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molby: Commit


Commit MetaInfo

Revision621 (tree)
Time2019-08-17 00:55:27
Authortoshinagata1964

Log Message

Ruby document is updated.

Change Summary

Incremental Difference

--- trunk/Documents/src/molby_rb/AtomRef.html (revision 620)
+++ trunk/Documents/src/molby_rb/AtomRef.html (revision 621)
@@ -75,8 +75,7 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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>
--- trunk/Documents/src/molby_rb/Molecule.html (revision 620)
+++ trunk/Documents/src/molby_rb/Molecule.html (revision 621)
@@ -81,8 +81,7 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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">
@@ -2335,39 +2532,46 @@
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
23662567 </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>
2570+</p>
23672571 </div>
23682572 </div>
2369--->
23702573
2574+
23712575 <div id="method-M000226" class="method-detail">
23722576 <a name="M000226"></a>
23732577 <div class="method-heading">
@@ -2513,6 +2717,23 @@
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">
@@ -2545,39 +2766,7 @@
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>
25642769
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--->
2580-
25812770 <div id="method-M000243" class="method-detail">
25822771 <a name="M000243"></a>
25832772 <div class="method-heading">
@@ -2609,20 +2798,18 @@
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 @@
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 @@
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">
--- trunk/MolLib/Ruby_bind/ruby_bind.c (revision 620)
+++ trunk/MolLib/Ruby_bind/ruby_bind.c (revision 621)
@@ -5446,7 +5446,7 @@
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)
--- trunk/Scripts/crystal.rb (revision 620)
+++ trunk/Scripts/crystal.rb (revision 621)
@@ -443,6 +443,9 @@
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
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