Ruby document is updated.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@621 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/Documents/src/molby_rb/AtomRef.html b/Documents/src/molby_rb/AtomRef.html
index c24924f..77a7016 100644 (file)
--- a/Documents/src/molby_rb/AtomRef.html
+++ b/Documents/src/molby_rb/AtomRef.html
@@ -75,8 +75,7 @@ An <a href="AtomRef.html">AtomRef</a> object contains the parent <a href="Molecu
 <div id="method-anchor_list" class="method-detail">
 <a name="anchor_list"></a>
 <div class="method-heading">
-<span class="method-name">
-anchor_list       &rarr; [n1, w1, n2, w2, ...]<br />
+<span class="method-name">anchor_list       &rarr; [n1, w1, n2, w2, ...]<br />
 self.anchor_list = [n1, w1, n2, w2, ...]
 </span>
 </div>
@@ -90,8 +89,7 @@ Get/set the list of component atoms for a pi-anchor. N1, n2, ... are the compone
 <div id="method-aniso" class="method-detail">
 <a name="aniso"></a>
 <div class="method-heading">
-<span class="method-name">
-aniso       &rarr; [f11, f22, f33, f12, f13, f23]<br />
+<span class="method-name">aniso       &rarr; [f11, f22, f33, f12, f13, f23]<br />
 self.aniso = [f11, f22, f33, f12, f13, f23]<br />
 self.aniso = [f11, f22, f33, f12, f13, f23, type]
 </span>
@@ -140,8 +138,7 @@ The thermal parameters are described in crystallographic coordinates, so that th
 <div id="method-atom_type" class="method-detail">
 <a name="atom_type"></a>
 <div class="method-heading">
-<span class="method-name">
-atom_type       &rarr; String<br />
+<span class="method-name">atom_type       &rarr; String<br />
 self.atom_type = String
 </span>
 </div>
@@ -161,8 +158,7 @@ The atom type "X" and "x" are reserved as wildcards. When parameters are looked
 <div id="method-atom_type" class="method-detail">
 <a name="atomic_number"></a>
 <div class="method-heading">
-<span class="method-name">
-atomic_number       &rarr; Integer<br />
+<span class="method-name">atomic_number       &rarr; Integer<br />
 self.atomic_number = Integer
 </span>
 </div>
@@ -179,8 +175,7 @@ Get/set the atomic number. Setting an atomic number also causes change of the <a
 <div id="method-atom_type" class="method-detail">
 <a name="charge"></a>
 <div class="method-heading">
-<span class="method-name">
-charge       &rarr; Float<br />
+<span class="method-name">charge       &rarr; Float<br />
 self.charge = Float
 </span>
 </div>
@@ -194,8 +189,7 @@ Get/set the partial charge. The partial charge is a value used in molecular mech
 <div id="method-atom_type" class="method-detail">
 <a name="connects"></a>
 <div class="method-heading">
-<span class="method-name">
-connects       &rarr; Array of Integers<br />
+<span class="method-name">connects       &rarr; Array of Integers<br />
 </span>
 </div>
 <div class="method-description">
@@ -208,8 +202,7 @@ Get the connection table. A connection table is a list of atoms that are connect
 <div id="method-atom_type" class="method-detail">
 <a name="element"></a>
 <div class="method-heading">
-<span class="method-name">
-element       &rarr; String<br />
+<span class="method-name">element       &rarr; String<br />
 self.element = String<br />
 </span>
 </div>
@@ -229,8 +222,7 @@ Setting the chemical element also causes change of the <a href="AtomRef.html#ato
 <div id="method-atom_type" class="method-detail">
 <a name="exclusion"></a>
 <div class="method-heading">
-<span class="method-name">
-exclusion       &rarr; [[i1, i2, ...], [j1, j2, ...], [k1, k2, ...]]<br />
+<span class="method-name">exclusion       &rarr; [[i1, i2, ...], [j1, j2, ...], [k1, k2, ...]]<br />
 </span>
 </div>
 <div class="method-description">
@@ -249,8 +241,7 @@ This method requires that the <a href="MDArena.html">MDArena</a> object for the
 <div id="method-atom_type" class="method-detail">
 <a name="f"></a>
 <div class="method-heading">
-<span class="method-name">
-f       &rarr; <a href="Vector3D.html">Vector3D</a><br />
+<span class="method-name">f       &rarr; <a href="Vector3D.html">Vector3D</a><br />
 self.f = <a href="Vector3D.html">Vector3D</a><br />
 </span>
 </div>
@@ -264,8 +255,7 @@ Get the force value from the last MM/MD calculation. The value is in internal fo
 <div id="method-atom_type" class="method-detail">
 <a name="fix_force"></a>
 <div class="method-heading">
-<span class="method-name">
-fix_force       &rarr; Float<br />
+<span class="method-name">fix_force       &rarr; Float<br />
 self.fix_force = Float<br />
 </span>
 </div>
@@ -282,8 +272,7 @@ Get/set the force constant to fix the atom at the particular position during MM/
 <div id="method-atom_type" class="method-detail">
 <a name="fix_pos"></a>
 <div class="method-heading">
-<span class="method-name">
-fix_pos       &rarr; <a href="Vector3D.html">Vector3D</a><br />
+<span class="method-name">fix_pos       &rarr; <a href="Vector3D.html">Vector3D</a><br />
 self.fix_pos = <a href="Vector3D>html">Vector3D</a><br />
 </span>
 </div>
@@ -300,8 +289,7 @@ Get/set the position to fix the atom during MM/MD calculations. The <a href="Ato
 <div id="method-atom_type" class="method-detail">
 <a name="fract_r"></a>
 <div class="method-heading">
-<span class="method-name">
-fract_r       &rarr; <a href="Vector3D.html">Vector3D</a><br />
+<span class="method-name">fract_r       &rarr; <a href="Vector3D.html">Vector3D</a><br />
 self.fract_r = <a href="Vector3D.html">Vector3D</a><br />
 </span>
 </div>
@@ -315,8 +303,7 @@ Get/set the fractional coordinates as a <a href="Vector3D.html">Vector3D</a>. If
 <div id="method-atom_type" class="method-detail">
 <a name="fract_x"></a>
 <div class="method-heading">
-<span class="method-name">
-fract_x       &rarr; Float<br />
+<span class="method-name">fract_x       &rarr; Float<br />
 self.fract_x = Float<br />
 </span>
 </div>
@@ -330,8 +317,7 @@ Get/set the fractional coordinate x. If the crystallographic unit cell is not de
 <div id="method-atom_type" class="method-detail">
 <a name="fract_y"></a>
 <div class="method-heading">
-<span class="method-name">
-fract_y       &rarr; Float<br />
+<span class="method-name">fract_y       &rarr; Float<br />
 self.fract_y = Float<br />
 </span>
 </div>
@@ -345,8 +331,7 @@ Get/set the fractional coordinate y. If the crystallographic unit cell is not de
 <div id="method-atom_type" class="method-detail">
 <a name="fract_z"></a>
 <div class="method-heading">
-<span class="method-name">
-fract_z       &rarr; Float<br />
+<span class="method-name">fract_z       &rarr; Float<br />
 self.fract_z = Float<br />
 </span>
 </div>
@@ -360,8 +345,7 @@ Get/set the fractional coordinate z. If the crystallographic unit cell is not de
 <div id="method-atom_type" class="method-detail">
 <a name="hidden"></a>
 <div class="method-heading">
-<span class="method-name">
-hidden       &rarr; Boolean<br />
+<span class="method-name">hidden       &rarr; Boolean<br />
 self.hidden = Boolean<br />
 </span>
 </div>
@@ -375,8 +359,7 @@ Get/set the hidden flag. This is an atom attribute, and is independent with the
 <div id="method-atom_type" class="method-detail">
 <a name="index"></a>
 <div class="method-heading">
-<span class="method-name">
-index       &rarr; Integer<br />
+<span class="method-name">index       &rarr; Integer<br />
 </span>
 </div>
 <div class="method-description">
@@ -389,8 +372,7 @@ Get the atom index as an integer. This is a read-only attribute; if you want to
 <div id="method-atom_type" class="method-detail">
 <a name="int_charge"></a>
 <div class="method-heading">
-<span class="method-name">
-int_charge       &rarr; Integer<br />
+<span class="method-name">int_charge       &rarr; Integer<br />
 self.int_charge = Integer<br />
 </span>
 </div>
@@ -404,8 +386,7 @@ Get/set the integer charge. This is the integer charge of the atom as defined in
 <div id="method-atom_type" class="method-detail">
 <a name="mm_exclude"></a>
 <div class="method-heading">
-<span class="method-name">
-mm_exclude       &rarr; Integer<br />
+<span class="method-name">mm_exclude       &rarr; Integer<br />
 self.mm_exclude = Integer<br />
 </span>
 </div>
@@ -419,8 +400,7 @@ Get/set the flag whether to exclude this atom from MM/MD calculation. The atom i
 <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 class="method-name">molecule       &rarr; <a href="Molecule.html">Molecule</a><br />
 </span>
 </div>
 <div class="method-description">
@@ -433,8 +413,7 @@ Get the parent molecule object.
 <div id="method-name" class="method-detail">
 <a name="name"></a>
 <div class="method-heading">
-<span class="method-name">
-name       &rarr; String<br />
+<span class="method-name">name       &rarr; String<br />
 self.name = String<br />
 </span>
 </div>
@@ -448,8 +427,7 @@ Get/set the atom name. An atom name consists of up to 4 printable ASCII characte
 <div id="method-occupancy" class="method-detail">
 <a name="occupancy"></a>
 <div class="method-heading">
-<span class="method-name">
-occupancy       &rarr; Float<br />
+<span class="method-name">occupancy       &rarr; Float<br />
 self.occupancy = Float<br />
 </span>
 </div>
@@ -463,8 +441,7 @@ Get/set the occupancy.
 <div id="method-periodic_exclude" class="method-detail">
 <a name="periodic_exclude"></a>
 <div class="method-heading">
-<span class="method-name">
-periodic_exclude       &rarr; Integer<br />
+<span class="method-name">periodic_exclude       &rarr; Integer<br />
 self.periodic_exclude = Integer<br />
 </span>
 </div>
@@ -478,8 +455,7 @@ Get/set the flag whether to exclude this atom from periodic calculation. The ato
 <div id="method-r" class="method-detail">
 <a name="r"></a>
 <div class="method-heading">
-<span class="method-name">
-r       &rarr; <a href="Vector3D.html">Vector3D</a><br />
+<span class="method-name">r       &rarr; <a href="Vector3D.html">Vector3D</a><br />
 self.r = <a href="Vector3D.html">Vector3D</a><br />
 </span>
 </div>
@@ -493,8 +469,7 @@ Get/set the atom position as a <a href="Vector3D.html">Vector3D</a>. The atom po
 <div id="method-res_name" class="method-detail">
 <a name="res_name"></a>
 <div class="method-heading">
-<span class="method-name">
-res_name       &rarr; String<br />
+<span class="method-name">res_name       &rarr; String<br />
 </span>
 </div>
 <div class="method-description">
@@ -507,8 +482,7 @@ Get the residue name. A residue name consists of up to 4 printable ASCII charact
 <div id="method-res_seq" class="method-detail">
 <a name="res_seq"></a>
 <div class="method-heading">
-<span class="method-name">
-res_seq       &rarr; Integer<br />
+<span class="method-name">res_seq       &rarr; Integer<br />
 </span>
 </div>
 <div class="method-description">
@@ -521,8 +495,7 @@ Get the residue number. Residue numbers are 1-based, and the number 0 means "no
 <div id="method-seg_name" class="method-detail">
 <a name="seg_name"></a>
 <div class="method-heading">
-<span class="method-name">
-seg_name       &rarr; String<br />
+<span class="method-name">seg_name       &rarr; String<br />
 self.seg_name = String<br />
 </span>
 </div>
@@ -536,8 +509,7 @@ Get/set the segment name. A segment name consists of up to 4 printable ASCII cha
 <div id="method-seg_seq" class="method-detail">
 <a name="seg_seq"></a>
 <div class="method-heading">
-<span class="method-name">
-seg_seq       &rarr; Integer<br />
+<span class="method-name">seg_seq       &rarr; Integer<br />
 self.seg_seq = Integer<br />
 </span>
 </div>
@@ -551,8 +523,7 @@ Get/set the segment number.
 <div id="method-sigma" class="method-detail">
 <a name="sigma"></a>
 <div class="method-heading">
-<span class="method-name">
-sigma       &rarr; <a href="Vector3D.html">Vector3D</a><br />
+<span class="method-name">sigma       &rarr; <a href="Vector3D.html">Vector3D</a><br />
 sigma_x     &rarr; Float</a><br /> 
 sigma_y     &rarr; Float</a><br /> 
 sigma_z     &rarr; Float</a><br /> 
@@ -572,8 +543,7 @@ Get/set the "sigma" (standard deviation) for the fractional coordinates. Usually
 <div id="method-symop" class="method-detail">
 <a name="symop"></a>
 <div class="method-heading">
-<span class="method-name">
-symop       &rarr; nil or [sym, dx, dy, dz, base]<br />
+<span class="method-name">symop       &rarr; nil or [sym, dx, dy, dz, base]<br />
 self.symop = [sym, dx, dy, dz, base]<br />
 self.symop = nil
 </span>
@@ -591,8 +561,7 @@ Get/set the symmetry operation. If this atom is not symmetry expanded, then nil
 <div id="method-temp_factor" class="method-detail">
 <a name="temp_factor"></a>
 <div class="method-heading">
-<span class="method-name">
-temp_factor       &rarr; Float<br />
+<span class="method-name">temp_factor       &rarr; Float<br />
 self.temp_factor = Float<br />
 </span>
 </div>
@@ -606,8 +575,7 @@ Get/set the (isotropic) temperature factor. For anisotropic temperature factors,
 <div id="method-uff_type" class="method-detail">
 <a name="uff_type"></a>
 <div class="method-heading">
-<span class="method-name">
-uff_type       &rarr; String<br />
+<span class="method-name">uff_type       &rarr; String<br />
 self.uff_type = String<br />
 </span>
 </div>
@@ -621,8 +589,7 @@ Get/set the UFF atom type as a 5-character string.
 <div id="method-v" class="method-detail">
 <a name="v"></a>
 <div class="method-heading">
-<span class="method-name">
-v       &rarr; <a href="Vector3D.html">Vector3D</a><br />
+<span class="method-name">v       &rarr; <a href="Vector3D.html">Vector3D</a><br />
 self.v = <a href="Vector3D.html">Vector3D</a><br />
 </span>
 </div>
@@ -636,8 +603,7 @@ Get/set the velocity value from the last MM/MD calculation. The value is in Å f
 <div id="method-weight" class="method-detail">
 <a name="weight"></a>
 <div class="method-heading">
-<span class="method-name">
-weight       &rarr; Float<br />
+<span class="method-name">weight       &rarr; Float<br />
 self.weight = Float<br />
 </span>
 </div>
@@ -651,8 +617,7 @@ Get/set the atomic weight. This attribute is automatically updated when <a href=
 <div id="method-x" class="method-detail">
 <a name="x"></a>
 <div class="method-heading">
-<span class="method-name">
-x       &rarr; Float<br />
+<span class="method-name">x       &rarr; Float<br />
 self.x = Float<br />
 </span>
 </div>
@@ -666,8 +631,7 @@ Get/set the cartesian coordinate x. To handle crystallographic fractional coordi
 <div id="method-y" class="method-detail">
 <a name="y"></a>
 <div class="method-heading">
-<span class="method-name">
-y       &rarr; Float<br />
+<span class="method-name">y       &rarr; Float<br />
 self.y = Float<br />
 </span>
 </div>
@@ -681,8 +645,7 @@ Get/set the cartesian coordinate y. To handle crystallographic fractional coordi
 <div id="method-z" class="method-detail">
 <a name="z"></a>
 <div class="method-heading">
-<span class="method-name">
-z       &rarr; Float<br />
+<span class="method-name">z       &rarr; Float<br />
 self.z = Float<br />
 </span>
 </div>

diff --git a/Documents/src/molby_rb/Molecule.html b/Documents/src/molby_rb/Molecule.html
index 3403325..7a1b0c3 100644 (file)
--- a/Documents/src/molby_rb/Molecule.html
+++ b/Documents/src/molby_rb/Molecule.html
@@ -81,8 +81,7 @@ Many methods of <a href="Molecule.html">Molecule</a> are described as "undoable"
 <div id="method-M000323" class="method-detail">
 <a name="M000323"></a>
 <div class="method-heading">
-<span class="method-name">
-Molecule[]          &rarr; <a href="Molecule.html">Molecule</a><br />
+<span class="method-name">Molecule[]          &rarr; <a href="Molecule.html">Molecule</a><br />
 Molecule[n]         &rarr; <a href="Molecule.html">Molecule</a><br />
 Molecule[name]      &rarr; <a href="Molecule.html">Molecule</a><br />
 Molecule[name, k]   &rarr; <a href="Molecule.html">Molecule</a><br />
@@ -262,8 +261,7 @@ an empry array.
 <div id="method-M000245" class="method-detail">
 <a name="M000245"></a>
 <div class="method-heading">
-<span class="method-name">
-add(molecule2)       &rarr; self<br />
+<span class="method-name">add(molecule2)       &rarr; self<br />
 </span>
 </div>
 <div class="method-description">
@@ -333,6 +331,24 @@ This operation is undoable.
 </div>
 </div>
 
+
+<div id="method-add_formula" class="method-detail">
+<a name="add_formula"></a>
+<div class="method-heading">
+<span class="method-name">add_formula(mol, mult)       &rarr; self<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Add a molecular fragment to self. The new connection is created at the position of the dummy atoms. The 'first' dummy atom in self is kept untouched wherever possible.
+</p>
+<p>
+Mult (multiplicity) is the number of dummy atoms removed from each fragment. If unspecified, it is the same as the number of the dummy atoms in the added fragment.
+</p>
+</div>
+</div>
+
+ 
 <div id="method-add_gaussian_orbital_shell" class="method-detail">
 <a name="add_gaussian_orbital_shell"></a>
 <div class="method-heading">
@@ -376,6 +392,19 @@ Atype is a String, which is one of the following: &quot;td&quot; (tetrahedral),
 </div>
 </div>
 
+<div id="method-add_hydrogen_on_group" class="method-detail">
+<a name="add_hydrogen_on_group"></a>
+<div class="method-heading">
+<span class="method-name">add_hydrogen_on_group(group, atype, bond = 1.07, anum = 1)</span>
+</div>
+<div class="method-description">
+<p>
+Repeat <a href="#M000125">add_hydrogen</a> for the atoms in the given group. This operation is undoable.
+</p>
+</div>
+</div>
+
+
 <div id="method-M000256" class="method-detail">
 <a name="M000256"></a>
 <div class="method-heading">
@@ -557,6 +586,34 @@ the atom with the lowest index is returned.
 </div>
 </div>
 
+<div id="method-atom_radius" class="method-detail">
+<a name="atom_radius"></a>
+<div class="method-heading">
+  <span class="method-name">atom_radius = Float<br />
+  <span class="method-name">atom_radius &rarr; Float<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Set the atom radius (multiple of the vdw radius) used in drawing the model in normal (non-line) mode. (Default = 0.4) If no argument is given, the current value is returned.
+</p>
+</div>
+</div>
+
+<div id="method-atom_resolution" class="method-detail">
+<a name="atom_resolution"></a>
+<div class="method-heading">
+  <span class="method-name">atom_resolution = Integer<br />
+  <span class="method-name">atom_resolution &rarr; Integer<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Set the atom resolution used in drawing the model in normal (non-line) mode. (Default = 12; minimum = 6)  If no argument is given, the current value is returned.
+</p>
+</div>
+</div>
+
 <div id="method-M000211" class="method-detail">
 <a name="M000211"></a>
 <div class="method-heading">
@@ -588,6 +645,33 @@ Imaginary bonds between a pi-anchor and member atoms are not considered.
 </div>
 </div>
 
+<div id="method-bond_radius" class="method-detail">
+<a name="bond_radius"></a>
+<div class="method-heading">
+  <span class="method-name">bond_radius = Float<br />
+  <span class="method-name">bond_radius &rarr; Float<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Set the bond radius (in angstrom) used in drawing the model in normal (non-line) mode. (Default = 0.1) If no argument is given, the current value is returned.</p>
+</div>
+</div>
+
+<div id="method-bond_resolution" class="method-detail">
+<a name="bond_resolution"></a>
+<div class="method-heading">
+  <span class="method-name">bond_resolution = Integer<br />
+  <span class="method-name">bond_resolution &rarr; Integer<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Set the bond resolution used in drawing the model in normal (non-line) mode. (Default = 8; minimum = 4) If no argument is given, the current value is returned.
+ </p>
+</div>
+</div>
+
 <div id="method-M000212" class="method-detail">
 <a name="M000212"></a>
 <div class="method-heading">
@@ -909,6 +993,47 @@ Calculate the total charge (the sum of the "charge" attributes of atoms). If a g
 </div>
 </div>
 
+
+<div id="method-clear_basis_set" class="method-detail">
+<a name="clear_basis_set"></a>
+<div class="method-heading">
+<span class="method-name">clear_basis_set &rarr; self</span>
+</div>
+<div class="method-description">
+<p>
+Clear the existing basis set info. All gaussian coefficients, MO energies and coefficients, cube and marching cube information are discarded. Note: this operation is <b>not</b> undoable!
+</p>
+</div>
+</div>
+
+
+<div id="method-clear_mo_coefficients" class="method-detail">
+<a name="clear_mo_coefficients"></a>
+<div class="method-heading">
+<span class="method-name">clear_mo_coefficients &rarr; self</span>
+</div>
+<div class="method-description">
+<p>
+Clear the existing MO coefficients. Note: this operation is <b>not</b> undoable!
+</p>
+</div>
+</div>
+
+
+<div id="method-clear_surface" class="method-detail">
+<a name="clear_surface"></a>
+<div class="method-heading">
+<span class="method-name">clear_surface &rarr; self</span>
+</div>
+<div class="method-description">
+<p>
+Clear the MO surface if present.
+</p>
+<i>See Also:</i> <a href="Molecule.html#create_surface">Molecule#create_surface, 
+<a href="Molecule.html#set_surface_attr">Molecule#set_surface_attr</a>
+</div>
+</div>
+
 <div id="method-M000189" class="method-detail">
 <a name="M000189"></a>
 <div class="method-heading">
@@ -958,8 +1083,8 @@ Returns the number of bonds actually created. This operation is undoable.
 </div>
 </div>
 
-<div id="method-M000268" class="method-detail">
-<a name="M000268"></a>
+<div id="method-create_frame" class="method-detail">
+<a name="create_frame"></a>
 <div class="method-heading">
 <span class="method-name">create_frame(coordinates = nil) &rarr; Integer<br />
 create_frames(coordinates = nil) &rarr; Integer<br />
@@ -969,6 +1094,9 @@ create_frames(coordinates = nil) &rarr; Integer<br />
 <p>
 Same as <a href="Molecule.html#M000336">Molecule#insert_frames</a>(nil, coordinates).
 </p>
+<p>
+<i>See Also:</i> <a href="#remove_frames">Molecule#remove_frames</a>
+</p>
 </div>
 </div>
 
@@ -1022,54 +1150,32 @@ of component atoms (and their weights) can be retrived by <a href="AtomRef.html#
 </div>
 </div>
 
-<!--
-<div id="method-M000242" class="method-detail">
-<a name="create_pi_anchor_construct"></a>
+<div id="method-create_surface" class="method-detail">
+<a name="create_surface"></a>
 <div class="method-heading">
-<span class="method-name">create_pi_anchor_construct(n1, n2, n3 = nil, n4 = nil) &rarr; Integer
+<span class="method-name">create_surface(mo, attr = nil) &rarr; self<br />
 </span>
 </div>
 <div class="method-description">
 <p>
-Create a bond, angle, or dihedral including one or more pi anchor points.
-The arguments can either be an atom representation (atom index, atom name, res_seq:name)
-or a pi-anchor representation (pi-anchor index, pi-anchor name).
-The pi-anchor index is represented by a negative integer -N, which corresponds to the (N-1)-th pi anchor.
-Returns the index for the newly created construct.
-This operation is undoable.
+Create a MO surface. The argument mo is the MO index (1-based); if mo is negative, then it denotes the beta orbital. If mo is nil, then the attributes of the current surface are modified.
 </p>
-</div>
-</div>
-
-<div id="method-M000242" class="method-detail">
-<a name="count_pi_anchors"></a>
-<div class="method-heading">
-<span class="method-name">count_pi_anchors &rarr; Integer
-</span>
-</div>
-<div class="method-description">
 <p>
-Return the number of currently defined pi anchors.
+Attributes:
 </p>
+<ul>
+<li>:npoints : the approximate number of grid points</li>
+<li>:expand  : the scale factor to expand/shrink the display box size for each atom</li>
+<li>:thres   : the threshold for the isovalue surface</li>
+</ul>
 <p>
-<i>See Also:</i> <a href="Molecule.html#insert_pi_anchor">Molecule#insert_pi_anchor</a>
+If the molecule does not contain MO information, raises exception.
 </p>
-</div>
-</div>
-
-<div id="method-M000242" class="method-detail">
-<a name="count_pi_anchor_constructs"></a>
-<div class="method-heading">
-<span class="method-name">count_pi_anchor_constructs(IntGroup) &rarr; Integer
-</span>
-</div>
-<div class="method-description">
 <p>
-Returns the number of defined pi-anchor constructs.
+<i>See Also:</i> <a href="#clear_surface">Molecule#clear_surface</a>, <a href="#set_surface_attr">Molecule#set_surface_attr</a>
 </p>
 </div>
 </div>
--->
 
 <div id="method-M000318" class="method-detail">
 <a name="M000318"></a>
@@ -1532,8 +1638,7 @@ Get the atom attribute for the specified atom. Equivalent to <a href="Molecule.h
 <div id="method-get_bond_order" class="method-detail">
 <a name="get_bond_order"></a>
 <div class="method-heading">
-<span class="method-name">
-get_bond_order(idx) &rarr; Float <br />
+<span class="method-name">get_bond_order(idx) &rarr; Float <br />
 get_bond_orders(group) &rarr; Array
 </span>
 </div>
@@ -1559,6 +1664,78 @@ Copy the coordinates from the specified frame. If group is specified, then only
 </div>
 </div>
 
+<div id="method-get_graphic_color" class="method-detail">
+<a name="get_graphic_color"></a>
+<div class="method-heading">
+<span class="method-name">get_graphic_color(graphic_index) &rarr; value<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Get the color of graphic_index-th graphic object.</p>
+</div>
+</div>
+
+<div id="method-get_graphic_point" class="method-detail">
+<a name="get_graphic_point"></a>
+<div class="method-heading">
+<span class="method-name">get_graphic_point(graphic_index, point_index) &rarr; value
+get_graphic_points(graphic_index) &rarr; values
+</span>
+</div>
+<div class="method-description">
+<p>
+Get the point_index-th (or all) control point(s) of graphic_index-th graphic object.
+</p>
+</div>
+</div>
+
+<div id="method-get_mo_coefficients" class="method-detail">
+<a name="get_mo_coefficients"></a>
+<div class="method-heading">
+<span class="method-name">get_mo_coefficients(idx) &rarr; Array<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Get an array of MO coefficients for the given MO index (1-based).
+</p>
+</div>
+</div>
+
+<div id="method-get_mo_energy" class="method-detail">
+<a name="get_mo_energy"></a>
+<div class="method-heading">
+<span class="method-name">get_mo_energy(idx) &rarr; Float<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Get an array of MO coefficients for the given MO index (1-based).
+</p>
+</div>
+</div>
+
+<div id="method-get_property" class="method-detail">
+<a name="get_property"></a>
+<div class="method-heading">
+<span class="method-name">get_property(name[, index]) &rarr; value<br />
+get_property(name, group) &rarr; Array
+</span>
+</div>
+<div class="method-description">
+<p>
+Get molecular property. In the first form, a property value for a single frame is returned.
+(If index is omitted, then the value for the current frame is given)
+In the second form, an array of property values for the given frames is returned.
+If name is not one of known properties or a valid index integer, exception is raised.
+</p>
+<p>
+<i>See Also:</i> <a href="Molecule.html#property_names">Molecule#property_names</a>, <a href="Molecule.html#set_property">Molecule#set_property</a>
+</p>
+</div>
+</div>
+
 <div id="method-get_view_center" class="method-detail">
 <a name="get_view_center"></a>
 <div class="method-heading">
@@ -1628,6 +1805,17 @@ Unset the visibility flag of the graphic_index-th graphic object.
 </p></div>
 </div>
 
+<div id="method-hide_surface" class="method-detail">
+<a name="hide_surface"></a>
+<div class="method-heading">
+<span class="method-name">hide_surface &rarr; self</span>
+</div>
+<div class="method-description">
+<p>
+Hide the MO surface if present.
+</p>
+</div>
+
 <div id="method-M000215" class="method-detail">
 <a name="M000215"></a>
 <div class="method-heading">
@@ -1646,8 +1834,8 @@ improper is represented by an array of four atom indices.
 </div>
 </div>
 
-<div id="method-M000269" class="method-detail">
-<a name="M000269"></a>
+<div id="method-insert_frame" class="method-detail">
+<a name="insert_frame"></a>
 <div class="method-heading">
 <span class="method-name">insert_frame(integer, coordinates = nil) &rarr; <a href="IntGroup.html">IntGroup</a><br />
 insert_frames(intGroup = nil, coordinates = nil) &rarr; <a href="IntGroup.html">IntGroup</a><br />
@@ -1662,29 +1850,26 @@ coordinates is given, it should be an array of arrays of Vector3Ds, and
 those coordinates are set to the new frame. Otherwise, the current coordinates are copied to the new frame. Returns an <a href="IntGroup.html">IntGroup</a> representing
 the inserted frames if successful, nil if not.
 </p>
+<p>
+<i>See Also:</i> <a href="#create_frame">Molecule#create_frame</a>,
+<a href="#remove_frames">Molecule#remove_frames</a>
+</p>
 </div>
 </div>
 
-<!--
-<div id="method-M000242" class="method-detail">
-<a name="insert_pi_anchor"></a>
+<div id="method-insert_graphic" class="method-detail">
+<a name="insert_graphic"></a>
 <div class="method-heading">
-<span class="method-name">insert_pi_anchor(index, name, type, group [, weights]) &rarr; index<br />
+<span class="method-name">insert_graphic(index, kind, color, points, fill = nil) &rarr; integer<br />
 </span>
 </div>
 <div class="method-description">
 <p>
-Create a "pi anchor", which is an anchor point to define a metal-pi bond, and insert at the given index.
-If index is negative or no less than the current number of pi anchors, the new anchor is placed at the end of the anchor list.
-Name and type are Strings, and are similar to those in atoms.
-Group is a group of atoms to define a pi system to be bound to the metal.
-Weights (optional) is an Array of Floats, which determine the significance
-of the component atoms. If not given, then 1.0/N (N is the number of atoms
-in the group) is assumed for all atoms. This operation is undoable.
+Create a new graphic object and insert at the given graphic index (if -1, then append at the last).
+The meaning of the other arguments are the same as <a href="#create_graphic">Molecule#create_graphic</a>.
 </p>
 </div>
 </div>
--->
 
 <div id="method-M000210" class="method-detail">
 <a name="M000210"></a>
@@ -1744,6 +1929,18 @@ given, the current flag is returned.
 </div>
 </div>
 
+<div id="method-loadcif" class="method-detail">
+<a name="loadcif"></a>
+<div class="method-heading">
+<span class="method-name">loadcif(filename) &rarr; bool</span>
+</div>
+<div class="method-description">
+<p>
+Load a molecule from a CIF (crystal information file) file.
+</p>
+</div>
+</div>
+
 <div id="method-M000136" class="method-detail">
 <a name="M000136"></a>
 <div class="method-heading">
@@ -2335,38 +2532,45 @@ If the molecule has no associated document, then returns nil.
 </div>
 </div>
 
-<!--
-<div id="method-M000242" class="method-detail">
-<a name="pi_anchor"></a>
+<div id="method-plane" class="method-detail">
+<a name="plane"></a>
 <div class="method-heading">
-<span class="method-name">pi_anchor(index) &rarr; nil or [name, type, group, weights]<br />
+<span class="method-name">plane(group)  &rarr; Molby::Plane<br />
 </span>
 </div>
 <div class="method-description">
 <p>
-Return the attributes of the idx-th pi anchor if present, otherwise nil.
+Calculate best-fit plane for the given atoms. Returns a value of "Molby::Plane" type.
 </p>
 <p>
-<i>See Also:</i> <a href="Molecule.html#insert_pi_anchor">Molecule#insert_pi_anchor</a>
+Molby::Plane object has the following methods:
 </p>
+<ul>
+<li>inspect: returns a String describing the internal info.</li>
+<li>coeffs: an Array of coefficients [a, b, c, d].</li>
+<li>sigma: an Array of the standard deviations of the coefficients.</li>
+<li>distance: a distance and its standard deviation from the given atom (AtomRef) or a point (Vector3D).</li>
+<li>dihedral: a dihedral angle its standard deviation between this plane and another plane.</li>
+</ul>
 </div>
 </div>
--->
 
-<!--
-<div id="method-M000242" class="method-detail">
-<a name="pi_anchor_construct"></a>
+<div id="method-property_names" class="method-detail">
+<a name="property_names"></a>
 <div class="method-heading">
-<span class="method-name">pi_anchor_construct(index) &rarr; Array of Integers
+<span class="method-name">property_names       &rarr; Array<br />
 </span>
 </div>
 <div class="method-description">
 <p>
-Returns the elements representing the index-th pi anchor constructs.
+Get an array of property names
+</p>
+<p>
+<i>See Also:</i> <a href="Molecule.html#get_property">Molecule#get_property</a>, <a href="Molecule.html#set_property">Molecule#set_property</a>
 </p>
 </div>
 </div>
--->
+
 
 <div id="method-M000226" class="method-detail">
 <a name="M000226"></a>
@@ -2513,6 +2717,23 @@ If the given group corrensponds to all frames, then the current frame is retaine
 </div>
 </div>
 
+<div id="method-remove_frames" class="method-detail">
+<a name="remove_frames"></a>
+<div class="method-heading">
+<span class="method-name">remove_frames(IntGroup, wantCoordinates = false)<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Remove the frames at group. If wantsCoordinates is false (default), returns true if successful and nil otherwise. If wantsCoordinates is true, an array of arrays of the coordinates in the removed frames is returned if operation is successful. This operation is undoable.
+</p>
+<p>
+<i>See Also:</i> <a href="Molecule.html#create_frame">Molecule#create_frame</a>, 
+<a href="Molecule.html#insert_frame">Molecule#insert_frame</a>
+</p>
+</div>
+</div>
+
 <div id="method-remove_graphic" class="method-detail">
 <a name="remove_graphic"></a>
 <div class="method-heading">
@@ -2545,38 +2766,6 @@ This operation is undoable.
 </div>
 </div>
 
-<!--
-<div id="method-M000242" class="method-detail">
-<a name="remove_pi_anchor"></a>
-<div class="method-heading">
-<span class="method-name">remove_pi_anchor(index) &rarr; self<br />
-</span>
-</div>
-<div class="method-description">
-<p>
-Remove an existing "pi anchor". The bonds, angles, and dihedrals containing the pi anchor are also remove. This operation is undoable.
-</p>
-<p>
-<i>See Also:</i> <a href="Molecule.html#insert_pi_anchor">Molecule#insert_pi_anchor</a>
-</p>
-</div>
-</div>
-
-<div id="method-M000242" class="method-detail">
-<a name="remove_pi_anchor_constructs"></a>
-<div class="method-heading">
-<span class="method-name">remove_pi_anchor_constructs(IntGroup) &rarr; self <br />
-remove_pi_anchor_construct(IntGroup)
-</span>
-</div>
-<div class="method-description">
-<p>
-Remove pi anchor constructs (bond, angle, dihedral) with indices specified in IntGroup.
-This operation is undoable.
-</p>
-</div>
-</div>
--->
 
 <div id="method-M000243" class="method-detail">
 <a name="M000243"></a>
@@ -2609,20 +2798,18 @@ operation is undoable.
 </div>
 </div>
 
-<!--
-<div id="method-M000242" class="method-detail">
-<a name="replace_pi_anchor"></a>
+<div id="method-reorder_frames" class="method-detail">
+<a name="reorder_frames"></a>
 <div class="method-heading">
-<span class="method-name">replace_pi_anchor(index, name, type, group [, weights]) &rarr; index<br />
+<span class="method-name">reorder_frames(old_indices) &rarr; self<br />
 </span>
 </div>
 <div class="method-description">
 <p>
-Replace an existing "pi anchor", which is an anchor point to define a metal-pi bond, with the given parameters. For the meaning of the parameters, see the description in <a href="Molecule.html#insert_pi_anchor">Molecule#insert_pi_anchor</a>. This operation is undoable.
+Reorder the frames. The argument is an array of integers that specify the 'old' frame numbers. Thus, if the argument is [2,0,1], then the new frames 0/1/2 are the same as the old frames 2/0/1, respectively. The argument must have the same number of integers as the number of frames. This operation is undoable.
 </p>
 </div>
 </div>
--->
 
 <div id="method-M000216" class="method-detail">
 <a name="M000216"></a>
@@ -2815,6 +3002,18 @@ Returns an array of integers of size natoms, each entry designates the equivalen
 </div>
 </div>
 
+<div id="method-select_frame" class="method-detail">
+<a name="select_frame"></a>
+<div class="method-heading">
+<span class="method-name">select_frame(index) &rarr; bool<br />
+</span>
+</div>
+<div class="method-description">
+<p>
+Select the specified frame. If successful, returns true, otherwise returns false.</p>
+</div>
+</div>
+
 <div id="method-M000316" class="method-detail">
 <a name="M000316"></a>
 <div class="method-heading">
@@ -2946,6 +3145,38 @@ Set the name of an untitled molecule. This method requires that the molecule is
 </div>
 </div>
 
+<div id="method-set_property" class="method-detail">
+<a name="set_property"></a>
+<div class="method-heading">
+<span class="method-name">set_property(name, value[, index]) &rarr; value<br />
+set_property(name, values, group) &rarr; values</span>
+</div>
+<div class="method-description">
+<p>
+Set molecular property. A property is a floating-point number with a specified name, and can be set for each frame separately. The name of the property is given as a String. The value can be a single floating point number, which is set to the current frame.
+</p>
+<p>
+<i>See Also:</i> <a href="#get_property">Molecule#get_property</a>, 
+<a href="#property_names">Molecule#property_names</a>
+</p>
+</div>
+</div>
+
+<div id="method-set_surface_attr" class="method-detail">
+<a name="set_surface_attr"></a>
+<div class="method-heading">
+<span class="method-name">set_surface_attr(attr = nil) &rarr; self</span>
+</div>
+<div class="method-description">
+<p>
+Set the drawing attributes of the surface. Attr is a hash containing the attributes.
+</p>
+<p>
+<i>See Also:</i> <a href="#create_surface">Molecule#create_surface</a>, <a href="#clear_surface">Molecule#clear_surface</a>
+</p>
+</div>
+</div>
+
 <div id="method-M000264" class="method-detail">
 <a name="M000264"></a>
 <div class="method-heading">

diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c
index 7238677..817e3b7 100644 (file)
--- a/MolLib/Ruby_bind/ruby_bind.c
+++ b/MolLib/Ruby_bind/ruby_bind.c
@@ -5446,7 +5446,7 @@ s_Molecule_ErrorMessage(VALUE klass)
  *     set_error_message(String)
  *     Molecule.error_message = String
  *
- *  Get the error_message from the last load/save method. If no error, returns nil.
+ *  Set the error_message for the present load/save method.
  */
 static VALUE
 s_Molecule_SetErrorMessage(VALUE klass, VALUE sval)

diff --git a/Scripts/crystal.rb b/Scripts/crystal.rb
index 613c7c5..62fb6f8 100755 (executable)
--- a/Scripts/crystal.rb
+++ b/Scripts/crystal.rb
@@ -443,6 +443,9 @@ class Molby::Plane
     @metric_tensor = met
     self
   end
+  def coeffs
+    [@coeff.x, @coeff.x, @coeff.z, @const]
+  end
   def sigma
     [sqrt_safe(@error_matrix[0, 0]), sqrt_safe(@error_matrix[1, 1]), sqrt_safe(@error_matrix[2, 2]), sqrt_safe(@error_matrix[3, 3])]
   end

diff --git a/build-xcode/Molby.xcodeproj/project.xcworkspace/xcuserdata/toshi_n.xcuserdatad/UserInterfaceState.xcuserstate b/build-xcode/Molby.xcodeproj/project.xcworkspace/xcuserdata/toshi_n.xcuserdatad/UserInterfaceState.xcuserstate
index d2230b0..59c2ae6 100644 (file)
Binary files a/build-xcode/Molby.xcodeproj/project.xcworkspace/xcuserdata/toshi_n.xcuserdatad/UserInterfaceState.xcuserstate and b/build-xcode/Molby.xcodeproj/project.xcworkspace/xcuserdata/toshi_n.xcuserdatad/UserInterfaceState.xcuserstate differ