aboutsummaryrefslogtreecommitdiff
path: root/app/static/ketcher/doc/help.html
blob: 9f800fa1054d29c5e97c26003b49d4f4c6cbc397 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
<!DOCTYPE html><p><strong>Ketcher</strong> is a tool to draw molecular structures and chemical
reactions.</p>
<h1>Ketcher Overview</h1>
<p><strong>Ketcher</strong> is a tool to draw molecular structures and chemical
reactions. Ketcher operates in two modes, the Server mode with most
functions available and the client mode with limited functions
available.</p>
<p><strong>Ketcher</strong> consists of the following elements:</p>
<p><img src="main.png" alt="" title="Main window"></p>
<p><strong>Note</strong> : Depending on the screen size, some tools on the <em>Tool
palette</em> can be displayed in expanded or collapsed forms.</p>
<p>Using the <em>Tool palette</em>, you can</p>
<ul>
<li>
<p>draw and edit a molecule or reaction by clicking on and dragging
atoms, bonds, and other elements provided with the buttons on the
<em>Atoms</em> toolbar and <em>Tool palette</em>;</p>
</li>
<li>
<p>delete any element of the drawing (atom or bond) by clicking on it
with the Erase tool;</p>
</li>
<li>
<p>delete the entire molecule or its fragment by a lasso,
rectangular, or fragment selection with the Erase tool;</p>
</li>
<li>
<p>draw special structures (see the following sections);</p>
</li>
<li>
<p>select the entire molecule or its fragment in one of the following
ways (click on the button to see the list of available options):</p>
<ul>
<li>
<p>in the expanded form</p>
<p><img src="expanded.png" alt="" title="Expanded tool"></p>
</li>
<li>
<p>in the collapsed form</p>
<p><img src="collapsed.png" alt="" title="Collapsed tool"></p>
</li>
</ul>
</li>
</ul>
<p>To select one atom or bond, click Lasso or Rectangle Selection tool,
and then click the atom or bond.</p>
<p>To select the entire structure:</p>
<ul>
<li>
<p>Select the Fragment Selection tool and then click the object.</p>
</li>
<li>
<p>Select the Lasso or Rectangle Selection tool, and then drag the
mouse to select the object.</p>
</li>
<li>
<p><code>Ctrl-click</code> with the Lasso or Rectangle Selection tool.</p>
</li>
</ul>
<p>To select multiple atoms, bonds, structures, or other objects, do one
of the following:</p>
<ul>
<li>
<p><code>Shift-click</code> with the Lasso or Rectangle Selection tool selects
some (connected or not) atoms/bonds.</p>
</li>
<li>
<p>With the Lasso or Rectangle Selection tool click and drag the
mouse around the atoms, bonds, or structures that you want to
select.</p>
</li>
</ul>
<p><strong>Note</strong> : <code>Ctrl+Shift-click</code> with the Lasso or Rectangle Selection tool
selects several structures.</p>
<p>You can use the buttons of the <em>Main</em> toolbar:</p>
<p><img src="toolbar.png" alt="" title="Tolbar"></p>
<ul>
<li>
<p><strong>Clear Canvas</strong> (1) button to start drawing a new molecule; this
command clears the drawing area;</p>
</li>
<li>
<p><strong>Open…</strong> (2) and <strong>Save As…</strong> (3) buttons to import a molecule
from a molecular file or save it to a supported molecular file
format;</p>
</li>
<li>
<p><strong>Undo</strong> / <strong>Redo</strong> (4), <strong>Cut</strong> (5), <strong>Copy</strong> (6), <strong>Paste</strong> (7),
<strong>Zoom In</strong> / <strong>Out</strong> (8), and <strong>Scaling</strong> (9) buttons to perform
the corresponding actions;</p>
</li>
<li>
<p><strong>Layout</strong> button (10) to change the position of the structure to
work with it with the most convenience;</p>
</li>
<li>
<p><strong>Clean Up</strong> button (11) to improve the appearance of the
structure by assigning them uniform bond lengths and angles.</p>
</li>
<li>
<p><strong>Aromatize</strong> / <strong>Dearomatize</strong> buttons (12) to mark aromatic
structures (to convert a structure to the Aromatic or Kekule
presentation);</p>
</li>
<li>
<p><strong>Calculate CIP</strong> button (13) to determine R/S and E/Z
configurations;</p>
</li>
<li>
<p><strong>Check Structure</strong> button (14) to check the following properties
of the structure:</p>
<p><img src="check.png" alt="" title="Structure Ckeck"></p>
</li>
<li>
<p><strong>Calculated Values</strong> button (15) to display some properties of
the structure:</p>
<p><img src="analyse.png" alt="" title="Calculated Values"></p>
</li>
<li>
<p><strong>Recognize Molecule</strong> button (16) to recognize a structure in the
image file and load it to the canvas;</p>
</li>
<li>
<p><strong>3D Viewer</strong> button (17) to open the structure in the
three-dimensional Viewer;</p>
</li>
<li>
<p><strong>Settings</strong> button (18) to make some settings for molecular
files:</p>
<p><img src="settings.png" alt="" title="Settings"></p>
</li>
<li>
<p><strong>Help</strong> button (19) to view Help;</p>
</li>
<li>
<p><strong>About</strong> button (20) to display version and copyright information
of the program.</p>
</li>
</ul>
<p><strong>Note</strong> : <strong>Layout,</strong> <strong>Clean Up,</strong> <strong>Aromatize</strong> / <strong>Dearomatize,</strong>
<strong>Calculate CIP,</strong> <strong>Check Structure,</strong> <strong>Calculated Values,</strong>
<strong>Recognize Molecule</strong> and <strong>3D View</strong> buttons are active only in the
Server mode.</p>
<h1>3D Viewer</h1>
<p>The structure appears in a modal window after clicking on the <strong>3D
Viewer</strong> button:</p>
<p><img src="miew.png" alt="" title="3D Viewer"></p>
<p>You can perform the following actions:</p>
<ul>
<li>
<p>Rotate the structure holding the left mouse button;</p>
</li>
<li>
<p>Zoom In/Out the structure;</p>
</li>
</ul>
<p>Ketcher Settings allow to change the appearance of the structure and background coloring.</p>
<p>“Lines” drawing method, “Bright” atom name coloring
method and “Light” background coloring are default.</p>
<h1>Drawing Atoms</h1>
<p>To draw/edit atoms you can:</p>
<ul>
<li>
<p>select an atom in the Atoms toolbar and click inside the drawing
area;</p>
</li>
<li>
<p>if the desired atom is absent in the toolbar, click on
the <img src="periodic-table.png" alt=""> button to invoke the Periodic Table and
click on the desired atom (available options: <em>Single</em> – selection
of a single atom, <em>List</em> – choose an atom from the list of selected
options (To allow one atom from a list of atoms of your choice at
that position), <em>Not List</em> - exclude any atom on your list at that
position).</p>
<p><img src="periodic-dialog.png" alt="" title="Periodic Table"></p>
</li>
<li>
<p>add an atom to the existing molecule by selecting an atom in the
<em>Atoms</em> toolbar, clicking on an atom in the molecule, and dragging
the cursor; the atom will be added with a single bond; vacant
valences will be filled with the corresponding number of hydrogen
atoms;</p>
</li>
<li>
<p>change an atom by selecting an atom in the <em>Atoms</em> toolbar and
clicking on the atom to be changed; in the case a wrong valence thus
appears the atom will be underlined in red;</p>
</li>
<li>
<p>change an atom by clicking on an existing atom with the
<em>Selection</em> tool and waiting for a couple of seconds for the text
box to appear; type another atom symbol in the text box:</p>
<p><img src="inline-edit.png" alt="" title="Change Atom"></p>
</li>
<li>
<p>change the charge of an atom by selecting the Charge Plus or
Charge Minus tool and clicking consecutively on an atom to
increase/decrease its charge</p>
<p><img src="charge.png" alt="" title="Ions"></p>
</li>
<li>
<p>change an atom or its properties by double-clicking on the atom to
invoke the Atom Properties dialog (the dialog also provides atom
query features):</p>
<p><img src="atom-dialog.png" alt="" title="Atom Properties"></p>
</li>
<li>
<p>click on the Periodic Table button, open the Extended table and
select a corresponding Generic group or Special Node:</p>
<p><img src="periodic-dialog-ext.png" alt="" title="Generic Groups"></p>
</li>
</ul>
<h1>Drawing Bonds</h1>
<p>To draw/edit bonds you can:</p>
<ul>
<li>
<p>Click an arrow on the Bond tool <img src="bond.png" alt=""> in the Tools palette
to open the drop-down list with the following bond types:</p>
<p><img src="bonds.png" alt=""></p>
<p>For the full screen format, the Bond tool from the Tools palette
splits into three: _Single Bond,_<em>Single Up Bond,</em> and <em>Any
Bond</em>,which include the corresponding bond types:</p>
<p><img src="bond-types.png" alt=""></p>
</li>
<li>
<p>select a bond type from the drop down list and click inside the
drawing area; a bond of the selected type will be drawn;</p>
</li>
<li>
<p>click on an atom in the molecule; a bond of the selected type will
be added to the atom at the angle of 120 degrees;</p>
</li>
<li>
<p>add a bond to the existing molecule by clicking on an atom in the
molecule and dragging the cursor; in this case you can set the angle
manually;</p>
</li>
<li>
<p>change the bond type by clicking on it;</p>
</li>
<li>
<p>use the Chain Tool <img src="chain.png" alt=""> to draw consecutive single
bonds;</p>
</li>
<li>
<p>change a bond or its properties by double-clicking on the bond to
invoke the Bond Properties dialog:</p>
<p><img src="bond-dialog.png" alt="" title="Bond Properties"></p>
</li>
<li>
<p>clicking on a drawn stereo bond changes its direction.</p>
</li>
<li>
<p>clicking with the Single Bond tool or Chain tool switches the bond type
cyclically: Single-Double-Triple-Single.</p>
</li>
</ul>
<h1>Drawing R-Groups</h1>
<p>Use the <em>R-Group</em> toolbox <img src="rgroup.png" alt=""> to draw R-groups in Markush
structures:</p>
<p><img src="rgroup-types.png" alt=""></p>
<p>Selecting the <em>R-Group</em> <em>Label</em> Tool and clicking on an atom in the
structure invokes the dialog to select the R-Group label for a current
atom position in the structure:</p>
<p><img src="rgroup-dialog.png" alt=""></p>
<p>Selecting the R-Group label and clicking <strong>OK</strong> converts the structure
into a Markush structure with the selected R-Group label:</p>
<p><img src="rgroup-example1.png" alt=""></p>
<p><strong>Note</strong> : You can choose several R-Group labels simultaneously:</p>
<p><img src="rgroup-example2.png" alt=""></p>
<p>Particular chemical fragments that may be substituted for a given
R-Group form a set of R-Group members. R-Group members can be any
structural fragment, including functional groups and single atoms or
atom lists.</p>
<p>To create a set of R-Group members:</p>
<ol>
<li>
<p>Draw a structure to become an R-Group member.</p>
</li>
<li>
<p>Select the structure using the <em>R-Group Fragment Tool</em> to invoke
the R-Group dialog; in this dialog select the label of the
R-Group to assign the fragment to.</p>
</li>
<li>
<p>Click on <strong>OK</strong> to convert the structure into an R-Group member.</p>
</li>
</ol>
<p>An R-Group attachment point is the atom in an R-Group member fragment
that attaches the fragment to the initial Markush structure.</p>
<p>Selecting the <em>Attachment Point Tool</em> and clicking on an atom in the
R-Group fragment converts this atom into an attachment point. If the
R-Group contains more than one attachment point, you can specify one
of them as primary and the other as secondary. You can select between
either the primary or secondary attachment point using the dialog that
appears after clicking on the atom:</p>
<p><img src="attpoints-dialog.png" alt=""></p>
<p>If there are two attachment points on an R-Group member, there must be
two corresponding attachments (bonds) to the R-Group atom that has the
same R-Group label. Clicking on <strong>OK</strong> in the above dialog creates the
attachment point.</p>
<p>Schematically, the entire process of the R-Group member creation can
be presented as:</p>
<p><img src="rgroup-example3.png" alt=""></p>
<p><img src="rgroup-example4.png" alt=""></p>
<h1>R-Group Logic</h1>
<p><strong>Ketcher</strong> enables one to add logic when using R-Groups. To access
the R-Group logic:</p>
<ol>
<li>
<p>Create an R-Group member fragment as described above.</p>
</li>
<li>
<p>Move the cursor over the entire fragment for the green frame to
appear, then click inside the fragment. The following dialog
appears:</p>
<p><img src="rlogic-dialog.png" alt=""></p>
</li>
<li>
<p>Specify <strong>Occurrence</strong> to define how many of an R-Group
occurs. If an R-Group atom appears several times in the initial
structure, you will specify <strong>Occurrence</strong>&quot;&gt;n&quot;, n
being the number of occurrences; if it appears once, you see
&quot;R1 &gt; 0&quot;.</p>
</li>
<li>
<p>Specify H at <strong>unoccupied</strong> R-Group sites ( <strong>RestH</strong> ): check or
clear the checkbox.</p>
</li>
<li>
<p>Specify the logical <strong>Condition</strong>. Use the R-Group condition <strong>If
R(i) Then</strong> to specify whether the presence of an R-Group is
dependent on the presence of another R-Group.</p>
</li>
</ol>
<h1>Marking S-Groups</h1>
<p>To mark S-Groups, use the <em>S-Group tool</em> <img src="sgroup.png" alt=""> and the
following dialog that appears after selecting a fragment with this
tool:</p>
<p><img src="sgroup-dialog.png" alt="" title="S-Group Dialog"></p>
<p>Available S-Group types:</p>
<p><em>Generic</em></p>
<p>Generic is a pair of brackets without any labels.</p>
<p><em>Multiple group</em></p>
<p>A Multiple group indicates a number of replications of a fragment or a part of a
structure in contracted form.</p>
<p><em>SRU Polymer</em></p>
<p>The Structural Repeating Unit (SRU) brackets enclose the structural
repeating of a polymer. You have three available patterns:
head-to-tail (the default), head-to-head, and either/unknown.</p>
<p><em>Superatom</em></p>
<p>An abbreviated structure (abbreviation) is all or part of a structure
(molecule or reaction component) that has been abbreviated to a text
label. Structures that you abbreviate keep their chemical
significance, but their underlying structure is hidden. The current
version can't display contracted structures but correctly
saves/reads them into/from files.</p>
<h1>Data S-Groups</h1>
<p>The <em>Data S-Groups Tool</em> <img src="sdata.png" alt=""> is a separate tool for
comfortable use with the accustomed set of descriptors (like Attached
Data in <strong>Marvin</strong> Editor).</p>
<p>You can attach data to an atom, a fragment, a single bond, or a
group. The defined set of <em>Names</em> and <em>Values</em> is introduced for each
type of selected elements:</p>
<p><img src="sdata-dialog.png" alt=""></p>
<ul>
<li>
<p>Select the appropriate S-Group Field Name.</p>
</li>
<li>
<p>Select or type the appropriate Field Value.</p>
</li>
<li>
<p>Labels can be specified as Absolute, Relative or Attached.</p>
</li>
</ul>
<h1>Changing Structure Display</h1>
<p>Use the <em>Flip/Rotate</em> tool <img src="transform.png" alt=""> to change the structure
display:</p>
<p><img src="transform-types.png" alt=""></p>
<p>For the full screen format, the <em>Flip/Rotate</em> tool is split into
separate buttons:</p>
<p><img src="rotate.png" alt=""></p>
<p><em>Rotate Tool</em></p>
<p>This tool allows rotating objects.</p>
<ul>
<li>If some objects are selected, the tool rotates the selected objects.</li>
<li>If no objects are selected, or all objects are selected, the tool rotates the whole canvas</li>
<li>The default rotation step is 15 degrees.</li>
<li>Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step</li>
</ul>
<p>Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.</p>
<p><em>Flip Tool</em></p>
<p>This tool flips the objects horizontally or vertically.</p>
<ul>
<li>If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally</li>
<li>If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally</li>
<li>If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically</li>
<li>If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically</li>
</ul>
<h1>Drawing Reactions</h1>
<p>To draw/edit reactions you can</p>
<ul>
<li>
<p>draw reagents and products as described above;</p>
</li>
<li>
<p>use options of the <em>Reaction Arrow Tool</em> <img src="reaction.png" alt=""> to draw an
arrow and pluses in the reaction equation and map same atoms in
reagents and products.</p>
<p><img src="reaction-types.png" alt=""></p>
</li>
</ul>
<p><strong>Note</strong> : Reaction Auto-Mapping Tool is available only in the Server
mode.</p>
<h1>Templates toolbar</h1>
<p>You can add templates (rings or other predefined structures) to the
structure using the <em>Templates</em> toolbar together with the <em>Custom
Templates</em> button located at the bottom:</p>
<p><img src="template.png" alt=""></p>
<p>To add a ring to the molecule, select a ring from the toolbar and
click inside the drawing area, or click on an atom or a bond in the
molecule.</p>
<p>Rules of using templates:</p>
<ul>
<li>
<p>Selecting a template and clicking on an atom in the existing
structure adds the template to the structure connected with a single
bond:</p>
<p><img src="template-example1.png" alt=""></p>
</li>
<li>
<p>Selecting a template and dragging the cursor from an atom in the
existing structure adds the template directly to this atom resulting
in the fused structure:</p>
<p><img src="template-example2.png" alt=""></p>
</li>
<li>
<p>Dragging the cursor from an atom in the existing structure results
in the single bond attachment if the cursor is dragged to more than
the bond length; otherwise the fused structure is drawn.</p>
</li>
<li>
<p>Selecting a template and clicking on a bond in the existing
structure created a bond-to-bond fused structure:</p>
<p><img src="template-example3.png" alt=""></p>
</li>
<li>
<p>The bond in the initial structure is replaced with the bond in the
template.</p>
</li>
<li>
<p>This procedure doesn't change the length of the bond in the
initial structure.</p>
</li>
<li>
<p>Dragging the cursor relative to the initial bond applies the
template at the corresponding side of the bond.</p>
</li>
</ul>
<p><strong>Note</strong> : The added template will be fused by the default attachment
atom or bond preset in the program.</p>
<p><strong>Note</strong> : User is able to define the attachment atom and bond by clicking
the Edit button for template structure.</p>
<p>The <em>Custom Templates</em> button <img src="template-lib.png" alt="">invokes the scrolling
list of templates available in the program; both built-in and created
by user:</p>
<p><img src="template-dialog.png" alt=""></p>
<p>To create a user template:</p>
<ul>
<li>draw a structure.</li>
<li>click the Save as button.</li>
<li>click the Save to Templates button.</li>
<li>enter a name and define the attachment atom and bond.</li>
</ul>
<h1>Working with Files</h1>
<p>Ketcher supports the following molecular formats that can be entered
either manually or from files:</p>
<ul>
<li>
<p>MDL Molfile or RXN file;</p>
</li>
<li>
<p>Daylight SMILES (Server mode only);</p>
</li>
<li>
<p>Daylight SMARTS (Server mode only);</p>
</li>
<li>
<p>InChi string (Server mode only);</p>
</li>
<li>
<p>CML file (Server mode only).</p>
</li>
</ul>
<p>You can use the <strong>Open…</strong> and <strong>Save As…</strong> buttons of the <em>Main</em>
toolbar to import a molecule from a molecular file or save it to a
supported molecular file format. The <em>Open Structure</em> dialog enables
one to either browse for a file (Server mode) or manually input, e.g.,
the Molfile ctable for the molecule to be imported:</p>
<p><img src="open.png" alt=""></p>
<p>The <em>Save Structure</em> dialog enables one to save the molecular file:</p>
<p><img src="save.png" alt=""></p>
<p><strong>Note</strong> : In the standalone version only mol/rxn are supported for
Open and mol/rxn/SMILES for Save.</p>
<h1>Hotkeys</h1>
<p>You can use keyboard hotkeys (including Numeric keypad) for some
features/commands of the Editor. To display the hotkeys just place the
cursor over a toolbar button. If a hotkey is available for the button,
it will appear in brackets after the description of the button.</p>
<table>
<thead>
<tr>
<th>Key</th>
<th>Action</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>Esc</code></td>
<td>Switching between the Lasso/Rectangle/Fragment Selection tools</td>
</tr>
<tr>
<td><code>Del</code></td>
<td>Delete the selected objects</td>
</tr>
<tr>
<td><code>0</code></td>
<td>Draw Any bond.</td>
</tr>
<tr>
<td><code>1</code></td>
<td>Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types.</td>
</tr>
<tr>
<td><code>2</code></td>
<td>Double / Double Cis/Trans bond</td>
</tr>
<tr>
<td><code>3</code></td>
<td>Draw a triple bond.</td>
</tr>
<tr>
<td><code>4</code></td>
<td>Draw an aromatic bond.</td>
</tr>
<tr>
<td><code>5</code></td>
<td>Charge Plus/Charge Minus</td>
</tr>
<tr>
<td><code>A</code></td>
<td>Draw any atom</td>
</tr>
<tr>
<td><code>H</code></td>
<td>Draw a hydrogen</td>
</tr>
<tr>
<td><code>C</code></td>
<td>Draw a carbon</td>
</tr>
<tr>
<td><code>N</code></td>
<td>Draw a nitrogen</td>
</tr>
<tr>
<td><code>O</code></td>
<td>Draw an oxygen</td>
</tr>
<tr>
<td><code>S</code></td>
<td>Draw a sulfur</td>
</tr>
<tr>
<td><code>F</code></td>
<td>Draw a fluorine</td>
</tr>
<tr>
<td><code>P</code></td>
<td>Draw a phosphorus</td>
</tr>
<tr>
<td><code>I</code></td>
<td>Draw an iodine</td>
</tr>
<tr>
<td><code>T</code></td>
<td>Basic templates. Consecutive pressing switches between different templates</td>
</tr>
<tr>
<td><code>Shift+t</code></td>
<td>Open template library</td>
</tr>
<tr>
<td><code>Alt+r</code></td>
<td>Rotate tool</td>
</tr>
<tr>
<td><code>Alt+v</code></td>
<td>Flip vertically</td>
</tr>
<tr>
<td><code>Alt+h</code></td>
<td>Flip horizontally</td>
</tr>
<tr>
<td><code>Ctrl+g</code></td>
<td>S-Group tool / Data S-Group tool</td>
</tr>
<tr>
<td><code>Ctrl+d</code></td>
<td>Align and select all S-Group data</td>
</tr>
<tr>
<td><code>Ctrl+r</code></td>
<td>Switching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool</td>
</tr>
<tr>
<td><code>Ctrl+Shift+r</code></td>
<td>R-Group Fragment Tool</td>
</tr>
<tr>
<td><code>Ctrl+Del</code></td>
<td>Clear canvas</td>
</tr>
<tr>
<td><code>Ctrl+o</code></td>
<td>Open</td>
</tr>
<tr>
<td><code>Ctrl+s</code></td>
<td>Save As</td>
</tr>
<tr>
<td><code>Ctrl+z</code></td>
<td>Undo</td>
</tr>
<tr>
<td><code>Ctrl+Shift+z</code></td>
<td>Redo</td>
</tr>
<tr>
<td><code>Ctrl+x</code></td>
<td>Cut selected objects</td>
</tr>
<tr>
<td><code>Ctrl+c</code></td>
<td>Copy selected objects</td>
</tr>
<tr>
<td><code>Ctrl+v</code></td>
<td>Paste selected objects</td>
</tr>
<tr>
<td><code>+</code></td>
<td>Zoom In</td>
</tr>
<tr>
<td><code>-</code></td>
<td>Zoom Out</td>
</tr>
<tr>
<td><code>Ctrl+l</code></td>
<td>Layout</td>
</tr>
<tr>
<td><code>Ctrl+Shift+l</code></td>
<td>Clean Up</td>
</tr>
<tr>
<td><code>Ctrl+p</code></td>
<td>Calculate CIP</td>
</tr>
<tr>
<td><code>?</code></td>
<td>Help</td>
</tr>
</tbody>
</table>
<p><strong>Note</strong> : Please, use <code>Ctrl+V</code> to paste the selected object in
Google Chrome and Mozilla Firefox browsers.</p>
<p><strong>Note 2</strong> : Probably, you have forbidden access to the local storage.
If you are using IE10 or IE11 and didn’t forbid access to local storage
intentionally, you can pay attention here: <a href="https://stackoverflow.com/a/20848924">https://stackoverflow.com/a/20848924</a></p>