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Molby: コミット

Molecular Modeling Software


コミットメタ情報

リビジョンb581b6ced7bcb7ff8603d9131d4823413d771df7 (tree)
日時2019-08-17 00:55:27
作者toshinagata1964 <toshinagata1964@a2be...>
コミッターtoshinagata1964

ログメッセージ

Ruby document is updated.

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

変更サマリ

差分

--- 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
7575 <div id="method-anchor_list" class="method-detail">
7676 <a name="anchor_list"></a>
7777 <div class="method-heading">
78-<span class="method-name">
79-anchor_list &rarr; [n1, w1, n2, w2, ...]<br />
78+<span class="method-name">anchor_list &rarr; [n1, w1, n2, w2, ...]<br />
8079 self.anchor_list = [n1, w1, n2, w2, ...]
8180 </span>
8281 </div>
@@ -90,8 +89,7 @@ Get/set the list of component atoms for a pi-anchor. N1, n2, ... are the compone
9089 <div id="method-aniso" class="method-detail">
9190 <a name="aniso"></a>
9291 <div class="method-heading">
93-<span class="method-name">
94-aniso &rarr; [f11, f22, f33, f12, f13, f23]<br />
92+<span class="method-name">aniso &rarr; [f11, f22, f33, f12, f13, f23]<br />
9593 self.aniso = [f11, f22, f33, f12, f13, f23]<br />
9694 self.aniso = [f11, f22, f33, f12, f13, f23, type]
9795 </span>
@@ -140,8 +138,7 @@ The thermal parameters are described in crystallographic coordinates, so that th
140138 <div id="method-atom_type" class="method-detail">
141139 <a name="atom_type"></a>
142140 <div class="method-heading">
143-<span class="method-name">
144-atom_type &rarr; String<br />
141+<span class="method-name">atom_type &rarr; String<br />
145142 self.atom_type = String
146143 </span>
147144 </div>
@@ -161,8 +158,7 @@ The atom type "X" and "x" are reserved as wildcards. When parameters are looked
161158 <div id="method-atom_type" class="method-detail">
162159 <a name="atomic_number"></a>
163160 <div class="method-heading">
164-<span class="method-name">
165-atomic_number &rarr; Integer<br />
161+<span class="method-name">atomic_number &rarr; Integer<br />
166162 self.atomic_number = Integer
167163 </span>
168164 </div>
@@ -179,8 +175,7 @@ Get/set the atomic number. Setting an atomic number also causes change of the <a
179175 <div id="method-atom_type" class="method-detail">
180176 <a name="charge"></a>
181177 <div class="method-heading">
182-<span class="method-name">
183-charge &rarr; Float<br />
178+<span class="method-name">charge &rarr; Float<br />
184179 self.charge = Float
185180 </span>
186181 </div>
@@ -194,8 +189,7 @@ Get/set the partial charge. The partial charge is a value used in molecular mech
194189 <div id="method-atom_type" class="method-detail">
195190 <a name="connects"></a>
196191 <div class="method-heading">
197-<span class="method-name">
198-connects &rarr; Array of Integers<br />
192+<span class="method-name">connects &rarr; Array of Integers<br />
199193 </span>
200194 </div>
201195 <div class="method-description">
@@ -208,8 +202,7 @@ Get the connection table. A connection table is a list of atoms that are connect
208202 <div id="method-atom_type" class="method-detail">
209203 <a name="element"></a>
210204 <div class="method-heading">
211-<span class="method-name">
212-element &rarr; String<br />
205+<span class="method-name">element &rarr; String<br />
213206 self.element = String<br />
214207 </span>
215208 </div>
@@ -229,8 +222,7 @@ Setting the chemical element also causes change of the <a href="AtomRef.html#ato
229222 <div id="method-atom_type" class="method-detail">
230223 <a name="exclusion"></a>
231224 <div class="method-heading">
232-<span class="method-name">
233-exclusion &rarr; [[i1, i2, ...], [j1, j2, ...], [k1, k2, ...]]<br />
225+<span class="method-name">exclusion &rarr; [[i1, i2, ...], [j1, j2, ...], [k1, k2, ...]]<br />
234226 </span>
235227 </div>
236228 <div class="method-description">
@@ -249,8 +241,7 @@ This method requires that the <a href="MDArena.html">MDArena</a> object for the
249241 <div id="method-atom_type" class="method-detail">
250242 <a name="f"></a>
251243 <div class="method-heading">
252-<span class="method-name">
253-f &rarr; <a href="Vector3D.html">Vector3D</a><br />
244+<span class="method-name">f &rarr; <a href="Vector3D.html">Vector3D</a><br />
254245 self.f = <a href="Vector3D.html">Vector3D</a><br />
255246 </span>
256247 </div>
@@ -264,8 +255,7 @@ Get the force value from the last MM/MD calculation. The value is in internal fo
264255 <div id="method-atom_type" class="method-detail">
265256 <a name="fix_force"></a>
266257 <div class="method-heading">
267-<span class="method-name">
268-fix_force &rarr; Float<br />
258+<span class="method-name">fix_force &rarr; Float<br />
269259 self.fix_force = Float<br />
270260 </span>
271261 </div>
@@ -282,8 +272,7 @@ Get/set the force constant to fix the atom at the particular position during MM/
282272 <div id="method-atom_type" class="method-detail">
283273 <a name="fix_pos"></a>
284274 <div class="method-heading">
285-<span class="method-name">
286-fix_pos &rarr; <a href="Vector3D.html">Vector3D</a><br />
275+<span class="method-name">fix_pos &rarr; <a href="Vector3D.html">Vector3D</a><br />
287276 self.fix_pos = <a href="Vector3D>html">Vector3D</a><br />
288277 </span>
289278 </div>
@@ -300,8 +289,7 @@ Get/set the position to fix the atom during MM/MD calculations. The <a href="Ato
300289 <div id="method-atom_type" class="method-detail">
301290 <a name="fract_r"></a>
302291 <div class="method-heading">
303-<span class="method-name">
304-fract_r &rarr; <a href="Vector3D.html">Vector3D</a><br />
292+<span class="method-name">fract_r &rarr; <a href="Vector3D.html">Vector3D</a><br />
305293 self.fract_r = <a href="Vector3D.html">Vector3D</a><br />
306294 </span>
307295 </div>
@@ -315,8 +303,7 @@ Get/set the fractional coordinates as a <a href="Vector3D.html">Vector3D</a>. If
315303 <div id="method-atom_type" class="method-detail">
316304 <a name="fract_x"></a>
317305 <div class="method-heading">
318-<span class="method-name">
319-fract_x &rarr; Float<br />
306+<span class="method-name">fract_x &rarr; Float<br />
320307 self.fract_x = Float<br />
321308 </span>
322309 </div>
@@ -330,8 +317,7 @@ Get/set the fractional coordinate x. If the crystallographic unit cell is not de
330317 <div id="method-atom_type" class="method-detail">
331318 <a name="fract_y"></a>
332319 <div class="method-heading">
333-<span class="method-name">
334-fract_y &rarr; Float<br />
320+<span class="method-name">fract_y &rarr; Float<br />
335321 self.fract_y = Float<br />
336322 </span>
337323 </div>
@@ -345,8 +331,7 @@ Get/set the fractional coordinate y. If the crystallographic unit cell is not de
345331 <div id="method-atom_type" class="method-detail">
346332 <a name="fract_z"></a>
347333 <div class="method-heading">
348-<span class="method-name">
349-fract_z &rarr; Float<br />
334+<span class="method-name">fract_z &rarr; Float<br />
350335 self.fract_z = Float<br />
351336 </span>
352337 </div>
@@ -360,8 +345,7 @@ Get/set the fractional coordinate z. If the crystallographic unit cell is not de
360345 <div id="method-atom_type" class="method-detail">
361346 <a name="hidden"></a>
362347 <div class="method-heading">
363-<span class="method-name">
364-hidden &rarr; Boolean<br />
348+<span class="method-name">hidden &rarr; Boolean<br />
365349 self.hidden = Boolean<br />
366350 </span>
367351 </div>
@@ -375,8 +359,7 @@ Get/set the hidden flag. This is an atom attribute, and is independent with the
375359 <div id="method-atom_type" class="method-detail">
376360 <a name="index"></a>
377361 <div class="method-heading">
378-<span class="method-name">
379-index &rarr; Integer<br />
362+<span class="method-name">index &rarr; Integer<br />
380363 </span>
381364 </div>
382365 <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
389372 <div id="method-atom_type" class="method-detail">
390373 <a name="int_charge"></a>
391374 <div class="method-heading">
392-<span class="method-name">
393-int_charge &rarr; Integer<br />
375+<span class="method-name">int_charge &rarr; Integer<br />
394376 self.int_charge = Integer<br />
395377 </span>
396378 </div>
@@ -404,8 +386,7 @@ Get/set the integer charge. This is the integer charge of the atom as defined in
404386 <div id="method-atom_type" class="method-detail">
405387 <a name="mm_exclude"></a>
406388 <div class="method-heading">
407-<span class="method-name">
408-mm_exclude &rarr; Integer<br />
389+<span class="method-name">mm_exclude &rarr; Integer<br />
409390 self.mm_exclude = Integer<br />
410391 </span>
411392 </div>
@@ -419,8 +400,7 @@ Get/set the flag whether to exclude this atom from MM/MD calculation. The atom i
419400 <div id="method-atom_type" class="method-detail">
420401 <a name="molecule"></a>
421402 <div class="method-heading">
422-<span class="method-name">
423-molecule &rarr; <a href="Molecule.html">Molecule</a><br />
403+<span class="method-name">molecule &rarr; <a href="Molecule.html">Molecule</a><br />
424404 </span>
425405 </div>
426406 <div class="method-description">
@@ -433,8 +413,7 @@ Get the parent molecule object.
433413 <div id="method-name" class="method-detail">
434414 <a name="name"></a>
435415 <div class="method-heading">
436-<span class="method-name">
437-name &rarr; String<br />
416+<span class="method-name">name &rarr; String<br />
438417 self.name = String<br />
439418 </span>
440419 </div>
@@ -448,8 +427,7 @@ Get/set the atom name. An atom name consists of up to 4 printable ASCII characte
448427 <div id="method-occupancy" class="method-detail">
449428 <a name="occupancy"></a>
450429 <div class="method-heading">
451-<span class="method-name">
452-occupancy &rarr; Float<br />
430+<span class="method-name">occupancy &rarr; Float<br />
453431 self.occupancy = Float<br />
454432 </span>
455433 </div>
@@ -463,8 +441,7 @@ Get/set the occupancy.
463441 <div id="method-periodic_exclude" class="method-detail">
464442 <a name="periodic_exclude"></a>
465443 <div class="method-heading">
466-<span class="method-name">
467-periodic_exclude &rarr; Integer<br />
444+<span class="method-name">periodic_exclude &rarr; Integer<br />
468445 self.periodic_exclude = Integer<br />
469446 </span>
470447 </div>
@@ -478,8 +455,7 @@ Get/set the flag whether to exclude this atom from periodic calculation. The ato
478455 <div id="method-r" class="method-detail">
479456 <a name="r"></a>
480457 <div class="method-heading">
481-<span class="method-name">
482-r &rarr; <a href="Vector3D.html">Vector3D</a><br />
458+<span class="method-name">r &rarr; <a href="Vector3D.html">Vector3D</a><br />
483459 self.r = <a href="Vector3D.html">Vector3D</a><br />
484460 </span>
485461 </div>
@@ -493,8 +469,7 @@ Get/set the atom position as a <a href="Vector3D.html">Vector3D</a>. The atom po
493469 <div id="method-res_name" class="method-detail">
494470 <a name="res_name"></a>
495471 <div class="method-heading">
496-<span class="method-name">
497-res_name &rarr; String<br />
472+<span class="method-name">res_name &rarr; String<br />
498473 </span>
499474 </div>
500475 <div class="method-description">
@@ -507,8 +482,7 @@ Get the residue name. A residue name consists of up to 4 printable ASCII charact
507482 <div id="method-res_seq" class="method-detail">
508483 <a name="res_seq"></a>
509484 <div class="method-heading">
510-<span class="method-name">
511-res_seq &rarr; Integer<br />
485+<span class="method-name">res_seq &rarr; Integer<br />
512486 </span>
513487 </div>
514488 <div class="method-description">
@@ -521,8 +495,7 @@ Get the residue number. Residue numbers are 1-based, and the number 0 means "no
521495 <div id="method-seg_name" class="method-detail">
522496 <a name="seg_name"></a>
523497 <div class="method-heading">
524-<span class="method-name">
525-seg_name &rarr; String<br />
498+<span class="method-name">seg_name &rarr; String<br />
526499 self.seg_name = String<br />
527500 </span>
528501 </div>
@@ -536,8 +509,7 @@ Get/set the segment name. A segment name consists of up to 4 printable ASCII cha
536509 <div id="method-seg_seq" class="method-detail">
537510 <a name="seg_seq"></a>
538511 <div class="method-heading">
539-<span class="method-name">
540-seg_seq &rarr; Integer<br />
512+<span class="method-name">seg_seq &rarr; Integer<br />
541513 self.seg_seq = Integer<br />
542514 </span>
543515 </div>
@@ -551,8 +523,7 @@ Get/set the segment number.
551523 <div id="method-sigma" class="method-detail">
552524 <a name="sigma"></a>
553525 <div class="method-heading">
554-<span class="method-name">
555-sigma &rarr; <a href="Vector3D.html">Vector3D</a><br />
526+<span class="method-name">sigma &rarr; <a href="Vector3D.html">Vector3D</a><br />
556527 sigma_x &rarr; Float</a><br />
557528 sigma_y &rarr; Float</a><br />
558529 sigma_z &rarr; Float</a><br />
@@ -572,8 +543,7 @@ Get/set the "sigma" (standard deviation) for the fractional coordinates. Usually
572543 <div id="method-symop" class="method-detail">
573544 <a name="symop"></a>
574545 <div class="method-heading">
575-<span class="method-name">
576-symop &rarr; nil or [sym, dx, dy, dz, base]<br />
546+<span class="method-name">symop &rarr; nil or [sym, dx, dy, dz, base]<br />
577547 self.symop = [sym, dx, dy, dz, base]<br />
578548 self.symop = nil
579549 </span>
@@ -591,8 +561,7 @@ Get/set the symmetry operation. If this atom is not symmetry expanded, then nil
591561 <div id="method-temp_factor" class="method-detail">
592562 <a name="temp_factor"></a>
593563 <div class="method-heading">
594-<span class="method-name">
595-temp_factor &rarr; Float<br />
564+<span class="method-name">temp_factor &rarr; Float<br />
596565 self.temp_factor = Float<br />
597566 </span>
598567 </div>
@@ -606,8 +575,7 @@ Get/set the (isotropic) temperature factor. For anisotropic temperature factors,
606575 <div id="method-uff_type" class="method-detail">
607576 <a name="uff_type"></a>
608577 <div class="method-heading">
609-<span class="method-name">
610-uff_type &rarr; String<br />
578+<span class="method-name">uff_type &rarr; String<br />
611579 self.uff_type = String<br />
612580 </span>
613581 </div>
@@ -621,8 +589,7 @@ Get/set the UFF atom type as a 5-character string.
621589 <div id="method-v" class="method-detail">
622590 <a name="v"></a>
623591 <div class="method-heading">
624-<span class="method-name">
625-v &rarr; <a href="Vector3D.html">Vector3D</a><br />
592+<span class="method-name">v &rarr; <a href="Vector3D.html">Vector3D</a><br />
626593 self.v = <a href="Vector3D.html">Vector3D</a><br />
627594 </span>
628595 </div>
@@ -636,8 +603,7 @@ Get/set the velocity value from the last MM/MD calculation. The value is in Å f
636603 <div id="method-weight" class="method-detail">
637604 <a name="weight"></a>
638605 <div class="method-heading">
639-<span class="method-name">
640-weight &rarr; Float<br />
606+<span class="method-name">weight &rarr; Float<br />
641607 self.weight = Float<br />
642608 </span>
643609 </div>
@@ -651,8 +617,7 @@ Get/set the atomic weight. This attribute is automatically updated when <a href=
651617 <div id="method-x" class="method-detail">
652618 <a name="x"></a>
653619 <div class="method-heading">
654-<span class="method-name">
655-x &rarr; Float<br />
620+<span class="method-name">x &rarr; Float<br />
656621 self.x = Float<br />
657622 </span>
658623 </div>
@@ -666,8 +631,7 @@ Get/set the cartesian coordinate x. To handle crystallographic fractional coordi
666631 <div id="method-y" class="method-detail">
667632 <a name="y"></a>
668633 <div class="method-heading">
669-<span class="method-name">
670-y &rarr; Float<br />
634+<span class="method-name">y &rarr; Float<br />
671635 self.y = Float<br />
672636 </span>
673637 </div>
@@ -681,8 +645,7 @@ Get/set the cartesian coordinate y. To handle crystallographic fractional coordi
681645 <div id="method-z" class="method-detail">
682646 <a name="z"></a>
683647 <div class="method-heading">
684-<span class="method-name">
685-z &rarr; Float<br />
648+<span class="method-name">z &rarr; Float<br />
686649 self.z = Float<br />
687650 </span>
688651 </div>
--- 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"
8181 <div id="method-M000323" class="method-detail">
8282 <a name="M000323"></a>
8383 <div class="method-heading">
84-<span class="method-name">
85-Molecule[] &rarr; <a href="Molecule.html">Molecule</a><br />
84+<span class="method-name">Molecule[] &rarr; <a href="Molecule.html">Molecule</a><br />
8685 Molecule[n] &rarr; <a href="Molecule.html">Molecule</a><br />
8786 Molecule[name] &rarr; <a href="Molecule.html">Molecule</a><br />
8887 Molecule[name, k] &rarr; <a href="Molecule.html">Molecule</a><br />
@@ -262,8 +261,7 @@ an empry array.
262261 <div id="method-M000245" class="method-detail">
263262 <a name="M000245"></a>
264263 <div class="method-heading">
265-<span class="method-name">
266-add(molecule2) &rarr; self<br />
264+<span class="method-name">add(molecule2) &rarr; self<br />
267265 </span>
268266 </div>
269267 <div class="method-description">
@@ -333,6 +331,24 @@ This operation is undoable.
333331 </div>
334332 </div>
335333
334+
335+<div id="method-add_formula" class="method-detail">
336+<a name="add_formula"></a>
337+<div class="method-heading">
338+<span class="method-name">add_formula(mol, mult) &rarr; self<br />
339+</span>
340+</div>
341+<div class="method-description">
342+<p>
343+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.
344+</p>
345+<p>
346+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.
347+</p>
348+</div>
349+</div>
350+
351+
336352 <div id="method-add_gaussian_orbital_shell" class="method-detail">
337353 <a name="add_gaussian_orbital_shell"></a>
338354 <div class="method-heading">
@@ -376,6 +392,19 @@ Atype is a String, which is one of the following: &quot;td&quot; (tetrahedral),
376392 </div>
377393 </div>
378394
395+<div id="method-add_hydrogen_on_group" class="method-detail">
396+<a name="add_hydrogen_on_group"></a>
397+<div class="method-heading">
398+<span class="method-name">add_hydrogen_on_group(group, atype, bond = 1.07, anum = 1)</span>
399+</div>
400+<div class="method-description">
401+<p>
402+Repeat <a href="#M000125">add_hydrogen</a> for the atoms in the given group. This operation is undoable.
403+</p>
404+</div>
405+</div>
406+
407+
379408 <div id="method-M000256" class="method-detail">
380409 <a name="M000256"></a>
381410 <div class="method-heading">
@@ -557,6 +586,34 @@ the atom with the lowest index is returned.
557586 </div>
558587 </div>
559588
589+<div id="method-atom_radius" class="method-detail">
590+<a name="atom_radius"></a>
591+<div class="method-heading">
592+ <span class="method-name">atom_radius = Float<br />
593+ <span class="method-name">atom_radius &rarr; Float<br />
594+</span>
595+</div>
596+<div class="method-description">
597+<p>
598+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.
599+</p>
600+</div>
601+</div>
602+
603+<div id="method-atom_resolution" class="method-detail">
604+<a name="atom_resolution"></a>
605+<div class="method-heading">
606+ <span class="method-name">atom_resolution = Integer<br />
607+ <span class="method-name">atom_resolution &rarr; Integer<br />
608+</span>
609+</div>
610+<div class="method-description">
611+<p>
612+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.
613+</p>
614+</div>
615+</div>
616+
560617 <div id="method-M000211" class="method-detail">
561618 <a name="M000211"></a>
562619 <div class="method-heading">
@@ -588,6 +645,33 @@ Imaginary bonds between a pi-anchor and member atoms are not considered.
588645 </div>
589646 </div>
590647
648+<div id="method-bond_radius" class="method-detail">
649+<a name="bond_radius"></a>
650+<div class="method-heading">
651+ <span class="method-name">bond_radius = Float<br />
652+ <span class="method-name">bond_radius &rarr; Float<br />
653+</span>
654+</div>
655+<div class="method-description">
656+<p>
657+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>
658+</div>
659+</div>
660+
661+<div id="method-bond_resolution" class="method-detail">
662+<a name="bond_resolution"></a>
663+<div class="method-heading">
664+ <span class="method-name">bond_resolution = Integer<br />
665+ <span class="method-name">bond_resolution &rarr; Integer<br />
666+</span>
667+</div>
668+<div class="method-description">
669+<p>
670+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.
671+ </p>
672+</div>
673+</div>
674+
591675 <div id="method-M000212" class="method-detail">
592676 <a name="M000212"></a>
593677 <div class="method-heading">
@@ -909,6 +993,47 @@ Calculate the total charge (the sum of the "charge" attributes of atoms). If a g
909993 </div>
910994 </div>
911995
996+
997+<div id="method-clear_basis_set" class="method-detail">
998+<a name="clear_basis_set"></a>
999+<div class="method-heading">
1000+<span class="method-name">clear_basis_set &rarr; self</span>
1001+</div>
1002+<div class="method-description">
1003+<p>
1004+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!
1005+</p>
1006+</div>
1007+</div>
1008+
1009+
1010+<div id="method-clear_mo_coefficients" class="method-detail">
1011+<a name="clear_mo_coefficients"></a>
1012+<div class="method-heading">
1013+<span class="method-name">clear_mo_coefficients &rarr; self</span>
1014+</div>
1015+<div class="method-description">
1016+<p>
1017+Clear the existing MO coefficients. Note: this operation is <b>not</b> undoable!
1018+</p>
1019+</div>
1020+</div>
1021+
1022+
1023+<div id="method-clear_surface" class="method-detail">
1024+<a name="clear_surface"></a>
1025+<div class="method-heading">
1026+<span class="method-name">clear_surface &rarr; self</span>
1027+</div>
1028+<div class="method-description">
1029+<p>
1030+Clear the MO surface if present.
1031+</p>
1032+<i>See Also:</i> <a href="Molecule.html#create_surface">Molecule#create_surface,
1033+<a href="Molecule.html#set_surface_attr">Molecule#set_surface_attr</a>
1034+</div>
1035+</div>
1036+
9121037 <div id="method-M000189" class="method-detail">
9131038 <a name="M000189"></a>
9141039 <div class="method-heading">
@@ -958,8 +1083,8 @@ Returns the number of bonds actually created. This operation is undoable.
9581083 </div>
9591084 </div>
9601085
961-<div id="method-M000268" class="method-detail">
962-<a name="M000268"></a>
1086+<div id="method-create_frame" class="method-detail">
1087+<a name="create_frame"></a>
9631088 <div class="method-heading">
9641089 <span class="method-name">create_frame(coordinates = nil) &rarr; Integer<br />
9651090 create_frames(coordinates = nil) &rarr; Integer<br />
@@ -969,6 +1094,9 @@ create_frames(coordinates = nil) &rarr; Integer<br />
9691094 <p>
9701095 Same as <a href="Molecule.html#M000336">Molecule#insert_frames</a>(nil, coordinates).
9711096 </p>
1097+<p>
1098+<i>See Also:</i> <a href="#remove_frames">Molecule#remove_frames</a>
1099+</p>
9721100 </div>
9731101 </div>
9741102
@@ -1022,54 +1150,32 @@ of component atoms (and their weights) can be retrived by <a href="AtomRef.html#
10221150 </div>
10231151 </div>
10241152
1025-<!--
1026-<div id="method-M000242" class="method-detail">
1027-<a name="create_pi_anchor_construct"></a>
1153+<div id="method-create_surface" class="method-detail">
1154+<a name="create_surface"></a>
10281155 <div class="method-heading">
1029-<span class="method-name">create_pi_anchor_construct(n1, n2, n3 = nil, n4 = nil) &rarr; Integer
1156+<span class="method-name">create_surface(mo, attr = nil) &rarr; self<br />
10301157 </span>
10311158 </div>
10321159 <div class="method-description">
10331160 <p>
1034-Create a bond, angle, or dihedral including one or more pi anchor points.
1035-The arguments can either be an atom representation (atom index, atom name, res_seq:name)
1036-or a pi-anchor representation (pi-anchor index, pi-anchor name).
1037-The pi-anchor index is represented by a negative integer -N, which corresponds to the (N-1)-th pi anchor.
1038-Returns the index for the newly created construct.
1039-This operation is undoable.
1161+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.
10401162 </p>
1041-</div>
1042-</div>
1043-
1044-<div id="method-M000242" class="method-detail">
1045-<a name="count_pi_anchors"></a>
1046-<div class="method-heading">
1047-<span class="method-name">count_pi_anchors &rarr; Integer
1048-</span>
1049-</div>
1050-<div class="method-description">
10511163 <p>
1052-Return the number of currently defined pi anchors.
1164+Attributes:
10531165 </p>
1166+<ul>
1167+<li>:npoints : the approximate number of grid points</li>
1168+<li>:expand : the scale factor to expand/shrink the display box size for each atom</li>
1169+<li>:thres : the threshold for the isovalue surface</li>
1170+</ul>
10541171 <p>
1055-<i>See Also:</i> <a href="Molecule.html#insert_pi_anchor">Molecule#insert_pi_anchor</a>
1172+If the molecule does not contain MO information, raises exception.
10561173 </p>
1057-</div>
1058-</div>
1059-
1060-<div id="method-M000242" class="method-detail">
1061-<a name="count_pi_anchor_constructs"></a>
1062-<div class="method-heading">
1063-<span class="method-name">count_pi_anchor_constructs(IntGroup) &rarr; Integer
1064-</span>
1065-</div>
1066-<div class="method-description">
10671174 <p>
1068-Returns the number of defined pi-anchor constructs.
1175+<i>See Also:</i> <a href="#clear_surface">Molecule#clear_surface</a>, <a href="#set_surface_attr">Molecule#set_surface_attr</a>
10691176 </p>
10701177 </div>
10711178 </div>
1072--->
10731179
10741180 <div id="method-M000318" class="method-detail">
10751181 <a name="M000318"></a>
@@ -1532,8 +1638,7 @@ Get the atom attribute for the specified atom. Equivalent to <a href="Molecule.h
15321638 <div id="method-get_bond_order" class="method-detail">
15331639 <a name="get_bond_order"></a>
15341640 <div class="method-heading">
1535-<span class="method-name">
1536-get_bond_order(idx) &rarr; Float <br />
1641+<span class="method-name">get_bond_order(idx) &rarr; Float <br />
15371642 get_bond_orders(group) &rarr; Array
15381643 </span>
15391644 </div>
@@ -1559,6 +1664,78 @@ Copy the coordinates from the specified frame. If group is specified, then only
15591664 </div>
15601665 </div>
15611666
1667+<div id="method-get_graphic_color" class="method-detail">
1668+<a name="get_graphic_color"></a>
1669+<div class="method-heading">
1670+<span class="method-name">get_graphic_color(graphic_index) &rarr; value<br />
1671+</span>
1672+</div>
1673+<div class="method-description">
1674+<p>
1675+Get the color of graphic_index-th graphic object.</p>
1676+</div>
1677+</div>
1678+
1679+<div id="method-get_graphic_point" class="method-detail">
1680+<a name="get_graphic_point"></a>
1681+<div class="method-heading">
1682+<span class="method-name">get_graphic_point(graphic_index, point_index) &rarr; value
1683+get_graphic_points(graphic_index) &rarr; values
1684+</span>
1685+</div>
1686+<div class="method-description">
1687+<p>
1688+Get the point_index-th (or all) control point(s) of graphic_index-th graphic object.
1689+</p>
1690+</div>
1691+</div>
1692+
1693+<div id="method-get_mo_coefficients" class="method-detail">
1694+<a name="get_mo_coefficients"></a>
1695+<div class="method-heading">
1696+<span class="method-name">get_mo_coefficients(idx) &rarr; Array<br />
1697+</span>
1698+</div>
1699+<div class="method-description">
1700+<p>
1701+Get an array of MO coefficients for the given MO index (1-based).
1702+</p>
1703+</div>
1704+</div>
1705+
1706+<div id="method-get_mo_energy" class="method-detail">
1707+<a name="get_mo_energy"></a>
1708+<div class="method-heading">
1709+<span class="method-name">get_mo_energy(idx) &rarr; Float<br />
1710+</span>
1711+</div>
1712+<div class="method-description">
1713+<p>
1714+Get an array of MO coefficients for the given MO index (1-based).
1715+</p>
1716+</div>
1717+</div>
1718+
1719+<div id="method-get_property" class="method-detail">
1720+<a name="get_property"></a>
1721+<div class="method-heading">
1722+<span class="method-name">get_property(name[, index]) &rarr; value<br />
1723+get_property(name, group) &rarr; Array
1724+</span>
1725+</div>
1726+<div class="method-description">
1727+<p>
1728+Get molecular property. In the first form, a property value for a single frame is returned.
1729+(If index is omitted, then the value for the current frame is given)
1730+In the second form, an array of property values for the given frames is returned.
1731+If name is not one of known properties or a valid index integer, exception is raised.
1732+</p>
1733+<p>
1734+<i>See Also:</i> <a href="Molecule.html#property_names">Molecule#property_names</a>, <a href="Molecule.html#set_property">Molecule#set_property</a>
1735+</p>
1736+</div>
1737+</div>
1738+
15621739 <div id="method-get_view_center" class="method-detail">
15631740 <a name="get_view_center"></a>
15641741 <div class="method-heading">
@@ -1628,6 +1805,17 @@ Unset the visibility flag of the graphic_index-th graphic object.
16281805 </p></div>
16291806 </div>
16301807
1808+<div id="method-hide_surface" class="method-detail">
1809+<a name="hide_surface"></a>
1810+<div class="method-heading">
1811+<span class="method-name">hide_surface &rarr; self</span>
1812+</div>
1813+<div class="method-description">
1814+<p>
1815+Hide the MO surface if present.
1816+</p>
1817+</div>
1818+
16311819 <div id="method-M000215" class="method-detail">
16321820 <a name="M000215"></a>
16331821 <div class="method-heading">
@@ -1646,8 +1834,8 @@ improper is represented by an array of four atom indices.
16461834 </div>
16471835 </div>
16481836
1649-<div id="method-M000269" class="method-detail">
1650-<a name="M000269"></a>
1837+<div id="method-insert_frame" class="method-detail">
1838+<a name="insert_frame"></a>
16511839 <div class="method-heading">
16521840 <span class="method-name">insert_frame(integer, coordinates = nil) &rarr; <a href="IntGroup.html">IntGroup</a><br />
16531841 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
16621850 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
16631851 the inserted frames if successful, nil if not.
16641852 </p>
1853+<p>
1854+<i>See Also:</i> <a href="#create_frame">Molecule#create_frame</a>,
1855+<a href="#remove_frames">Molecule#remove_frames</a>
1856+</p>
16651857 </div>
16661858 </div>
16671859
1668-<!--
1669-<div id="method-M000242" class="method-detail">
1670-<a name="insert_pi_anchor"></a>
1860+<div id="method-insert_graphic" class="method-detail">
1861+<a name="insert_graphic"></a>
16711862 <div class="method-heading">
1672-<span class="method-name">insert_pi_anchor(index, name, type, group [, weights]) &rarr; index<br />
1863+<span class="method-name">insert_graphic(index, kind, color, points, fill = nil) &rarr; integer<br />
16731864 </span>
16741865 </div>
16751866 <div class="method-description">
16761867 <p>
1677-Create a "pi anchor", which is an anchor point to define a metal-pi bond, and insert at the given index.
1678-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.
1679-Name and type are Strings, and are similar to those in atoms.
1680-Group is a group of atoms to define a pi system to be bound to the metal.
1681-Weights (optional) is an Array of Floats, which determine the significance
1682-of the component atoms. If not given, then 1.0/N (N is the number of atoms
1683-in the group) is assumed for all atoms. This operation is undoable.
1868+Create a new graphic object and insert at the given graphic index (if -1, then append at the last).
1869+The meaning of the other arguments are the same as <a href="#create_graphic">Molecule#create_graphic</a>.
16841870 </p>
16851871 </div>
16861872 </div>
1687--->
16881873
16891874 <div id="method-M000210" class="method-detail">
16901875 <a name="M000210"></a>
@@ -1744,6 +1929,18 @@ given, the current flag is returned.
17441929 </div>
17451930 </div>
17461931
1932+<div id="method-loadcif" class="method-detail">
1933+<a name="loadcif"></a>
1934+<div class="method-heading">
1935+<span class="method-name">loadcif(filename) &rarr; bool</span>
1936+</div>
1937+<div class="method-description">
1938+<p>
1939+Load a molecule from a CIF (crystal information file) file.
1940+</p>
1941+</div>
1942+</div>
1943+
17471944 <div id="method-M000136" class="method-detail">
17481945 <a name="M000136"></a>
17491946 <div class="method-heading">
@@ -2335,38 +2532,45 @@ If the molecule has no associated document, then returns nil.
23352532 </div>
23362533 </div>
23372534
2338-<!--
2339-<div id="method-M000242" class="method-detail">
2340-<a name="pi_anchor"></a>
2535+<div id="method-plane" class="method-detail">
2536+<a name="plane"></a>
23412537 <div class="method-heading">
2342-<span class="method-name">pi_anchor(index) &rarr; nil or [name, type, group, weights]<br />
2538+<span class="method-name">plane(group) &rarr; Molby::Plane<br />
23432539 </span>
23442540 </div>
23452541 <div class="method-description">
23462542 <p>
2347-Return the attributes of the idx-th pi anchor if present, otherwise nil.
2543+Calculate best-fit plane for the given atoms. Returns a value of "Molby::Plane" type.
23482544 </p>
23492545 <p>
2350-<i>See Also:</i> <a href="Molecule.html#insert_pi_anchor">Molecule#insert_pi_anchor</a>
2546+Molby::Plane object has the following methods:
23512547 </p>
2548+<ul>
2549+<li>inspect: returns a String describing the internal info.</li>
2550+<li>coeffs: an Array of coefficients [a, b, c, d].</li>
2551+<li>sigma: an Array of the standard deviations of the coefficients.</li>
2552+<li>distance: a distance and its standard deviation from the given atom (AtomRef) or a point (Vector3D).</li>
2553+<li>dihedral: a dihedral angle its standard deviation between this plane and another plane.</li>
2554+</ul>
23522555 </div>
23532556 </div>
2354--->
23552557
2356-<!--
2357-<div id="method-M000242" class="method-detail">
2358-<a name="pi_anchor_construct"></a>
2558+<div id="method-property_names" class="method-detail">
2559+<a name="property_names"></a>
23592560 <div class="method-heading">
2360-<span class="method-name">pi_anchor_construct(index) &rarr; Array of Integers
2561+<span class="method-name">property_names &rarr; Array<br />
23612562 </span>
23622563 </div>
23632564 <div class="method-description">
23642565 <p>
2365-Returns the elements representing the index-th pi anchor constructs.
2566+Get an array of property names
2567+</p>
2568+<p>
2569+<i>See Also:</i> <a href="Molecule.html#get_property">Molecule#get_property</a>, <a href="Molecule.html#set_property">Molecule#set_property</a>
23662570 </p>
23672571 </div>
23682572 </div>
2369--->
2573+
23702574
23712575 <div id="method-M000226" class="method-detail">
23722576 <a name="M000226"></a>
@@ -2513,6 +2717,23 @@ If the given group corrensponds to all frames, then the current frame is retaine
25132717 </div>
25142718 </div>
25152719
2720+<div id="method-remove_frames" class="method-detail">
2721+<a name="remove_frames"></a>
2722+<div class="method-heading">
2723+<span class="method-name">remove_frames(IntGroup, wantCoordinates = false)<br />
2724+</span>
2725+</div>
2726+<div class="method-description">
2727+<p>
2728+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.
2729+</p>
2730+<p>
2731+<i>See Also:</i> <a href="Molecule.html#create_frame">Molecule#create_frame</a>,
2732+<a href="Molecule.html#insert_frame">Molecule#insert_frame</a>
2733+</p>
2734+</div>
2735+</div>
2736+
25162737 <div id="method-remove_graphic" class="method-detail">
25172738 <a name="remove_graphic"></a>
25182739 <div class="method-heading">
@@ -2545,38 +2766,6 @@ This operation is undoable.
25452766 </div>
25462767 </div>
25472768
2548-<!--
2549-<div id="method-M000242" class="method-detail">
2550-<a name="remove_pi_anchor"></a>
2551-<div class="method-heading">
2552-<span class="method-name">remove_pi_anchor(index) &rarr; self<br />
2553-</span>
2554-</div>
2555-<div class="method-description">
2556-<p>
2557-Remove an existing "pi anchor". The bonds, angles, and dihedrals containing the pi anchor are also remove. This operation is undoable.
2558-</p>
2559-<p>
2560-<i>See Also:</i> <a href="Molecule.html#insert_pi_anchor">Molecule#insert_pi_anchor</a>
2561-</p>
2562-</div>
2563-</div>
2564-
2565-<div id="method-M000242" class="method-detail">
2566-<a name="remove_pi_anchor_constructs"></a>
2567-<div class="method-heading">
2568-<span class="method-name">remove_pi_anchor_constructs(IntGroup) &rarr; self <br />
2569-remove_pi_anchor_construct(IntGroup)
2570-</span>
2571-</div>
2572-<div class="method-description">
2573-<p>
2574-Remove pi anchor constructs (bond, angle, dihedral) with indices specified in IntGroup.
2575-This operation is undoable.
2576-</p>
2577-</div>
2578-</div>
2579--->
25802769
25812770 <div id="method-M000243" class="method-detail">
25822771 <a name="M000243"></a>
@@ -2609,20 +2798,18 @@ operation is undoable.
26092798 </div>
26102799 </div>
26112800
2612-<!--
2613-<div id="method-M000242" class="method-detail">
2614-<a name="replace_pi_anchor"></a>
2801+<div id="method-reorder_frames" class="method-detail">
2802+<a name="reorder_frames"></a>
26152803 <div class="method-heading">
2616-<span class="method-name">replace_pi_anchor(index, name, type, group [, weights]) &rarr; index<br />
2804+<span class="method-name">reorder_frames(old_indices) &rarr; self<br />
26172805 </span>
26182806 </div>
26192807 <div class="method-description">
26202808 <p>
2621-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.
2809+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.
26222810 </p>
26232811 </div>
26242812 </div>
2625--->
26262813
26272814 <div id="method-M000216" class="method-detail">
26282815 <a name="M000216"></a>
@@ -2815,6 +3002,18 @@ Returns an array of integers of size natoms, each entry designates the equivalen
28153002 </div>
28163003 </div>
28173004
3005+<div id="method-select_frame" class="method-detail">
3006+<a name="select_frame"></a>
3007+<div class="method-heading">
3008+<span class="method-name">select_frame(index) &rarr; bool<br />
3009+</span>
3010+</div>
3011+<div class="method-description">
3012+<p>
3013+Select the specified frame. If successful, returns true, otherwise returns false.</p>
3014+</div>
3015+</div>
3016+
28183017 <div id="method-M000316" class="method-detail">
28193018 <a name="M000316"></a>
28203019 <div class="method-heading">
@@ -2946,6 +3145,38 @@ Set the name of an untitled molecule. This method requires that the molecule is
29463145 </div>
29473146 </div>
29483147
3148+<div id="method-set_property" class="method-detail">
3149+<a name="set_property"></a>
3150+<div class="method-heading">
3151+<span class="method-name">set_property(name, value[, index]) &rarr; value<br />
3152+set_property(name, values, group) &rarr; values</span>
3153+</div>
3154+<div class="method-description">
3155+<p>
3156+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.
3157+</p>
3158+<p>
3159+<i>See Also:</i> <a href="#get_property">Molecule#get_property</a>,
3160+<a href="#property_names">Molecule#property_names</a>
3161+</p>
3162+</div>
3163+</div>
3164+
3165+<div id="method-set_surface_attr" class="method-detail">
3166+<a name="set_surface_attr"></a>
3167+<div class="method-heading">
3168+<span class="method-name">set_surface_attr(attr = nil) &rarr; self</span>
3169+</div>
3170+<div class="method-description">
3171+<p>
3172+Set the drawing attributes of the surface. Attr is a hash containing the attributes.
3173+</p>
3174+<p>
3175+<i>See Also:</i> <a href="#create_surface">Molecule#create_surface</a>, <a href="#clear_surface">Molecule#clear_surface</a>
3176+</p>
3177+</div>
3178+</div>
3179+
29493180 <div id="method-M000264" class="method-detail">
29503181 <a name="M000264"></a>
29513182 <div class="method-heading">
--- a/MolLib/Ruby_bind/ruby_bind.c
+++ b/MolLib/Ruby_bind/ruby_bind.c
@@ -5446,7 +5446,7 @@ s_Molecule_ErrorMessage(VALUE klass)
54465446 * set_error_message(String)
54475447 * Molecule.error_message = String
54485448 *
5449- * Get the error_message from the last load/save method. If no error, returns nil.
5449+ * Set the error_message for the present load/save method.
54505450 */
54515451 static VALUE
54525452 s_Molecule_SetErrorMessage(VALUE klass, VALUE sval)
--- a/Scripts/crystal.rb
+++ b/Scripts/crystal.rb
@@ -443,6 +443,9 @@ class Molby::Plane
443443 @metric_tensor = met
444444 self
445445 end
446+ def coeffs
447+ [@coeff.x, @coeff.x, @coeff.z, @const]
448+ end
446449 def sigma
447450 [sqrt_safe(@error_matrix[0, 0]), sqrt_safe(@error_matrix[1, 1]), sqrt_safe(@error_matrix[2, 2]), sqrt_safe(@error_matrix[3, 3])]
448451 end
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
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