + Vector3D[0.00001, 0, 0]
-        amend_by_symmetry(pp)
-        t1 = calc_angle(i, j, k)
-        apn.fract_r = r + Vector3D[0, 0.00001, 0]
-        amend_by_symmetry(pp)
-        t2 = calc_angle(i, j, k)
-        apn.fract_r = r + Vector3D[0, 0, 0.00001]
-        amend_by_symmetry(pp)
-        t3 = calc_angle(i, j, k)
-        apn.fract_r = r
-        amend_by_symmetry(pp)
-        printf " dt/dv[%d] cal %10.5g %10.5g %10.5g\n", n, c[0], c[1], c[2]
-        printf " dt/dv[%d] est %10.5g %10.5g %10.5g\n", n, (t1 - t0) / 0.00001, (t2 - t0) / 0.00001, (t3 - t0) / 0.00001
-      end
       sig += c[0] * c[0] * s[0] * s[0] + c[1] * c[1] * s[1] * s[1] + c[2] * c[2] * s[2] * s[2]
     }
     dd = dtdr12 * p0[4] + dtdr23 * p1[4] + dtdr13 * p2[4] + dtdr24 * p3[4]
@@ -919,63 +880,79 @@ end
 
 def cmd_bond_angle_with_sigma
   mol = self
-  Dialog.new("Bond & Angle with Sigma:" + self.name, "Close", nil) {
+  Dialog.new("Bond & Angle with Sigma:" + self.name, nil, nil) {
     values = []
        clicked = []
        sel = mol.selection
-       on_get_value = proc { |it, row, col|
-         val = values[row][col]
-         if col == 0
-           val = val.collect { |i| ap = mol.atoms[i]; "#{ap.res_seq}:#{ap.name}" }.join("-")
-         elsif col >= 2 && col <= 4
-           val ||= "."
-         end
-         val
+       on_get_value = proc { |it, row, col| values[row][col + 2] }
+       atom_name = proc { |ap|
+         (ap.molecule.nresidues >= 2 ? "#{ap.res_seq}:" : "") + ap.name
        }
     layout(1,
          item(:table, :width=>480, :height=>300, :tag=>"table",
-           :columns=>["Bond/Angle", "value(sigma)", "symop1", "symop2", "symop3"],
+           :columns=>[["Bond/Angle", 140], "value(sigma)", "symop1", "symop2", "symop3"],
                :on_count=> proc { values.count },
-               :on_get_value=> on_get_value)
+               :on_get_value=> on_get_value),
+         layout(2,
+           item(:view, :width=>480, :height=>1), -1,
+           item(:button, :title=>"Dump to Console", :tag=>"dump",
+                 :action=>proc { print "\n"; values.each { |val| print val[2..-1].join("  ") + "\n" } },
+                 :enabled=>false),
+               [item(:button, :title=>"Close", :action=>proc { hide }), {:align=>:right}])
        )
        on_document_modified = proc {
          newsel = mol.selection
-         puts "newsel = #{newsel}"
+         val1 = val2 = nil
          if sel != newsel
-           n0 = sel.count
            n1 = newsel.count
-           if n1 == 1      #  New atom is clicked
+               if n1 == 0
+                 #  Clear selection
+                 clicked.clear
+               elsif n1 == 1 && !clicked.include?(newsel[0])
+                 #  New atom
+                 clicked.clear
                  clicked[0] = newsel[0]
-                 clicked[1..-1] = []
-                 if n0 == 1
-                   values[-1][0] = [clicked[0]]
-                 else
-                   values.push([[clicked[0]], "---", nil, nil, nil])
-                 end
-               elsif n1 == 2   #  Bond
-                 puts "new bond"
-                 if newsel.include?(clicked[0])
-                   if newsel[0] == clicked[0]
-                         clicked[1] = newsel[1]
-                       else
-                         clicked[1] = newsel[0]
-                       end
+                 val1 = [[clicked[0]], "---", "", "", ""]
+               elsif n1 == 2 && clicked.length == 1
+                 #  New bond
+                 if newsel[0] == clicked[0]
+                   clicked[1] = newsel[1]
+                 elsif newsel[1] == clicked[0]
+                   clicked[1] = newsel[0]
                  else
                    clicked[0] = newsel[0]
                        clicked[1] = newsel[1]
                  end
-                 clicked[2..-1] = []
-                 puts "clicked = #{clicked.inspect}"
-                 val = mol.bond_angle_with_sigma(clicked)
-                 puts "val = #{val.inspect}"
-                 if n0 == 1
-                   values[-1] = val[0]
-                 else
-                   values.push(val[0])
-                 end
+                 val1 = mol.bond_angle_with_sigma(clicked)[0]
+               elsif n1 == 3 && clicked.length == 2 && newsel.include?(clicked[0]) && newsel.include?(clicked[1])
+                 #  New angle
+                 clicked[2] = (newsel - clicked)[0]
+                 val1 = mol.bond_angle_with_sigma(clicked[1..2])[0]
+                 val2 = mol.bond_angle_with_sigma(clicked)[0]
+               else
+                 return
+               end
+               [val1, val2].each { |val|
+                 next unless val
+                 label = ""
+                 n = val[0].length
+                 n.times { |i|
+                   label += atom_name.call(mol.atoms[val[0][i]])
+                       if val[0][i + 1]
+                         label += (mol.bond_exist?(val[0][i], val[0][i + 1]) ? "-" : "...")
+                       end
+                 }
+                 val[1, 0] = label
+                 val.unshift(n)  #  val = [count, indices, label, value(sigma), symop1, symop2, symop3]
+               }
+           if values[-1] && values[-1][0] == 1
+                 values.pop
                end
+               values.push(val1) if val1
+               values.push(val2) if val2
                sel = newsel
                item_with_tag("table")[:refresh] = true
+               item_with_tag("dump")[:enabled] = (values.length > 0)
          end
        }
     listen(mol, "documentModified", on_document_modified)