summaryrefslogtreecommitdiff
path: root/Master/texmf-dist/doc/latex/chemfig/chemfig_doc_en.tex
blob: 3b6b069ee053bda9b4352c460aed1cf2effd23c3 (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
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
%  _________________________________________________________________
% |                                                                 |
% |                                                                 |
% |                      ChemFig Documentation                      |
% |                                                                 |
% |                        November 21, 2010                        |
% |                                                                 |
% |_________________________________________________________________|
%
% This is chemfig_doc_en.tex, the LaTeX code of the chemfig English
% documentation. Translation by Theo Hopman (hopman.theo@gmail.com).
%
% Maintainer: Christian Tellechea
% E-mail    : unbonpetit@gmail.com
%             Comments, bug reports and suggestions are welcome.
% Licence   : Released under the LaTeX Project Public License v1.3c or
%             later, see http://www.latex-project.org/lppl.txt
% Copyright : Christian Tellechea 2010
%
% The "chemfig" package consists of the 6 following files:
%   chemfig.sty
%   README
%   chemfig_doc_en.tex, chemfig_doc_en.pdf (english manual)
%   chemfig_doc_fr.tex, chemfig_doc_fr.pdf (french manual)
%
% -------------------------------------------------------------------
% This work may be distributed and/or modified under the
% conditions of the LaTeX Project Public License, either version 1.3
% of this license or (at your option) any later version.
% The latest version of this license is in
%
%     http://www.latex-project.org/lppl.txt
%
% and version 1.3 or later is part of all distributions of LaTeX
% version 2005/12/01 or later.
% -------------------------------------------------------------------
% This work has the LPPL maintenance status `maintained'.
%
% The Current Maintainer of this work is Christian Tellechea
% -------------------------------------------------------------------
\documentclass[10pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage[a4paper,margin=2.5cm,head=5mm,headsep=5mm,footskip=10mm]{geometry}
\usepackage[bottom]{footmisc}
\usepackage{lmodern}
\usepackage{amsmath}
\usepackage{array}
\usepackage{xspace}
\usepackage{fancybox}
\usepackage{textcomp}
\usepackage{xstring}
\usepackage{enumitem}
\usepackage{chemfig}
\usetikzlibrary{decorations.pathmorphing}
\usepackage{emerald}
\usepackage[protrusion=true,expansion,final,babel=true]{microtype}
\usepackage{fancyhdr}
	\fancyhead[L]{\small\bfseries\CF}
	\fancyhead[C]{}
	\fancyhead[R]{\scriptsize\slshape \leftmark}
	\fancyfoot[l]{\tiny \LaTeX ed by Christian \textsc{Tellechea}, the \today.}
	\fancyfoot[c]{}
	\fancyfoot[r]{\thepage}

\makeatletter

\newcommand\disable@lig[1]{%
	\catcode`#1\active
	\begingroup
		\lccode`\~`#1\relax
		\lowercase{\endgroup\def~{\leavevmode\kern\z@\string#1}}%
}

\newif\if@exstar

\newcommand\exemple{\@ifstar{\@exstartrue\exemple@}{\@exstarfalse\exemple@}}

\newcommand\exemple@[2][65]{%
	\par\nobreak\vskip5pt
	\def\part@coeff{#1}%
	\def\code@name{#2}%
	\relax\leavevmode\null
	\bgroup
		\obeylines\frenchspacing
		\let\do\@makeother\dospecials
		\@makeother:%
		\@vobeyspaces
		\disable@lig,\disable@lig-%
		\exemple@@
}

\newcommand\exemple@@[1]{%
	\def\@tempa##1#1{%
		\xdef\left@content{##1}%
		\egroup
		\begingroup
			\endlinechar\m@ne\everyeof{\relax}\catcode`\^^M=10
			\@makeother:\@makeother~\@makeother!\@makeother?\@makeother;%
			\expandafter\grab@toks\scantokens{##1}%
		\endgroup
		\exemple@@@
		}%
	\@tempa
}

\begingroup
\catcode`#=12
\gdef\exemple@@@%
{%
	\begingroup
		\StrSubstitute\left@content{##}#[\left@content]%
		\if@exstar
			\edef\part@left{\the\dimexpr\linewidth-2\fboxsep-2\fboxrule}%
			\let\part@right\part@left
		\else
			\edef\part@left{\the\dimexpr0.\part@coeff\linewidth-\fboxsep-\fboxrule}%
			\edef\part@right{\the\dimexpr\linewidth-0.\part@coeff\linewidth-\fboxsep-\fboxrule}%
		\fi
		\edef\saved@boxsep{\the\fboxsep}%
		\fboxsep1pt\relax
		\boxput*(0,1)%
			{\colorbox{black}{{%
				\leavevmode\kern1.5pt\relax
				\color{white}\ECFAugie\footnotesize
				\vphantom{Cp}\code@name
				}\kern1.5pt\relax}}%
			{\fboxsep\saved@boxsep
			\fbox{%
				\if@exstar
					\parbox[c]\part@left{%
						\vskip5pt\relax\ttfamily\footnotesize\left@content
						\vskip3pt\hrule\vskip3pt
						\everypar{{\color{lightgray}\rlap{\vrule height0.1pt width\part@right depth0.1pt}}}%
						\par\normalfont
						\subst@in\right@content\par\def
						\subst@in\right@content\def{\hfill\null\par\hfill}%
						\hfill\right@content\hfill\null}%
				\else
					\parbox[c]\part@left{\vskip5pt\relax\ttfamily\footnotesize\left@content}%
					\parbox[c]\part@right{%
						\vskip5pt\relax
						\everypar{{\color{lightgray}\rlap{\vrule height0.1pt width\part@right depth0.1pt}}}%
						\normalfont\footnotesize
						\right@content}%
				\fi
				}%
			}%
		\vskip7.5pt\relax
	\endgroup
}
\endgroup

\long\def\if@instr#1#2{%
	\long\def\if@instr@i##1#2##2\@nil{\ifx\@empty##2\@empty\expandafter\@secondoftwo\else\expandafter\@firstoftwo\fi}%
	\if@instr@i#1\relax#2\@nil
}

\long\def\subst@in#1#2#3{%
	\long\def\subst@in@i##1#2##2\@nil{##1#3##2}%
	\expandafter\if@instr\expandafter{#1}{#2}%
		{\expandafter\expandafter\expandafter\def\expandafter\expandafter\expandafter#1\expandafter\expandafter\expandafter{\expandafter\subst@in@i#1\@nil}%
		\subst@in#1{#2}{#3}%
		}\relax
}

\long\def\grab@toks#1\relax{\gdef\right@content{#1}}

\newcommand\falseverb[1]{{\ttfamily\detokenize{#1}}}

\long\def\centerverb#1{%
	\def\centerverb@i##1#1{##1\hfill\null\par\egroup}
	\bgroup
		\ttfamily\@noligs
		\parskip3.5pt\par\hfill
		\let\do\@makeother\dospecials
		\@vobeyspaces
		\centerverb@i}
\makeatother

\usepackage[english]{babel}
\def\degres{\ensuremath{{}^\circ}}

\newcommand\CF{{\ECFAugie ChemFig}\xspace}
\newcommand\TIKZ{ti\textit kz\xspace}
\newcommand\molht[1]{\begingroup\parskip3.5pt\par\hfill\chemfig{#1}\hfill\null\par\endgroup}
\newcommand\boxednode[2]{\fbox{$\mathrm{#1}\vphantom{M_1}$}_{#2}}
\newcommand\boxedfalseverb[1]{{\fboxsep0pt\fbox{\vphantom|\falseverb{#1}}}}

\usepackage[plainpages=false,pdfpagelabels,bookmarks=true,bookmarksopen=true,colorlinks=true,hyperfootnotes=false,filecolor=black,linkcolor=blue,urlcolor=magenta,pdfauthor={Christian TELLECHEA},pdftitle={ChemFig},pdfsubject={Dessiner des molécules 2D avec LaTeX},pdfkeywords={ChemFig},pdfcreator={LaTeX}]{hyperref}

\csname @addtoreset\endcsname{section}{part}
\usepackage{titlesec}
\titleformat{\part}[display]
	{\normalfont\Large\filcenter\sffamily\bfseries}%
	{\LARGE\MakeUppercase{\partname~\thepart}}%
	{1pc}%
	{\titlerule\vspace{1pc}\Huge}

\newcommand*\nouveau[1][0pt]{\leavevmode\llap{\footnotesize\itshape\bfseries\color{red}New\kern\dimexpr15pt+#1\relax}}

\begin{document}
\begin{titlepage}
	\catcode`!12
	\begin{tikzpicture}[remember picture,overlay]
		\filldraw[blue!75](current page.south west) rectangle ([yshift=2cm,xshift=-3cm]current page.center);
		\shade [left color=blue!75,right color=white]([yshift=2cm,xshift=-3cm]current page.center) rectangle ([xshift=3cm]current page.south);
		\filldraw[black](current page.north west) rectangle ([yshift=7cm]current page.east);
		\shade[top color=black,bottom color=blue]([yshift=7cm]current page.east)rectangle([yshift=2.5cm]current page.west);
		\filldraw[black!55!blue!100]([yshift=2.5cm]current page.east)rectangle([yshift=2cm]current page.west);
	\end{tikzpicture}
	\begin{center}
		\color{white}\ECFAugie\fontsize{50pt}{50pt}\selectfont\CF\par
		\Large v\csname CF@ver\endcsname\par\bigskip
		\footnotesize\csname CF@en@date\endcsname\par
		\normalsize Christian Tellechea\par\vskip1.5cm
		\huge A \LaTeX{} package for drawing molecules%
	\end{center}
	\vskip4cm
	\begin{center}
		\scriptsize
		\setatomsep{3em}%
		\chemfig{-[::-30](-[5])(-[7])-[::+60]-[::-60]O-[::+60](=[::-45]O)-[::+90]HN>:[::-60](-[::+60]**6(------))-[::-30](<:[2]OH)-[::-60](=[6]O)-[::+60]O>:[::-60]*7(---?(<[::-120]OH)-(<|[1]CH_3)(<:[::-90]CH_3)-(-[1](<[::+80]HO)-[0](=[::+60]O)-[7](<|[::+130]CH_3)(-[::+75](<|[2]OH)-[::-60]-[::-60](<[::+30]O-[::-90])-[::-60](<[::+90])(<:[::+30]O-[7](-[6]CH_3)=[0]O)-[::-60])-[6]-[5,1.3]?(<:[7]O-[5](=[::-60]O)-[6]**6(------)))=(-[2]CH_3)-)}%
		\par
		{\ECFAugie\small Taxotere}%
	\end{center}
	\vskip1.5cm
	\hfill
	\hbox to 0pt{\hss
		\scriptsize
		\setbondoffset{1pt}
		\setatomsep{2em}
		\chemfig{(-[:-150]R')(-[:-30]R)=[2]N-[:30]OH}%
		\kern-1em
		\chemrel[\chemfig{\chemabove{H}{\kern10pt\oplus}}]{<>}%
		\kern-0.5em
		\chemfig{(-[@{a0}:-150]R')(-[:-30]R)=[2]@{a1}N-[@{b0}:30]@{b1}\chemabove{O}{\oplus}H_2}%
		\chemmove[red,-stealth,shorten <=2pt]{%
			\draw(a0)..controls +(135:2mm) and +(215:4mm).. (a1);
			\draw(b0)..controls +(120:2mm) and +(180:3mm).. ([yshift=7pt]b1.180);
		}
		\kern-1.5em
		\chemrel[\chemfig{{-}H_2O}]{<>}%
		$\left[\begin{tabular}{c}
		\chemfig{R'-N=@{a1}\chemabove{C}\oplus-R}\\
		\tikz\draw[stealth-stealth](0,3mm)--(0,-3mm);\\
		\chemfig{R'-\chemabove{N}\oplus~C-R}
		\end{tabular}\right]$%
		\chemrel[\chemfig{H_2@{a0}\lewis{0:2:,O}}]{<>}%
		\chemmove[red,-stealth,shorten <=3pt]{%
			\draw(a0)..controls+(90:10mm)and+(45:10mm)..([yshift=6pt]a1.45);
		}%
		\chemfig{*6(R\rlap{$'$}-N=(-R)-\chemabove{O}\oplus H_2)}%
		\chemrel[\chemfig{{-}\chemabove{H}{\kern10pt\oplus}}]{<>}%
		\chemfig{*6(R\rlap{$'$}-N=(-R)-OH)}%
		\chemrel{-stealth}%
		\chemfig{*6(R\rlap{$'$}-\chembelow{N}{H}-(-R)(=[2]O))}\par\bigskip
		\hss}\hfill\null
	\begin{center}
		\ECFAugie\small The Beckmann rearrangement%
	\end{center}
\end{titlepage}
\parindent0pt\pagestyle{fancy}
\tableofcontents
\parskip\medskipamount
\vspace{2cm}

\fbox{\vbox{\hsize\dimexpr\linewidth-2\fboxrule-2\fboxsep\relax\noindent\color{red}\bfseries The translation of the new features is not done yet, but should be available within a few weeks. The corresponding text, still in french, is gray in this manual. I apologize for the inconvenience.}}
\vspace{2cm}

\setitemize{leftmargin=3em,topsep=0pt,parsep=0pt,itemsep=0pt}
\part{Introduction}
\begingroup\color{gray}% !!! Nouveau
\section{Nouveautés de la version 0.3}
\nouveau Suite à des demandes d'utilisateurs et des lacunes qui devaient de toutes façons être comblées, voici les nouveautés de la version 0.3 :
\begin{enumerate}
	\item Amélioration de la commande \verb-\definesubmol- qui accepte les séquences de contrôle comme alias. On peut aussi choisir un alias dont la substitution est différente selon l'orientation de la liaison qui lui arrive dessus. Voir page~\pageref{definesubmol};
	\item Le caractère ``\verb-|-'' force la fin d'un atome. Si on écrit ``D|ef'' alors, \CF verra deux atomes ``D'' et ``ef''. Lire page~\pageref{decoupage.atomes};
	\item Le caractère ``\verb-#-'' est reconnu lorsqu'il suit un caractère de liaison. Il doit être suivi d'un argument entre parenthèses qui contient le retrait de début et de fin qui s'appliqueront à cette liaison. Voir page~\pageref{modif.retrait}.
	\item La macro \verb-\chemfig- admet des arguments optionnels qui seront passés à l'environnement ``tikzpicture'' dans lequel elle est dessinée. Lire page~\pageref{arguments.optionnels};
	\item Mise en place de la représentation des mouvement d'électrons et des mécanismes réactionnels avec la syntaxe ``\verb-@{<nom>}-'' devant un atome ou
	  ``\verb-@{<nom>,<coeff>}-'' au tout début de l'argument d'une liaison.\par
	  Cette syntaxe permet de placer un nœud (au sens de \TIKZ) qui deviendra l'extrémité des flèches dessinées. Le tracé des flèches est fait par la macro \verb-\chemmove- dont l'argument optionnel devient celui de l'environnement ``tikzpicture'' dans lequel sont faites les flèches. Lire page~\pageref{mecanismes-reactionnels};
	\item Pour le mécanisme d'alignement vertical des atomes sur une même horizontale, la commande \verb-\chemskipalign- permet d'ignorer ce mécanisme pour le groupe d'atomes dans lequel elle est écrite. Voir page~\pageref{chemskipalign};
	\item La commande \verb-\chemname- permet d'afficher un nom sous une molécule. La commande \verb-\chemnameinit- initialise l'alignement des noms. Lire page~\pageref{chemname};
	\item les dessins des décorations qu'effectue la commande \verb-\lewis- ont été améliorés;
	\item Corrections de bugs et optimisation du code.
\end{enumerate}
\endgroup% !!! fin

\section{Foreword}
This package has seen the light of day thanks to the assistance of Christophe \textsc{Casseau}, who had the idea after being confronted with the complexity of the syntax of the \href{http://www.ctan.org/tex-archive/help/Catalogue/entries/ppchtex.html}{\texttt{\textbf{ppchtex}}} package.

Throughout the writing of the code, he helped me find interesting features. He always encouraged me to write more advanced features even though I was sometimes (nearly always?) reluctant; if \CF has the features it does, it is in large part thanks to him. I thank him as well for his testing of beta versions of this package, and for his contributions to the writing of this manual.\medskip

\begingroup
\leftskip0.1\linewidth
\rightskip0.1\linewidth
\itshape\small
Experience shows that is it has been difficult to combine drawing of molecules with the typographic quality of a program like \LaTeX, leaving little choice for the user who wishes to have a vector format for these drawings. After having abandoned the \emph{ppchtex} package (developed for con\TeX t and available under \LaTeX) because of the complexity of its syntax, I turned to the world of programs outside \LaTeX. The difficulty in this case is finding a compromise between quality and price. After many unsuccessful attempts I found the only option was a new package, and I would like to thank Christian \textsc{Tellechea} for bringing it to life. To meet my requirements, \CF needed to be easy to use but still have advanced features, something well nigh impossible. Yet he was able to put together a very flexible \TeX{} code which makes it a pleasure for me to write my molecules. I hope it will be the same for you readers looking for a package useful in the field of chemistry.\smallskip

\hfill Christophe \textsc{Casseau}\kern0.1\linewidth
\endgroup\medskip

Finally, I wish to warmly thank Theo \textsc{Hopman} for offering to translate this manual into English.

\section{Presenting \CF}
To use this package, start by adding the following code to the preamble:
\centerverb/\usepackage{chemfig}/
\smallskip

The most important command for drawing molecules is \verb|\chemfig{<code>}|. The argument \verb|code| is a set of characters describing the structure of the molecule according to the rules which are described in this manual.

Care has been taken to make it possible to draw the greatest possible number of molecular configurations, while maintaining a simple, flexible, and intuitive syntax. Despite this, the \verb-<code>- which describes the 2D structure of the molecule increases in complexity in proportion to that of the molecule being drawn.

The command \verb|\chemfig| draws a molecule using the commands provided by the \TIKZ package, placed inside a \verb|tikzpicture| environment. The choice of \TIKZ implies that:
\begin{itemize}
\item the user has a choice of compilation method: pdf\LaTeX{} can be used equally well in dvi mode (tex $\longrightarrow$ dvi $\longrightarrow$ ps $\longrightarrow$ pdf) or in pdf mode (tex $\longrightarrow$ pdf). In effect \TIKZ, via the underlying pgf, gives identical graphical results in the two modes;
\item the bounding box is automatically calculated by \TIKZ and the user need not worry about any overlap with the text. However, care must be taken with alignment when the molecule is drawn in a paragraph. In the following example, we have drawn the bounding box for the molecule: {\fboxsep0pt \fbox{\chemfig{H_3C-C(-[:-30]OH)=[:30]O}}}. \CF always places the first atom of the molecule on the baseline of the preceding code.
\end{itemize}
\newpage

\part{\CF for the impatient}
This part is a non-exhaustive overview of the features of \CF. The goal is to introduce the basic ideas, allowing the user to get started drawing molecules as quickly as possible. This part does not go into detail; advanced use and a more formal approach to \CF commands will be discussed in the following parts.

\section{Syntax}
The command \verb|\chemfig| is used in the following way:
\centerverb/\chemfig{<atom1><bond type>[<angle>,<coeff>,<n1>,<n2>,<tikz code>]<atom2>}/

\begin{itemize}
\item \verb-<angle>- is the bond angle between the two atoms;
\item \verb-<coeff>- is a coefficient multiplying the default bond length;
\item \verb-<n1>- and \verb-<n2>- are the numbers of the departure and arrival atoms of the bond;
\item \verb-<tikz code>- is additional options concerning the colour or style of a bond.
\end{itemize}
\medskip
Each bond takes optional arguments which are placed in square brackets. These arguments can adjust everything one needs for the bond. Each argument has a default value, so one can simply write:
\exemple{The water molecule}|\chemfig{H-O-H}|

In all the examples, the grey line represents the baseline.

\section{The different types of bonds}
For \CF, bonds between two atoms are one of nine types, represented by the characters \boxedfalseverb-, \boxedfalseverb=, \boxedfalseverb~, \boxedfalseverb>, \boxedfalseverb<, \boxedfalseverb{>:}, \boxedfalseverb{<:}, \boxedfalseverb{>|} and \boxedfalseverb{<|} :\label{types.liaisons}
\begin{center}
\begin{tabular}{>{\centering\arraybackslash}m{1.7cm}>{\centering\arraybackslash}m{3cm}>{\centering\arraybackslash}m{2cm}m{4cm}}
\hline
Bond \#&Code                 &Result      &Bond type\\\hline
1            &\verb+\chemfig{A-B}+ &\chemfig{A-B} &Single\\
2            &\verb+\chemfig{A=B}+ &\chemfig{A=B} &Double\\
3            &\verb+\chemfig{A~B}+ &\chemfig{A~B} &Triple\\
4            &\verb+\chemfig{A>B}+ &\chemfig{A>B} &right Cram, plain\\
5            &\verb+\chemfig{A<B}+ &\chemfig{A<B} &left Cram, plain\\
6            &\verb+\chemfig{A>:B}+&\chemfig{A>:B}&right Cram, dashed\\
7            &\verb+\chemfig{A<:B}+&\chemfig{A<:B}&left Cram, dashed\\
8            &\verb+\chemfig{A>|B}+&\chemfig{A>|B}&right Cram, hollow\\
9            &\verb+\chemfig{A<|B}+&\chemfig{A<|B}&left Cram, hollow\\\hline
\end{tabular}
\end{center}
\label{setdoublesep}The command \verb-\setdoublesep{<dim>}- adjusts the spacing between the lines in double or triple bonds. This spacing is 2pt by default.

\section{Different types of diagrams}
\subsection{Complete structural diagram}
\exemple{Ethane}|\chemfig{C(-[2]H)(-[4]H)(-[6]H)-C(-[2]H)(-[6]H)-H}|

Each bond takes several optional arguments. The first optional argument defines the \verb-<angle>- of the bond. Angles increase counterclockwise. If no angle is give then its default value is 0\degres.

Note: the parentheses allow multiple bonds from the same atom; see ``Branched molecules'', page~\pageref{molecules.ramifiees}.

There are many ways of specifying the angle of a bond.
\begin{description}
\item[Predefined angles] When the optional argument contains a whole number, this represents the angle that the bond makes with the horizontal, in multiples of 45\degres.

\exemple{Predefined angles}|\chemfig{(-[1]1)(-[2]2)(-[3]3)(-[4]4)(-[5]5)(-[6]6)(-[7]7)-0}|

\item[Absolute angle] To give an angle in degrees relative to the horizontal, the optional argument must take this form: \verb-[:<absolute angle>]-. The \verb-<absolute angle>- may be positive or negative, and may have decimal places. It is reduced to the interval $[0,360)$.
\item[Relative angle] It is often useful to give the bond angle relative to the preceding bond. This syntax is used:\verb-[::<relative angle>]-. The \verb-<relative angle>- may be positive or negative, and may have decimal places.  
\end{description}

\subsection{Condensed structural diagram}
\exemple{Hex-1-ene}|\chemfig{H_3C-{{(CH_2)}_3}-CH=CH_2}|

It is sometimes useful to change the length of a bond. In the preceding example, the first two bonds need to be lengthened; they are too short compared to the double bond. To do this, the \verb|<coeff>| is needed in the optional arguments.

\exemple{Hex-1-ene}|\chemfig{H_3C-[,1.5]{{(CH_2)}_3}-[,1.5]CH=CH_2}|

Notes:
\begin{itemize}
	\item in the notation \verb|[,1.5]|, the comma indicates that the value placed in brackets corresponds to the second argument (\verb|coeff|). To give a value for the fourth argument one would write \verb|[,,,2]|;
	\item characters between braces are not interpreted by \CF, which allows (for example) groupings of atoms to be written inside parentheses without having them treated as part of a branched molecule (see page~\pageref{molecules.ramifiees}).
\end{itemize}

\subsection{Cram representation}
Another way of showing the bond angle between two atoms.
\exemple{Methane}|\chemfig{C(-[5]H)(-[2]H)(<[:-70]H)(<:[:-20]H)}|

\subsection{Skeleton diagram}
The simplest input, only covalent bonds are listed with their possible settings.
\exemple{But-2-ene}|\chemfig{-[:30]=[:-30,,,,red]-[:30]}|

The double bond lines are drawn on either side of where the single bond line would be. To keep graphical consistency between skeleton diagrams of various compounds it is useful to shift the second double bond line above or below the single bond line. Just follow the \verb-=- symbol with \verb-^- or \verb-_-, as shown below:
\exemple{Comparison between double bonds and shifted double bonds}/\chemfig{-[:-30]=[:30]-[:-30]} \chemfig{-[:-30]=^[:30]-[:-30]}\par
\chemfig{=[:-30]-[:30]=[:-30]} \chemfig{=_[:-30]-[:30]=^[:-30]}/

\subsection{Lewis diagrams}
The syntax is as follows:
\centerverb/\lewis{<position index><electron state>,<atom>}/
\smallskip

The electron states can be a lone pair, an empty electron slot, or a single electron. By default the electron state is a lone pair. A single electron is represented by the character \boxedfalseverb. and an empty slot by \boxedfalseverb|.

\exemple{Chloromethane and water}|\chemfig{C(-[2]H)(-[4]H)(-[6]H)-\lewis{260,Cl}}\hspace{1cm}
\chemfig{[:40]H-\lewis{13,O}-[::-80]H}|

Note: the positions take whole number values between 0 and 7.
\exemple{Positions}/\lewis{0.2.4.6.,C}\hspace{1cm}
\lewis{0|2.46.,C}\hspace{1cm}
\lewis{1357,Ar}/

\section{Branched molecules}\label{molecules.ramifiees}
To indicate a branch, simply follow the atom holding the branch with a \verb-<code>- in parentheses. This \verb-<code>- is the code of the submolecule which will be attached to the atom. Multiple branches can be attached to the same atom, and these can be nested.

\exemple{Alkanes}|\chemfig{H_3C-CH(-[2]CH_3)-CH_3}
\hspace{.5cm}\chemfig{-(-[2])(-[6])-}|

In this type of representation it is sometimes necessary to connect to distant atoms. To do this, the character \verb|?| is used, which creates a hook between two atoms. The function
\centerverb/?[<name>,<bond>,<tikz>]/
takes three arguments: the name of the hook, the bond type, and tikz code. The following example shows how to make two different hooks.

\exemple*{Cocaine}|\chemfig{H_2C(-C?[a]H-[:-30]CH_2-[:30]C?[b]H-O-CO-C_6H_5)
-[2]CH_2-[,1.7]CH(-[3]N?[a]-[3]H_3C)(-[,1.35]C?[b]H-CO-OCH_3)}|

\section{Rings}
\CF can easily draw regular polygons. The syntax is the following:
\centerverb/\chemfig{*n(<code for the molecule>)}/
\smallskip

\exemple{Some rings}|
\chemfig{*3(---)}\hspace{.5cm}
\chemfig{*5(-=-=-)}\hspace{.5cm}
\chemfig{*6(-=-=-=)}|

Branches are used in the same way as before.

\exemple{Rings and branches}|\chemfig{*4(-(--[1]*4(----))---)}|

Note: a ring does not start or finish with the atom or group of atoms with which one wants to close the ring. The chemical entity on which the ring is based must be outside the ring definition.

\exemple{Proper coding}|\chemfig{A*4(-B-C-D-)}|

\exemple{Bad coding}|\chemfig{*4(A-B-C-D-)}\hspace{1cm}
	\chemfig{*4(-B-C-D-A)}|

\section{Ions}
The \verb|chemfig| commands enters the math mode\footnote{There is a problem with the placement of groups of atoms containing exponents or subscripts. See page~\pageref{alignement.vertical}.} of \TeX, so it is very simple to write an ion. A negative charge ($-$) must always be enclosed in braces to avoid \CF confusing it with the symbol for a single bond.

\exemple{Acetate ion}|\chemfig{-(-[1]O^{-})=[7]O}|

For purists it is possible to circle the charge of an ion by using the commands \verb|\ominus| and \verb|\oplus|.

To meet all requirements, there are two other commands \verb|\chemabove| and \verb|\chembelow| which allow placement of charges above or below the current atom.

\exemple{Some ions}|\chemfig{-(-[1]O^{\ominus})=[7]O}
\hspace{1cm}
\chemfig{\lewis{35,O}=\lewis{26,Cl}-\chemabove
{\lewis{026,O}}{\ominus}}
\vskip5pt
\chemfig{-\chemabove{N}{\scriptstyle\oplus}(=[1]O)-[7]O^{\ominus}}|

For those who are extremely picky, the commands \verb|\chemabove| and \verb|\chembelow| accept an optional argument which sets the distance between the charge and the atom.
\exemple{Charge position}|\chemfig{\lewis{35,O}=C-\chemabove
[3pt]{\lewis{246,O}}{\hspace{.5cm}\ominus}}|

\section{Chemical equations}
Here is an example of a chemical reaction:
\exemple*{Chemical reaction}/\chemfig{**6(------)} \hspace{.5cm} + \hspace{.5cm} \chemfig{H_3C-Cl}
\hspace{.5cm} $\xrightarrow{catalyst}$ \hspace{.5cm} 
\chemfig{**6(---(-)---)} \hspace{.5cm} + \hspace{.5cm} \chemfig{H-Cl}/

\CF adds two new commands \verb-\chemsign- and \verb-\chemrel- which slightly simplify the preceding syntax.

\exemple*{Using the \CF commands}|\setchemrel{0pt}{1.2em}{6em}
\chemfig{**6(------)}\chemsign[0.5cm]+\chemfig{H_3C-Cl}
\chemrel[\itshape\tiny Catalyst]{->}
\chemfig{**6(---(-)---)}\chemsign[0.5cm]+\chemfig{H-Cl}|
\newpage

\part{Operation of \CF}
This part is devoted to describing the most common features of \CF. The outline of this description far exceeds that of ``\CF for the impatient``, but the user will find here explanations sufficient to draw most molecules. The presentation of features is done from a theoretical angle, and the goal of this part is not to draw real molecules but to give the user a formal description of the functionality of \CF. The ``Advanced usage'', page~\pageref{utilisation.avancee}, will be more practical and will illustrate advanced features for the most demanding uses. It will also highlight methods of building real molecules, page~\pageref{exemples.commentes}. Finally, the last part will give examples of molecules and the code used to draw them.

\section{Groups of atoms}
Drawing a molecule consists inherently of connecting groups of atoms with lines. Thus, in the molecule \chemfig{O=O}, there are two groups of atoms, each consisting of a single atom ``O''.

{\fboxsep1pt
However, in this molecule
\molht{H_3C-C(-[:-30]OH)=[:30]O}
there are four groups of atoms: ``$\mathrm{H_3C}$'', ``C'', ``O'' and ``OH''. For reasons which we shall see later, \CF splits each group into single atoms. Each atom extends up to the next capital letter or one of these special characters: {\ttfamily \boxedfalseverb{-} \boxedfalseverb{=} \boxedfalseverb{~} \boxedfalseverb{(} \boxedfalseverb{!} \boxedfalseverb{*} \boxedfalseverb{<} \boxedfalseverb{>} \boxedfalseverb{@}}. \CF ignores all characters inside braces when splitting groups into atoms.

Therefore the first group of atoms ``$\mathrm{H_3C}$'' is split into two atoms: $\boxednode{H_3}{}$ and $\boxednode C{}$. In terms of chemistry, of course, these are not real atoms; $\mathrm{H_3}$, for example, consists of three hydrogen atoms. In what follows the word atom refers to \CF's definition. Thus \CF sees the preceding molecule as follows:
\renewcommand*\printatom[1]{\fbox{\ensuremath{\mathrm{#1}}}}
\molht{H_3C-[,1.75]C(=[:30,1.5]O)(-[:-30,1.5]OH)}}

\section{Different types of bonds}
As we have already seen (see page~\pageref{types.liaisons}), bonds can be one of nine types, each corresponding to the characters \boxedfalseverb-, \boxedfalseverb=, \boxedfalseverb~, \boxedfalseverb>, \boxedfalseverb<, \boxedfalseverb{>:}, \boxedfalseverb{<:}, \boxedfalseverb{>|} and \boxedfalseverb{<|}.

\label{longueur.liaison}We must understand that when a bond is made between two atoms, these atoms are contained within invisible rectangular boxes. The centres of these two rectangles are separated by an adjustable distance $\Delta$ called the ``interatomic distance''. Furthermore, bonds do not connect to the exact edges of the rectangles: a length $\delta$, also adjustable, separates the edges of the rectangles and the beginning and end of the bond line. The rectangular boxes are made visible in the diagram below to help understanding.
\begin{center}
\begin{tikzpicture}[every node/.style={anchor=base,inner sep=1.5pt,outer sep=0pt,minimum size=0pt},baseline]
	\node[draw] at(0,0)(aa){\huge A};
	\node[draw]at(4,0)(bb){\huge B};
	\path[shorten <=5pt,shorten >=5pt,draw](aa)--(bb)coordinate[pos=0](al) coordinate[pos=1](bl);
	\node[draw,circle,fill,blue,minimum size=1.5pt,inner sep=0pt]at(al){};
	\node[draw,circle,fill,blue,minimum size=1.5pt,inner sep=0pt]at([xshift=5pt]al){};
	\node[draw,circle,fill,blue,minimum size=1.5pt,inner sep=0pt]at(bl){};
	\node[draw,circle,fill,blue,minimum size=1.5pt,inner sep=0pt]at([xshift=-5pt]bl){};
	\draw[blue,dash pattern=on 1pt off 1pt](bl)--([yshift=0.7cm]bl);
	\draw[blue,dash pattern=on 1pt off 1pt]([xshift=-5pt]bl)--([xshift=-5pt,yshift=0.7cm]bl);
	\draw[<->]([yshift=0.6cm]bl.center)--([xshift=-5pt,yshift=0.6cm]bl.center) node [midway,above,draw=none]{$\delta$};
	\draw[blue,dash pattern=on 1pt off 1pt](al)--([yshift=0.7cm]al);
	\draw[blue,dash pattern=on 1pt off 1pt]([xshift=5pt]al)--([xshift=5pt,yshift=0.7cm]al);
	\draw[<->]([yshift=0.6cm]al.center)--([xshift=5pt,yshift=0.6cm]al.center) node [midway,above,draw=none]{$\delta$};
	\node[draw,circle,fill,red,minimum size=2pt,inner sep=0pt]at(aa){};
	\node[draw,circle,fill,red,minimum size=2pt,inner sep=0pt]at(bb){};
	\draw[<->]([yshift=1cm]aa.center)--([yshift=1cm]bb.center) node [midway,above,draw=none] {$\Delta$} ;
	\draw[red,dash pattern=on 2pt off2pt](aa.center)--([yshift=1.1cm]aa.center);
	\draw[red,dash pattern=on 2pt off2pt](bb.center)--([yshift=1.1cm]bb.center);
\end{tikzpicture}
\end{center}

\label{setatomsep}The macro \verb-\setatomsep{<dimension>}- adjusts the interatomic distance $\Delta$. If the \verb-<dimension>- is empty, it takes the default value of 3em. This command, like all other settings commands, affects all the following molecules. 

\exemple{Interatomic distance}|\setatomsep{2em}\chemfig{A-B}\par
\setatomsep{50pt}\chemfig{A-B}|

\label{setbondoffset}The command \verb-\setbondoffset{<dimension>}- sets the spacing $\delta$ between the bond line and the atom. If the \verb-<dimension>- is empty, $\delta$ takes the default value of 2pt.
\exemple{Trimming bonds}|\setbondoffset{0pt}\chemfig{A-B}\par
	\setbondoffset{5pt}\chemfig{A-B}|

If one bond is followed immediately by another, then \CF inserts an empty group \verb-{}-. Around this empty group the separation $\delta$ is zero:
\exemple{Empty groups}/\chemfig{A-B=-=C}\par
\chemfig{A>B><>|<C}/

\begingroup\color{gray}% !!! Nouveau
\nouveau\label{modif.retrait}On peut spécifier l'espacement $\delta$ pour une seule liaison avec le caractère \verb-#-. Ce caractère doit se situer \emph{immédiatement} après le signe de liaison et dispose d'un argument obligatoire entre parenthèses de la forme ``\verb-#(<dim1>,<dim2>)-'', où \verb-<dim1>- représente l'espacement $\delta$ au début de la liaison et \verb-<dim2>- celui de la fin. Si \verb-<dim2>- est omis, l'espacement en fin de liaison prend la valeur de $\delta$ en vigueur à ce moment. On peut observer sur cet exemple comment le retrait, réglé à 4pt pour être plus visible, est rendu nul pour la liaison arrivant sur ``B'', puis partant de ``B'' et enfin pour les deux à la fois :
\begingroup
\catcode`\#12
\exemple{Réglage fin du retrait des liaisons}/\setbondoffset{4pt}
\chemfig{A-B-C}\par
\chemfig{A-#(,0pt)B-C}\par
\chemfig{A-B-#(0pt)C}\par
\chemfig{A-#(,0pt)B-#(0pt)C}/
\endgroup
\endgroup% !!! fin

By default, all atoms within groups of atoms are typeset in math mode (spaces are ignored). They may therefore contain math mode specific commands such as subscripts or superscripts\footnote{There is a problem with the placement of groups of atoms containing exponents or subscripts. See page~\pageref{alignement.vertical}.}:
\exemple{Math mode}|\chemfig{A_1B^2-C _ 3 ^ 4}|

There are settings specifically for Cram bonds. This syntax is used: \label{setcrambond}
\centerverb/\setcrambond{<dim1>}{<dim2>}{<dim3>}/
\smallskip

Any empty argument takes its default value. The three arguments are:
\begin{itemize}
	\item \verb-<dim1>- is the size of the base of the triangle, and is 1.5pt by default;
	\item \verb-<dim2>- is the thickness of the dots, and is 1pt by default;
	\item \verb-<dim3>- is the spacing between the dots, and is 2pt by default.
\end{itemize}

Here is an example where the three dimensions are changed:

\exemple{Modified Cram bonds}-\setcrambond{10pt}{0.4pt}{1pt}
	\chemfig{A>B>:C>|D}-

\section{Bond angle}
Each bond takes an optional argument in brackets. This optional argument can adjust every aspect of a bond, and consists of five optional fields separated by commas. The first of these fields defines the bond angle. Angles increase counterclockwise, and are relative to the horizontal. If the angle field is empty, the angle takes its default value of 0\degres. We will see later how to change this default.

There are several ways of specifying the bond angle.
\subsection{Predefined angles}
When the angle field contains an integer, this represents the angle the bond makes relative to the horizontal, in multiples of 45\degres. For example, \verb-[0]- specifies an angle of 0\degres, \verb-[1]- is 45\degres, and so on up to \verb-[7]- which specifies an angle of 315\degres. The integer may lie outside the interval $[0,7]$, in which case the angle is reduced to the interval $[0,360)$.

\exemple{Predefined angles}|\chemfig{A-B-[1]C-[3]-D-[7]E-[6]F}|

These angles remain valid if the atoms are empty, and this is the case for all the features we will see below:
\exemple{Predefined angles with empty groups}|\chemfig{--[1]-[3]--[7]-[6]}|

\subsection{Absolute angles}
If one wishes to specify an angle in degrees relative to the horizontal, then the optional angle field must take this form: \verb-[:<absolute angle>]-. If necessary, the \verb-<absolute angle>- is reduced to the interval $[0,360)$:
\exemple{Absolute angles}/\chemfig{A-[:30]B=[:-75]C-[:10]D-[:90]>|[:60]-[:-20]E-[:0]~[:-75]F}/

\subsection{Relative angles}\label{angle.relatif}
It is often useful to specify a bond angle relative to the preceding bond. This syntax must be then be used: \verb-[::<relative angle>]-. The sign of the \verb-<relative angle>- can be omitted if it is a \verb-+-.

Here is a molecule where the first bond has an absolute angle of $-5\degres$, and the rest of the bond angles are incremented by 20\degres:
\exemple{Result of relative angles}|\chemfig{A-[:-5]-[::+20]-[::20]B-[::+20]-[::20]C-[::20]}|

One can ``break'' a chain of relative angles by putting an absolute or predefined angle where desired. Here, atom ``B'' is followed by a bond at  an absolute angle of 315\degres.
\exemple{Result of relative angles followed by absolute}|\chemfig{A-[:-5]-[::20]-[::20]B-[7]-[::20]C-[::20]}|

\section{Length of a bond}
Rather than speaking of length of a bond, we should use the term interatomic spacing. If effect, only the interatomic spacing is adjustable with \verb-\setatomsep- as we have seen on page~\pageref{longueur.liaison}. Once this parameter is set, the length of a bond depends on the content of atoms and, to a lesser extent, the angle the bond makes with the horizontal. It should be obvious that two ``slimmer'' atoms will have larger edge separations than two which are larger. This can be seen easily in the following example where an ``I'' atom is narrower than an ``M'' atom, which means that the bond between the ``I'' atoms is longer than that between the ``M'' atoms:
\exemple{Influence of the size of atoms}|\chemfig{I-I}\par
\chemfig{M-M}|

This aspect of the size of atoms becomes particularly acute when the atom involves subscripts or superscripts. In this example, the bond is extremely short, to the point of confusion with a negative sign $-$:
\exemple{Too-short bond}|\chemfig{A^{++}_{2}-B^{-}_3}|

It is important to note that the exponent \verb+-+ is \emph{put inside braces}. If this were not done, \CF would stop the atom on this character, which is a bond character. The atom would then be ``\verb-B^-'', which would lead to unexpected results.

We see in the example above that is it sometimes necessary to increase (or perhaps reduce) the interatomic distance associated with a bond. For this, the optional argument to bonds is actually made up of several comma-separated fields. As we have seen, the first field specifies the angle.
The second field, if it is not empty, is a coefficient which multiplies the default interatomic distance $\Delta$. Thus, writing \verb+-[,2]+ asks that this bond have the default angle (first field is empty) and that the atoms it connects be separated by twice the default distance.
\exemple{Modified bond length}/\chemfig{A^{++}_{2}-[,2]B^{-}_3}\par
\chemfig{A-B-[,2]C=[,0.5]D}\par
\chemfig{-=[,1.5]-[,0.75]=[:-20,2]}/

\section{Departure and arrival atoms}
A group of atoms can contain several atoms. Suppose we want to connect the group ``ABCD'' to the group ``EFG'' with a bond. \CF calculates which atom of the first group and which of the second group are to be connected by looking at the angle of bond relative to the horizontal. If the angle is between (but not including) $-90\degres$ and 90\degres{} (modulo 360\degres) then the bond is made between the last atom of the first group and the first atom of the second group. In all other cases, the bond is made between the first atom of the first group and the last atom of the second group.

Here are some examples where the bond is in the interval $(-90,90)$, and where the bond is made between D and E:
\exemple{Default atom connections}|\chemfig{ABCD-[:75]EFG}\quad
	\chemfig{ABCD-[:-85]EFG}\quad
	\chemfig{ABCD-[1]EFG}|

In the  following examples, the angles are in the interval $[90,270]$ and so the bond is made between A and G:
\exemple[60]{Default atom connections}|\chemfig{ABCD-[:100]EFG}\quad
	\chemfig{ABCD-[:-110]EFG}\quad
	\chemfig{ABCD-[5]EFG}|

One may sometimes want the bond partners to be atoms other than those determined by \CF. The departure and arrival atoms can be set with the optional bond argument by writing:
\centerverb/[,,<integer 1>,<integer 2>]/
\smallskip

where \verb-<integer 1>- and \verb-<integer 2>- are the numbers of the desired departure and arrival atoms. These atoms must exist, otherwise an error message will be given.
\exemple{Specified atom connections}|\chemfig{ABCD-[:75,,2,3]EFG}\qquad
	\chemfig{ABCD-[:75,,,2]EFG}\qquad
	\chemfig{ABCD-[:75,,3,2]EFG}|

\section{Customization of bonds}
There is a fifth and last optional argument for bonds which is found after the fourth comma:
\centerverb/[,,,,<tikz code>]/
\smallskip

This \verb-<tikz code>- is passed directly to \TIKZ when the bond is drawn. There one can put characteristics such as colour (\verb-red-), dash type (\verb-dash pattern=on 2pt off 2pt-), thickness (\verb-line width=2pt-), or even decoration if the \TIKZ decoration library has been loaded. A bond can be made invisible by writing ``\verb-draw=none-''. To set several attributes, the syntax of \TIKZ is used, separating them by a comma:
\exemple{Passing tikz code}|\chemfig{A-[,,,,red]B}\par
	\chemfig{A-[,,,,dash pattern=on 2pt off 2pt]B}\par
	\chemfig{A-[,,,,line width=2pt]B}\par
	\chemfig{A-[,,,,red,line width=2pt]B}|

Numerous \TIKZ decoration libraries are available. For example, one can use the ``\verb-pathmorphing-'' library by putting \verb-\usetikzlibrary{decorations.pathmorphing}- in the preamble in order to draw wavy bonds:
\exemple{Wavy bonds}|\chemfig{A-[,3,,,decorate,decoration=snake]B}|

Cram bonds ignore thickness and dash settings.

\section{Default values}
At the beginning of each molecule, the default values for the optional arguments are initialized. They are:
\begin{itemize}
	\item 0\degres{} for the bond angle;
	\item 1 for the length multiplication coefficient;
	\item \verb-<empty>- for the numbers of the departure and arrival atoms, which lets \CF calculate these based on the bond angle;
	\item \verb-<empty>- for the parameters passed to \TIKZ.
\end{itemize}

These default values can be changed for the whole molecule by beginning the molecule code with
\centerverb/[<angle>,<coeff>,<n1>,<n2>,<tikz code]/
\smallskip

Thus, if the code of a molecule begins with \verb-[:20,1.5]-, then all the bonds will be at angle of 20\degres{} by default, and the interatomic distances will have a length 1.5 times the default length. These default values can be overridden at any time by giving an optional argument, such as for the bond which follows atom ``C'' in this example:
\exemple{Overriding default values}|\chemfig{[:20,1.5]A-B-C-[:-80,0.7]D-E-F}|

If something odd like \verb-[1,1.5,2,2,red,thick]- is written, then unless otherwise indicated all the bonds will have an angle of 45\degres{}, the interatomic distances will be 1.5 times the default distance, the bonds will begin and end on the second atom of each group, and the bonds will be red and thick:
\exemple{Default values}|\chemfig{[1,1.5,2,2,red,thick]ABC-DEF=GHI}|

\section{Branches}
\subsection{Principle}
Up to now, all the molecules have been linear, which is rare. A sub-molecule can be attached to an atom by following the atom with \verb-<code>- in parentheses. This \verb-<code>- is the code of the submolecule which will be attached to the atom.

In this example, the sub-molecule ``\verb/-[1]W-X/'' will be attached to atom ``B'': 
\exemple{A branch}|\chemfig{A-B(-[1]W-X)-C}|

There can be several sub-molecules which are to be attached to the same atom. Just have several parentheses containing the code for each sub-molecule:
\exemple{Multiple branches}|\chemfig{A-B(-[1]W-X)(-[6]Y-[7]Z)-C}|

The code of each sub-molecule can define its own default values, which will be valid throughout the whole sub-molecule. Here a sub-molecule ``\verb/[:60]-D-E/'' is attached to atom ``B'', with a default angle of 60\degres{} absolute. A second sub-molecule ``\verb/[::-60,1.5]-X-Y/'' is attached to ``B'' with a default bond angle 60\degres{} less than that of the preceding bond (which will be the one between ``A'' and ``B'') and with an interatomic distance 1.5 times the default value:
\exemple{Default values in branches}|\chemfig{A-B([:60]-D-E)([::-30,1.5]-X-Y)-C}|

Observe what happens if, at the beginning of the main molecule, one writes ``\verb/[:-45]/'':
\exemple{Effect of the default bond angle}|\chemfig{[:-45]A-B([:60]-D-E)([::-30,1.5]-X-Y)-C}|

We see that the angle between the bond \verb/B-C/ and the bond \verb/B-X/ stays at 30\degres{} because it is a relative angle for the sub-molecule ``\verb/-X-Y/''. By contrast, the branch ``\verb/-D-E/'' stays inclined at 60\degres{} to the horizontal, and does not follow the rotation given by the $-45\degres$ angle at the beginning; this is expected because ``\verb/-D-E/'' has an absolute angle. It is essential that all the angles be relative in order to rotate the whole molecule.

\subsection{Nesting}
Sub-molecules may be nested, and the rules seen in the preceding paragraphs stay in force:
\exemple{Nested branches}|\chemfig{A-B([1]-X([2]-Z)-Y)(-[7]D)-C}|

\subsection{Method}
Suppose now that we want to draw an acid anhydride molecule:
\chemfig{R-C(=[::+60]O)-[::-60]O-[::-60]C(=[::+60]O)-[::-60]R}

The best way to get this is to find the longest chain. Here, for example, we can draw the chain \verb/R-C-O-C-R/ taking into account angles and using only relative angles:
\exemple{Acid anhydride structure}|\chemfig{R-C-[::-60]O-[::-60]C-[::-60]R}|

To this structure we just have to add two ``\verb/=O/'' sub-molecules to each of the carbon atoms:
\exemple{Acid anhydride}|\chemfig{R-C(=[::+60]O)-[::-60]O-[::-60]C(=[::+60]O)-[::-60]R}|

Because we used only relative angles, we can rotate this molecule by giving a default angle of e.g. 75\degres:
\exemple[70]{Rotation of a molecule}|\chemfig{[:75]R-C(=[::+60]O)-[::-60]O-[::-60]C(=[::+60]O)-[::-60]R}|

\section{Connecting distant atoms}
We have seen how to connect atoms \emph{which are adjacent in the code}. It is often necessary to connect atoms which are not next to each other in the code. Let's call these particular bonds ``distant bonds''.

Let's take this molecule:
\exemple{Branched structure}|\chemfig{A-B(-[1]W-X)(-[7]Y-Z)-C}|

and suppose that we want to connect the atoms \verb/X/ and \verb/C/. In this case, \CF allows a ``hook'' to be placed \emph{immediately} after the atom of interest. The character used for a hook is ``\verb-?-'' because of its similarity to a hook. So, if one writes \verb/X?/ then the atom \verb/X/ will have a hook. Later in the code, all atoms followed by a \verb-?- will be connected to \verb/X/:
\exemple{Distant bond}|\chemfig{A-B(-[1]W-X?)(-[7]Y-Z)-C?}|

We could connect other atoms to X by following them with \verb-?-. Here it's the atoms \verb-C- and \verb-Z-:
\exemple{Several distant bonds}|\chemfig{A-B(-[1]W-X?)(-[7]Y-Z?)-C?}|

Now imagine if we were to leave the distant bonds \verb/X-C/ and \verb/X-Z/while adding another: \verb/A-W/. We must therefore ask for two \emph{different} hooks, one on \verb/A/ and the other on \verb/X/. Fortunately the character \verb/?/ has an optional argument:
\centerverb/?[<name>,<bond>,<tikz>]/
\smallskip

where each field takes its default value if it is empty:
\begin{itemize}
	\item The \verb-<name>- is the name of the hook: all alphanumeric characters (a\dots z, A\dots Z, 0\dots 9) are allowed\footnote{This is not exactly right. Actually all the characters that can be put between \texttt{\string\csname...\string\endcsname} are allowed.}. The name is \verb-a- by default. In the first occurrence of the hook with this name, only this field is used.
	\item \verb-<bond>- specifies how the atom with the current occurrence of the named hook is to be bonded to the atom with the first occurrence of the hook. There are two ways this can be done. First, this field can be an integer representing the desired bond type: 1=single bond, 2=double bond, etc. (See the table on page~\pageref{types.liaisons} for the bond codes.)

		Second, the field can be one of the bond character codes, provided that this character is \emph{between braces}.
	\item \verb-<tikz>- will be passed directly to \TIKZ as we have seen with regular bonds.
\end{itemize}

Here is our molecule with the required distant bonds, then with the bond \verb/A-W/ and \verb/X-C/ customized:
\exemple{Multiple distant bonds}|\chemfig{A?[a]-B(-[1]W?[a]-X?[b])(-[7]Y-Z?[b])-C?[b]}\par\medskip
	\chemfig{A?[a]-B(-[1]W?[a,2,red]-X?[b])(-[7]Y-
	Z?[b,1,{line width=2pt}])-C?[b,{>},blue]}|

Several different hooks can be written after an atom. Suppose that in this unfinished pentagon, we wish to connect \verb/A-E/, \verb/A-C/ and \verb/E-C/:
\exemple{An incomplete ring}|\chemfig{A-[:-72]B-C-[:72]D-[:144]E}|

Then we must do this:
\exemple{Multiple distant bonds}|\chemfig{A?[a]-[:-72]B-C?[a]?[b]-[:72]D-[:144]E?[a]?[b]}|

\section{Rings}
The preceding example shows how to draw a regular polygon, but the method used is tedious because the angles depend on the number of sides of the polygon.

\subsection{Syntax}
\CF can easily draw regular polygons. The idea is to attach a ring to an \verb/<atom>/ outside the ring with this syntax:
\centerverb/<atom>*<n>(<code>)/
\smallskip

\verb/<n>/ is the number of sides of the polygon and the \verb/<code>/ describes the bonds and groups of atoms which make up its edges and vertices. This code \emph{must} begin with a bond because the atom is outside the ring.

Here is a 5-ring, attached to the atom ``\verb/A/'':
\exemple{5-ring}|\chemfig{A*5(-B=C-D-E=)}|

A ring can also be drawn with one, several, or all the groups of atoms empty, as is the case for diagrams outside rings:
\exemple{5-ring with empty groups}|\chemfig{*5(-=--=)}|

A ring can be incomplete:
\exemple{Incomplete 5-ring}|\chemfig{*5(-B=C-D)}|
If a ring has a code which contains too many bonds and atom groups for the given number of vertices, all the bonds and groups over the maximum allowed are ignored:
\exemple{Truncated 5-ring}|\chemfig{A*5(-B=C-D-E=F-G=H-I)}|

It is possible to draw a circle or an arc in the inside of a ring. To do so, the following syntax is used:
\centerverb/<atom>**[<angle 1>,<angle 2>,<tikz>]<n>(<code>)/
\smallskip

where each field of the optional argument takes its default value if it is empty:
\begin{itemize}
	\item \verb/<angle 1>/ and \verb/<angle 2>/ are the absolute angles of the start and finish of the arc. These default to 0\degres{} and 360\degres{} respectively so that a circle is drawn by default;
	\item \verb/<tikz>/ is the code that will be passed to \TIKZ for drawing the arc.
\end{itemize}

\exemple{Rings and arcs}|\chemfig{**6(------)}\quad
	\chemfig{**[30,330]5(-----)}\quad
	\chemfig{**[0,270,dash pattern=on 2pt off 2pt]4(----)}|

\subsection{Angular position}
\subsubsection{At the start}
As can be seen in the examples above, the rule is that the attachment atom ``\verb/A/'' is always at the south-west of the ring. Furthermore, the ring is always constructed counterclockwise, and the last bond descends vertically onto the attachment atom:
\exemple{Angular position of rings}|\chemfig{A*4(-B-C-D-)}\qquad\chemfig{A*6(------)}|

If this angular position is not convenient, it is possible to specify another angle using the optional argument at the beginning of the molecule. Here is a 6-cycle which has been rotated by $+30\degres$, by $-30\degres$, and lastly by $+60\degres$:
\exemple[55]{Rotation of rings}|\chemfig{[:30]A*6(------)}\qquad
	\chemfig{[:-30]A*6(------)}\qquad
	\chemfig{[:60]A*6(------)}|

\subsubsection{After a bond}
When a ring does not begin a molecule and one or more bonds have already been drawn, the default angular position changes: the ring is drawn is such a way that the bond ending on the attachment atom bisects the angle formed by the first and last sides of the ring.

Here is a simple case:
\exemple{Bond ending on a ring}|\chemfig{A-B*5(-C-D-E-F-)}|

The rule remains valid, whatever the angle of the preceding bond:
\exemple{Bonds ending on a ring}|\chemfig{A-[:25]B*4(----)}\vskip5pt
	\chemfig{A=[:-30]*6(=-=-=-)}|

\subsection{Branches on a ring}
To have branches attached to the vertices of a ring, we use the syntax we have already seen:
\centerverb/<atom>(<code>)/
\smallskip

where the \verb/<code>/ is that of the sub-molecule and the \verb-<atom>- is at the vertex. Unique to rings, the default angle of the sub-molecule is not 0\degres{} but is calculated so that it will bisect the sides leaving the vertex:
\exemple{Branch on a ring}|\chemfig{X*6(-=-(-A-B=C)=-=-)}|

A sub-molecule can be attached to the first vertex of a ring, just like the other vertices:
\exemple{Ring and branches}|\chemfig{*5((-A=B-C)-(-D-E)-(=)-(-F)-(-G=)-)}|

If one wants the bond leaving a vertex not to be the bisector of its sides, one can tinker with the optional global parameter or the optional bond parameter:
\exemple[50]{Branches at specified angles}|\chemfig{*5(---([:90]-A-B)--)}\qquad
	\chemfig{*5(---(-[:90]A-B)--)}\qquad
	\chemfig{*5(---([::+0]-A-B)--)}|

It is worth noting that in the third example, where a relative angle of 0\degres{} was given, the bonds of the branch are drawn in line with the preceding bond in the ring. This is the rule on page~\pageref{angle.relatif} which specified that the reference angle was that of the bond last drawn.

We can now connect together rings with bonds:
\exemple{Connected rings}|\chemfig{*6(--(-*5(----(-*4(----))-))----)}|

\subsection{Nested rings}
To ``glue'' two rings together, the syntax is only slightly different: the vertex is specified where the other ring is going to start. Simply follow this vertex by the usual syntax for a ring. Here for example is a 5-ring which is attached to the second vertex of a 6-ring:
\exemple{Nested rings}|\chemfig{A*6(-B*5(----)=-=-=)}|

Note that the ring which is going to be attached to the main ring has an angular position such that two of the rings' sides coincide. In addition, the 5-ring has only four bonds ``\verb/----/''. In effect, the fifth will be useless because it is the second side of the 6-ring, which has already been drawn.

It is quite possible to glue multiple rings together:
\exemple{Multiple nested rings}|\chemfig{*5(--*6(-*4(-*5(----)--)----)---)}|

There is a case where a trick must be used. It can be seen in this example that the fourth side of the second 5-ring just passes through the centre of atom ``\verb-E-''.
\exemple{Flawed drawing}|\chemfig{A-B*5(-C-D*5(-X-Y-Z-)-E-F-)}|

This is normal because the second 5-ring (which is attached to atom ``\verb-D-'') is drawn \emph{before} \CF knows about atom ``\verb-E-''. In this case, it is necessary to use two hooks to draw the bond \verb/Z-E/:
\exemple{Distant bond and ring}|\chemfig{A-B*5(-C-D*5(-X-Y-Z?)-E?-F-)}|

We could also use a \verb-\phantom{E}- at the last vertex of the 5-ring:
\exemple{Using \string\phantom}/\chemfig{A-B*5(-C-D*5(-X-Y-Z-\phantom{E})-E-F-)}/

\subsection{Rings and groups of atoms}
Some care must be taken with rings when one or more vertices are made up of groups of atoms:
\exemple{Ring and groups of atoms}|\chemfig{AB*5(-CDE-F-GH-I-)}|

In order for the ring to have a regular shape, it is necessary to override the \CF mechanism which automatically calculates the departure and arrival atoms of bonds. Here, \verb/C-F/ and \verb/F-G/ must be connected by using the optional argument of these bonds:
\exemple{Forced departure and arrival atoms}|\chemfig{AB*5(-CDE-[,,1]F-[,,,1]GH-I-)}|

\begingroup\color{gray}% !!! Nouveau
\section{Représentation des déplacements d'électrons}\label{mecanismes-reactionnels}
\nouveau Depuis la version 0.3 de \CF, on peut représenter les déplacements d'électrons des effets mésomères ou des mécanismes réactionnels. Cela est rendu possible en marquant le point de départ et le point d'arrivée de la flèche que l'on utilise pour indiquer la migration des électrons à l'aide de la syntaxe ``\verb-@{<argument>}-''. Cette syntaxe permet de poser un nœud (au sens de \TIKZ) en rendant ce nœud accessible en dehors de l'argument de la commande \verb-\chemfig- grâce à l'option ``\texttt{remember picture}'' qui est passée à tous les environnements ``tikzpicture''. Cela suppose que le visualiseur prenne en charge le ``picture remembering'' et que la compilation soit lancée deux fois.

Deux cas de figure peuvent se présenter, on peut poser :
\begin{itemize}
	\item un nœud de dimension nulle sur une liaison en utilisant la syntaxe ``\verb-@{<nom>,<coeff>}-'' placée immédiatement au début de l'argument optionnel de la liaison concernée sans être suivi d'une virgule s'il y a un premier argument optionnel. Dans ce cas, le nœud portera le nom ``\verb-<nom>-'' et le \verb-<coeff>-, compris entre 0 et 1, déterminera où le nœud se situera sur la liaison. Si on utilise ``\verb-@{<nom>}-'', le \verb-<coeff>- prend la valeur de 0.5 par défaut ce qui signifie que le nœud est posé au milieu de la liaison;
	\item un nœud sur un atome en utilisant la syntaxe ``\verb-@{<nom>}-'' immédiatement avant l'atome concerné. Dans ce cas, le nœud a exactement le même encombrement que l'atome, il peut notamment être vide et donc avoir des dimensions nulles.
\end{itemize}
Une fois que la commande \verb-\chemfig- a dessiné la (ou les) molécule(s) et a posé les nœuds avec la syntaxe décrite ci dessus, on peut relier ces nœuds entre eux avec les instructions de \TIKZ. Ces instructions seront placées dans l'argument de la commande \verb-\chemmove-\footnote{En réalité, la commande \texttt{\string\chemmove} met son argument dans un environnement ``tikzpicture'' avec les options ``\texttt{remember picture,overlay}''.} et auront la syntaxe suivante si par exemple, on doit relier un nœud portant le nom ``\verb-<nom1>-'' au nœud portant le nom ``\verb-<nom2>-'' :
\centerverb|\chemmove[<opt>]{\draw[<opt tikz>](<nom1>)<link tikz>(<nom2>);}|
\smallskip

L'argument optionnel \verb-<opt>- de la commande \verb-\chemmove- sera ajouté à l'argument de l'environnement tikzpicture dans lequel seront tracées les liaisons entre les nœuds. Les instructions \verb-<opt tikz>- et \verb-<link tikz>- sont exhaustivement décrites dans la documentation de l'extension \TIKZ.

\subsection{Effets mésomères}
Pour fixer les idées prenons l'exemple d'un effet mésomère impliquant une double liaison et un doublet non liant conjugués. Commençons par la possible délocalisation des électrons de la double liaison. On va poser un nœud nommé ``db'' (double bond) au milieu de la double liaison et un nœud nommé ``a1'' sur l'extrémité de la double liaison.

\exemple{Effet mésomère 1}/\chemfig{@{a1}=_[@{db}::30]-[::-60]\lewis{2,X}}
\chemrel{<->}
\chemfig{\chemabove{\vphantom{X}}{\ominus}-[::30]=_[::-60]
\chemabove{X}{\scriptstyle\oplus}}
\chemmove{\draw[->](db).. controls +(80:8mm) and +(145:8mm).. (a1);}/

Comme on l'a dit, on remarque qu'il n'y pas de virgule derrière le nœud posé dans les arguments optionnels d'une liaison; On écrit ``\verb|=_[@{db}::30]|'' et non pas ``\verb|=_[@{db},::30]|'' comme on serait tenté de le faire.\\
Pour relier les nœuds ``db'' et ``a1'', nous avons utilisé la syntaxe suivante :
\centerverb|\chemmove{\draw[->](db)..controls +(80:8mm) and +(145:8mm)..(a1);}|
\medskip

Dans cet exemple nous demandons une flèche (\verb/[->]/) et nous utilisons 2 points de contrôle\footnote{Pour connaître toutes les façons de relier deux nœuds avec \TIKZ, lire la documentation de ce package.}. Ceux-ci seront situés en coordonnées polaires à 80\degres{} et 8~mm de ``db'' pour le premier et à 145\degres{} et 8~mm de ``a1'' pour le second. Il ne faut pas être effrayé par cette syntaxe qui peut paraître compliquée en première lecture car son utilisation se réduit dans la plupart des cas à un simple copier-coller dans lequel on modifie juste le nom des nœuds et les coordonnées polaires des points de contrôle. Ce que nous allons vérifier tout de suite avec l'ajout d'une flèche partant du doublet non liant (nœud ``dnl'') vers la liaison simple (nœud ``sb'').
\exemple{Effet mésomère 2}/\chemfig{@{a1}=_[@{db}::30]-[@{sb}::-60]@{dnl}\lewis{2,X}}
\chemrel{<->}
\chemfig{\chemabove{\vphantom{X}}{\ominus}-[::30]=_[::-60]
\chemabove{X}{\scriptstyle\oplus}}
\chemmove{\draw[->](db)..controls +(80:8mm) and +(145:8mm)..(a1);}
\chemmove{\draw[->](dnl)..controls +(90:4mm) and +(45:4mm)..(sb);}/

Pour notre nouvelle flèche nous avons fixé les points de contrôle comme suit : un angle de 90\degres{} à 4~mm de ``dnl'' et un angle de 45\degres{} à 4~mm de ``sb''. Mais nous ne sommes pas entièrement satisfaits car nous aimerions que la flèche ne touche pas le trait représentant le doublet non liant. Pour cela nous allons ajouter quelques options à notre flèche.
\exemple{Effet mésomère 3}/\chemfig{@{a1}=_[@{db}::30]-[@{sb}::-60]@{dnl}\lewis{2,X}}
\chemrel{<->}
\chemfig{\chemabove{\vphantom{X}}{\ominus}-[::30]=_[::-60]
\chemabove{X}{\scriptstyle\oplus}}
\chemmove{\draw[->](db).. controls +(80:8mm) and +(145:8mm).. (a1);}
\chemmove{\draw[->, shorten <=3pt, shorten >= 1pt]
    (dnl).. controls +(90:4mm) and +(70:6mm).. (sb);}/

L'option ``\verb|shorten <=3pt|'' indique que le point de départ de la flèche doit être raccourci de 3~pt de même ``\verb|shorten >=2pt|'' indique que le point d'arrivé doit être raccourci de 2~pt.

On peut utiliser toute la puissance des instructions de \TIKZ pour modifier le dessin de la flèche. Ici, nous changeons l'extrémité de la flèche partant de la double liaison, non plus écrite ``\verb|->|'' mais ``\verb|-stealth|'', nous la dessinons en pointillés d'épaisseur fine et rouge. Nous rajoutons également la lettre $\pi$ au dessus de la flèche en son milieu :
\exemple{Effet mésomère 4}/\chemfig{@{a1}=_[@{db}::30]-[@{sb}::-60]@{dnl}\lewis{2,X}}
\chemrel{<->}
\chemfig{\chemabove{\vphantom{X}}{\ominus}-[::30]=_[::-60]
\chemabove{X}{\scriptstyle\oplus}}
\chemmove{\draw[-stealth,thin,dash pattern= on 2pt off 2pt,red]
    (db).. controls +(80:8mm) and +(145:8mm)..
    node[sloped,above] {$\pi$} (a1);}
\chemmove{\draw[->, shorten <=3pt, shorten >= 1pt]
    (dnl).. controls +(90:4mm) and +(70:6mm).. (sb);}/

Dans l'exemple suivant nous allons voir comment indiquer la position de l'ancre de départ ou d'arrivée. Si nous écrivons
\exemple{Ancre de départ et d'arrivée 1}/\chemfig{@{x1}\lewis{1:,X}}
\hspace{2cm}
\chemfig{@{x2}\lewis{2|,X}}
\chemmove{\draw[->,shorten >=4pt]
    (x1).. controls +(90:1cm) and +(90:1cm).. (x2);}/

Nous constatons que l'ancre de départ de notre flèche ne pointe pas correctement sur nos électrons. La flèche part du milieu du bord supérieur du nœud. En effet, nous avons choisi un angle de départ de 90\degres{} et tikz fait donc partir la flèche de l’ancre ``x1.90'' qui correspond à l’intersection de la demi droite partant du centre du nœud ``x1'' et faisant un angle avec l’horizontale de 90\degres{} avec le bord du nœud qui est un rectangle. Pour obtenir le départ de la flèche d’où nous voulons, nous devons spécifier sa position. Après quelques tâtonnements, c’est ``x1.57'' :
\exemple{Ancres de départ et d'arrivée 2}/\chemfig{@{x1}\lewis{1:,X}}
\hspace{2cm}
\chemfig{@{x2}\lewis{2|,X}}
\chemmove{\draw[->,shorten <=4pt,shorten >=4pt]
    (x1.57).. controls +(60:1cm) and +(120:1cm).. (x2);}/

Dans certains cas il sera plus facile d'utiliser les coordonnées cartésiennes pour les points de contrôle. Ici, nous n'utilisons qu'un seul point de contrôle situé à 1~cm horizontalement de ``x1'' et 1,5~cm verticalement :
\exemple{Un seul point de contrôle}/\chemfig{@{x1}\lewis{1:,X}}
\hspace{2cm}
\chemfig{@{x2}\lewis{2|,X}}
\chemmove{\draw[->,shorten <=4pt,shorten >=4pt]
    (x1.57).. controls +(1cm,1.5cm).. (x2);}/

Dans ce cas nous plaçons un point de contrôle à 1~cm horizontalement et 2~cm verticalement de ``x1''. Tous les objets graphiques dessinées par l’intermédiaire de la commande \verb|\chemmove| sont faits en surimpression et ne seront pas comptés dans les boîtes englobantes. On peut le constater sur l’exemple précédent.

\subsection{Mécanismes réactionnels}
Grâce à l'option \verb|remenber picture| qui est passée à tous les environnements ``tikzpicture'' nous pouvons facilement dessiner les flèches indiquant les mécanismes réactionnels. Prenons comme exemple la première étape de la réaction d'estérification.
\exemple{Estérification: étape 1}/\setatomsep{7mm}
\setchemrel{}{}{5mm}
\chemfig{R-@{dnl}\lewis{26,O}-H}
\chemsign{+}
\chemfig{R-@{atoc}C([6]-OH)=[@{db}]O}
\chemrel[\chemfig{@{atoh}\chemabove{H}{\scriptstyle\oplus}}]{<>}
\chemmove[->,shorten <=2pt]{
    \draw[shorten >=2pt](dnl).. controls +(90:1cm) and +(north:1cm).. (atoc);
    \draw[shorten >=6pt](db).. controls +(north:5mm) and +(100:1cm).. (atoh);}/

L'utilisation de la commande \verb|\chemabove{<code>}{<materiel>}| ne change pas les dimensions de la boite englobante du \verb|<code>|. Pour cette raison on peut rencontrer certaines difficultés pour pointer sur le matériel indiquant la charge portée ($\oplus$ ou $\ominus$). Dans l'exemple ci-dessus la solution est de créer un point de contrôle avec un angle de 110\degres{} à 1~cm de ``atoh'' et de raccourcir la flèche de 6pt. Dans l'exemple suivant, seconde étape de la réaction d'estérification, on peut voir que la flèche peut prendre des formes plus compliquées sans forcément surcharger le code.
\exemple{Estérification: étape 2}/\setatomsep{7mm}
\setchemrel{}{}{5mm}
\chemfig{R-O-C(-[2]R)(-[6]OH)-@{dnl}\lewis{26,O}H}\hspace{1cm}
\chemfig{@{atoh}\chemabove{H}{\scriptstyle\oplus}}
\chemmove{\draw[->,shorten <=2pt, shorten >=7pt]
    (dnl).. controls +(south:1cm) and +(north:1.5cm).. (atoh);}/

Nous laissons le soin au lecteur d'écrire la suite\ldots

\section{Écrire un nom sous une molécule}\label{chemname}
\nouveau Pour plus de commodité, \CF permet d'écrire le nom d'une molécule sous celle-ci avec la commande
\centerverb/\chemname[<dim>]{\chemfig{<code de la molécule>}}{<nom>}/
\smallskip

La \verb-<dimension>-, qui vaut 1.5ex par défaut, sera insérée verticalement entre la ligne de base de la molécule et le haut des lettres du \verb-<nom>-. Le \verb-<nom>- sera centré par rapport à la molécule mais ce \verb-<nom>- ne peut pas contenir plusieurs paragraphes. Comme on le voit sur cet exemple : \chemname{\chemfig{H-O-H}}{\scriptsize\bfseries La molécule d'eau : $\mathrm{\mathbf{H_2O}}$}, le \verb-<nom>- qui est affiché sous la molécule est pris en compte dans la boîte englobante mais uniquement en ce qui concerne sa dimension \emph{verticale}. L'encombrement horizontal du \verb-<nom>- est toujours nul.

Voici une réaction avec les noms sous les molécules :
\exemple*{Affichage du nom des molécules}/
\chemname{\chemfig{R-C(-[:-30]OH)=[:30]O}}{Acide carboxylique}
\chemsign{+}
\chemname{\chemfig{R'OH}}{Alcool}
\chemrel{->}
\chemname{\chemfig{R-C(-[:-30]OR')=[:30]O}}{Ester}
\chemsign{+}
\chemname{\chemfig{H_2O}}{Eau}
/

Il y a quelques contraintes avec cette commande. Pour en pendre conscience, mettons que l'on ait inversé l'acide et l'alcool dans le membre de gauche :
\exemple*{Alignement des noms 1}/
\chemname{\chemfig{R'OH}}{Alcool}
\chemsign{+}
\chemname{\chemfig{R-C(-[:-30]OH)=[:30]O}}{Acide carboxylique}
\chemrel{->}
\chemname{\chemfig{R-C(-[:-30]OR')=[:30]O}}{Ester}
\chemsign{+}
\chemname{\chemfig{H_2O}}{Eau}
/

En fait, au dessous de la ligne de base de chaque molécule (en gris clair sur les exemples de ce manuel), pour écrire le \verb-<nom>-, la commande \verb-\chemname- insère 1.5ex${}+{}$\emph{la plus grande des profondeurs\footnote{En langage \TeX{}, la profondeur est la dimension qui s'étend verticalement sous la ligne de base.} des molécules rencontrées}. La macro \verb-\chemnameinit{<argument>}- initialise cette plus grande profondeur avec le contenu de l'\verb-<argument>-. Il convient donc :
\begin{itemize}
	\item d'écrire \verb-\chemnameinit{<plus profonde molécule>}- avant d'impliquer cette commande dans une réaction, sauf si cette réaction commence par la plus profonde molécule;
	\item d'écrire \verb-\chemnameinit{}- après avoir écrit tous les noms d'une réaction chimique afin d'éviter que la plus grande profondeur trouvée dans cette réaction n'interfère dans une réaction future.
\end{itemize}

Le code correct est donc d'utiliser \verb-\chemnameinit- avant et après la réaction :
\exemple*{Alignement des noms 2}/
\chemnameinit{\chemfig{R-C(-[:-30]OH)=[:30]O}}
\chemname{\chemfig{R'OH}}{Alcool}
\chemsign{+}
\chemname{\chemfig{R-C(-[:-30]OH)=[:30]O}}{Acide carboxylique}
\chemrel{->}
\chemname{\chemfig{R-C(-[:-30]OR')=[:30]O}}{Ester}
\chemsign{+}
\chemname{\chemfig{H_2O}}{Eau}
\chemnameinit{}
/

Enfin, pour écrire un nom sur plusieurs lignes, la commande \verb-\\- rencontrée dans un \verb-<nom>- effectue un retour à la ligne\footnote{Par contre, la commande \texttt{\textbackslash par} est interdite et provoquera une erreur à la compilation.} :
\exemple*{Nom sur 2 lignes}/
\chemname{\chemfig{R-C(-[:-30]OH)=[:30]O}}{Acide\\carboxylique}
\chemsign{+}
\chemname{\chemfig{R'OH}}{Alcool}
\chemrel{->}
\chemname{\chemfig{R-C(-[:-30]OR')=[:30]O}}{Ester}
\chemsign{+}
\chemname{\chemfig{H_2O}}{Eau}
\chemnameinit{}
/
\endgroup% !!!fin
\newpage

\part{Advanced usage}\label{utilisation.avancee}
\begingroup\color{gray}% !!! Nouveau
\section{Découpage des atomes}\label{decoupage.atomes}
\nouveau Le mécanisme de découpage des atomes, déjà décrit auparavant, fait s'étendre chaque atome jusqu'à la prochaine lettre majuscule ou l'un des caractères {\ttfamily \boxedfalseverb{-} \boxedfalseverb{=} \boxedfalseverb{~} \boxedfalseverb{(} \boxedfalseverb{!} \boxedfalseverb{*} \boxedfalseverb{<} \boxedfalseverb{>} \boxedfalseverb{@}}

Dans certains cas, ce découpage automatique produit des atomes incorrects ce qui peut se traduire par un affichage imparfait. Prenons cette molécule par exemple où l'on remarquera que le caractère ``\texttt('' est mis entre accolade de façon à éviter que \CF ne comprenne à tort qu'une ramification est créée :

\exemple*{Alcène}/\chemfig{CH_3CH_2-[:-60,,3]C(-[:-120]H_3C)=C(-[:-60]H)-[:60]C{(}CH_3{)}_3}/

On constate que la liaison qui arrive sur l'atome de carbone en haut à droite est trop courte. Cela se produit car, si l'on applique les règles de découpage de \CF dans le groupe d'atomes en haut à droite, les atomes sont découpés de cette façon : ``\texttt{\detokenize{C{(}}}'', ``\texttt{\detokenize{C}}'', ``\texttt{\detokenize{H_3{)}_3}}''. On comprend alors qu'en mode math, le premier atome qui contient une parenthèse ait une profondeur trop importante comme on le voit en rendant visibles les boites contenant les atomes :
\begin{center}
\fboxsep=0pt
\renewcommand*\printatom[1]{\fbox{\ensuremath{\mathrm{#1}}}}%
\chemfig{CH_3CH_2-[:-60,,3]C(-[:-120]H_3C)=C(-[:-60]H)-[:60]C{(}CH_3{)}_3}%
\end{center}
Le caractère ``|'' force la coupure de l'atome en cours lorsqu'il est rencontré. Ainsi, on peut écrire \texttt{C\textcolor{red}{|}\detokenize{{(CH_3)_3}}} pour faire en sorte que \CF ne découpe que 2 atomes ici : ``\texttt{\detokenize{C}}'' et ``\texttt{\detokenize{{(CH_3)_3}}}. Le problème de la liaison trop courte est ainsi résolu :

\exemple*{Alcène}/\chemfig{CH_3CH_2-[:-60,,3]C(-[:-120]H_3C)=C(-[:-60]H)-[:60]C|{(CH_3)_3}}/
\endgroup% !!! fin

\section{Displaying atoms}\label{perso.affichage}
Once a molecule has been split into atoms, the macro \verb-\printatom- is called internally by \CF in order to display each atom. Its sole argument is the code of the atom to be displayed (e.g. ``\verb-H_3-''). By default, this macro enters math mode and displays its argument with the math font family ``rm''. It is defined by the following code:

\hfill\verb-\newcommand*\printatom[1]{\ensuremath{\mathrm{#1}}}-\hfill\null

One can modify the code of this macro to customize how atoms are displayed. In the following example, we redefine \verb-\printatom- so that each atom will be enclosed in a rectangular box:
\exemple{Redefinition of \string\printatom}/\fboxsep=1pt
\renewcommand*\printatom[1]{\fbox{\ensuremath{\mathrm{##1}}}}
\chemfig{H_3C-C(=[:30]O)(-[:-30]OH)}/

Here is how to redefine it to use the ``sf'' font family of math mode:
\exemple{Atoms displayed with ``sf'' font family}/\renewcommand*\printatom[1]{\ensuremath{\mathsf{##1}}}
\chemfig{H_3C-C(=[:30]O)(-[:-30]OH)}/

\begingroup\color{gray}% !!! Nouveau
\section{Arguments optionnels}\label{arguments.optionnels}
\nouveau La commande \verb-\chemfig- admet deux arguments optionnels et sa syntaxe complète est la suivante :
\centerverb|\chemfig[<opt1>][<opt2>]{<code molécule>}|
\smallskip

Le premier argument optionnel \verb-<opt1>- contient des instructions \TIKZ qui seront passées à l'environnement tikzpicture dans lequel est dessinée la molécule. Le deuxième argument optionnel \verb-<opt2>- contient des instructions \TIKZ qui seront exécutées lors du dessin de chaque nœud\footnote{Ces instructions sont ajoutées à la fin de l'argument de \texttt{every node/.style\{<argument>\}}. Cet argument contient par défaut les instructions suivantes : ``{\ttfamily anchor=base,inner sep=0pt,outer sep=0pt,minimum size=0pt}''.}.

Par l'intermédiaire du premier argument optionnel, on peut choisir par exemple la couleur générale ou l'épaisseur des lignes :
\exemple{Choix du style}/\chemfig{A-B-[2]C}\par\medskip
\chemfig[line width=1.5pt]{A-B-[2]C}\par\medskip
\chemfig[red]{A-B-[2]C}/

Avec le second argument optionnel, on peut choisir la couleur des nœud dessinés par \TIKZ, et même modifier l'inclinaison du dessin :
\exemple{Choix des styles}/\chemfig{A-B-[2]C}\par\medskip
\chemfig[][red]{A-B-[2]C}\par\medskip
\chemfig[dash pattern=on 1pt off 2pt][red]{A-B-[2]C}\par\medskip
\chemfig[][rotate=20]{A-B-[2]C}/
\endgroup% !!! fin

\section{Vertical alignment}\label{alignement.vertical}
In some cases with condensed structural diagram of molecules having horizontal bonds, the placement of groups of atoms is incorrect.

Careful study of the following example shows that the groups of atoms are not correctly aligned on the baseline:
\exemple*{Vertical placement}/\Huge\setatomsep{2em}
\chemfig{A^1-B-C-D}\qquad
\chemfig{E_1-F-G-H}/

Surprisingly, the second atom is correctly aligned while the last two undergo a vertical shift which seems to be the results of the different height of the bounding box of the atoms ``\verb-A^1-'' and ``\verb-E_1''-.

In order to understand this phenomenon, we need to consider how \CF places groups of atoms relative to each other. Let us limit ourselves to the case of horizontal bonds in order to simplify terminology, although the algorithm is the same for other bonds. A horizontal bond leaves from the middle of the right side of the bounding box of the departure atom of this bond. The arrival atom is positioned in such a way that the middle of the left side of its bounding box is at the end of the bond. It follows that the vertical placement of the arrival atom depends on the height of the departure atom. To limit this phenomenon, \CF adds to each arrival atom the \verb-\vphantom- of the departure atom, but does not include it in the contents of the arrival atom; this \verb-\vphantom- is not intended to affect the following atoms.
\begingroup\color{gray}% !!! nouveau
Les atomes qui restent dans chaque groupe sont alignés de telle sorte que leur ligne de base coïncide avec la ligne de base de l'atome précédent.
\endgroup%!!! fin

The defective alignment can thus be explained. The atoms ``\verb-B-'' and ``\verb-F-'' are aligned correctly as they reflect the height of the atoms before them because of their \verb-\vphantom-. For the atoms ``\verb-C-'' and ``\verb-F-'', the heights of the immediately preceding atoms are taken into account, but those of the atoms ``\verb-A^1-'' and ``\verb-E_1-'' are ignored! It follows that these atoms are a little too high or too low, depending on the height of these bonds.

We can show this by making visible the bounding boxes of the atoms; one sees clearly that the atoms ``\verb-B-'' and ``\verb-F-'' have bounding boxes that reflect the heights of the immediately preceding atoms:
\exemple*{Vertical placement and bounding boxes}/\Huge\setatomsep{2em}
\fboxsep=0pt
\renewcommand\printatom[1]{\fbox{\ensuremath{\mathrm##1}}}
\chemfig{A^1-B-C-D}\qquad
\chemfig{E_1-F-G-H}/

Since there is no satisfactory manual solution, this problem can be worked around manually by putting \emph{inside} the third atom a \verb-\vphantom- having the same height as the first, so that the height affects the following atoms:
\exemple*{Vertical placement workaround}/\Huge\setatomsep{2em}
\chemfig{A^1-B-{\vphantom{A^1}C}-D}\qquad
\chemfig{E_1-F-{\vphantom{E_1}G}-H}/

\begingroup\color{gray}% !!! Nouveau
\nouveau \label{chemskipalign}Il est possible pour n'importe quel groupe d'atomes de désactiver momentanément le mécanisme d'ajustement d'alignement et neutraliser le \verb-\vphantom-. Il suffit pour cela de placer dans le groupe d'atomes la commande \verb-\chemskipalign- : l'alignement reprendra au groupe d'atomes suivant comme si le groupe d'atome contenant \verb-\chemskipalign- n'avait pas existé. On peut se rendre compte sur l'exemple suivant de l'effet de cette instruction qui a pour effet de placer le point de référence de la boîte contenant le premier atome au niveau de la liaison qui arrive de gauche. Les boîtes englobant les atomes ont été dessinées à la seconde ligne :

\exemple[60]{Désactivation du mécanisme d'alignement}/\large
\chemfig{A-.-B}\quad
\chemfig{A-\chemskipalign.-B}\par\bigskip
\fboxsep=0pt
\renewcommand\printatom[1]{\fbox{\ensuremath{\mathrm{##1}}}}
\chemfig{A-.-B}\quad
\chemfig{A-\chemskipalign.-B}/

Cette commande est à utiliser avec précaution car l'alignement des atomes dans le groupe d'atomes à venir peut être perturbé. En règle générale, tout se passera bien si le groupe d'atomes dans lequel figure \verb-\chemskipalign- contient \emph{un seul atome} dont la hauteur et la profondeur sont \emph{inférieures} à celles de l'atome qui précède et qui suit, et si les atomes qui précèdent et suivent ont leur profondeur et hauteur égales. Voici par exemple la mésaventure qui arrive lorsque le groupe d'atomes contient 2 atomes, ici ``\verb-\chemskipalign.-'' et ``\verb-B-'' :
\exemple{Conséquence de la commande \string\chemskipalign}/\large
\fboxsep=0pt
\renewcommand\printatom[1]{\fbox{\ensuremath{\mathrm{##1}}}}
\chemfig{A-\chemskipalign.B-C}/

Cette fonctionnalité peut parfois s'avérer utile. Mettons que l'on veuille dessiner la molécule
\begin{center}
	\catcode`;12
	\def\emptydisk{\chemskipalign\tikz\draw(0,0)circle(2pt);}%
	\def\fulldisk{\chemskipalign\tikz\fill(0,0)circle(2pt);}%
	\chemfig{A-#(,0pt)\emptydisk-#(0pt,0pt)\fulldisk-#(0pt)B}%
\end{center}
On peut définir les commandes qui vont dessiner les disques vides et pleins avec \TIKZ. Afin que ces disques soit à la bonne hauteur, c'est-à-dire à la hauteur de la liaison qui leur arrive dessus, on se servira de la commande \verb-\chemskipalign-. Pour que, à la deuxième ligne de l'exemple ci dessous, les liaisons ``collent'' aux disques, nous utiliserons la possibilité de modifier le retrait d'une liaison avec le caractère ``\verb-#-'', fonctionnalité qui a été vue à la page~\pageref{modif.retrait}.% ########## Ne pas traduire ce passage, merci ########## Pour les utilisateurs ayant chargé le package babel avec l'option ``frenchb'', il est nécessaire de désactiver le caractère actif ``\verb-;-'' qui marque la fin d'une instruction \TIKZ et qui sinon ne serait pas reconnu en tant que tel. C'est pourquoi on se place dans un groupe où l'on écrit l'instruction \verb-\shorthandoff{;}- :
\begingroup\catcode`;12 \catcode`#12
\exemple{Utilisation de \string\chemskipalign\ et #}/
\begingroup
\def\emptydisk{\chemskipalign\tikz\draw(0,0)circle(2pt);}
\def\fulldisk{\chemskipalign\tikz\fill(0,0)circle(2pt);}
\chemfig{A-\emptydisk-\fulldisk-B}\par
\chemfig{A-#(,0pt)\emptydisk-#(0pt,0pt)\fulldisk-#(0pt)B}
\endgroup/\endgroup
\endgroup% !!! fin

\section{Shifted double bonds}
All double bonds are made up of two line segments, and these segments are drawn on either side of the imaginary line along which a single bond would be drawn. It is possible to shift a double bond so that one of the line segments lies on the imaginary line. The other segment is then shifted above or below the bond. Actually, it is more correct to say ``left'' or ``right'' of the imaginary line, as the bond is traversed in the direction of drawing.

To shift the bond to the left, write ``\verb-=^-'' and to shift it to the right, write ``\verb-=_-'':
\exemple{Shifted double bonds}/\chemfig{A-=-B}\par
\chemfig{A-=^-B}\par
\chemfig{A-=_-B}/

In rings, double bonds are automatically shifted to the left. However, they can be shifted to the right by specifying it with ``\verb-=_-'':
\exemple{Shifted double bonds and rings}/\chemfig{*6(-=-=-=)}\qquad
\chemfig{*6(-=_-=_-=_)}/

Shifted bonds are particularly useful in drawing skeleton diagrams of molecules consisting of carbon chains with double bonds. They give a continuous zig-zag path, whereas the path will be broken with regular double bonds:
\exemple{Shifted bonds and skeleton diagrams}/\chemfig{-[:30]=[:-30]-[:30]=[:-30]-[:30]}\par
\chemfig{-[:30]=^[:-30]-[:30]=^[:-30]-[:30]}\par
\chemfig{-[:30]=_[:-30]-[:30]=_[:-30]-[:30]}/

\section{Delocalized double bonds}
It is sometimes necessary to draw a double bond so that one line segment is dashed while the other is solid\footnote{Thanks to Andreas \textsc{Bröermann} who suggested this feature and who gave me the solution to this problem.}. This feature is not hardcoded into \CF; instead \TIKZ, its ``decorations'' library and its programmable styles make it possible.

First of all, after having loaded the ``decorations'' library by putting \verb-\usetikzlibrary{decorations}- in the preamble, a decoration named ``ddbond'' (for Dashed Double Bond) is defined (lines 1 to 14) and then two \TIKZ styles called ``lddbond'' and ``rddbond'' (lines 15 and 16). For the former, the dashed line segment is on the left of the solid middle segment; for the latter it is on the right. These styles can be called with the fifth optional argument of bonds:
\exemple*{Custom decorations}|\pgfdeclaredecoration{ddbond}{initial}
{
  \state{initial}[width=4pt]
  {
    \pgfpathlineto{\pgfpoint{4pt}{0pt}}
    \pgfpathmoveto{\pgfpoint{2pt}{2pt}}
    \pgfpathlineto{\pgfpoint{4pt}{2pt}}
    \pgfpathmoveto{\pgfpoint{4pt}{0pt}}
  }
  \state{final}
  {
    \pgfpathlineto{\pgfpointdecoratedpathlast}
  }
}
\tikzset{lddbond/.style={decorate,decoration=ddbond}}
\tikzset{rddbond/.style={decorate,decoration={ddbond,mirror}}}
\setatomsep{4em}
\chemfig{[:-30]R-C-[::60]C(-[::60,,,,rddbond]O)-[,,,,lddbond]N(-[::-60]H)-[::60]C-R}|

\section{Saving a sub-molecule}\label{definesubmol}
\CF is capable of saving a \verb-<code>- as an alias for reuse in a more compact form in the code of a molecule. This is particularly useful when the \verb-<code>- appears several times.

To do this, one gives the command
\centerverb|\definesubmol{<name>}{<code>}|
\smallskip

which saves the \verb/<code>/ for recall in the code of the molecule via the shortcut ``\verb/!{name}/''.
\begingroup\color{gray}% !!! Nouveau
Ce \verb-<nom>- peut être :
\begin{itemize}
	\item une suite de caractères : tous les caractères alphanumériques pouvant se trouver entre \texttt{\string\csname} et \texttt{\string\endcsname} sont acceptés;
	\item \nouveau[30pt] une séquence de contrôle.
\end{itemize}

Dans tous les cas, si l'alias est déjà défini il est déconseillé de l'écraser avec une nouvelle définition faite avec \verb-\definesubmol-, d'ailleurs, un ``warning'' sera émis avertissant l'utilisateur que cet alias sera écrasé par le nouveau. Pour écraser la définition d'un alias faite au préalable, il faut utiliser :\label{redefinesubmol}
\endgroup% !!! fin
\centerverb|\redefinesubmol{<name>}{<code>}|
\smallskip

Here is a code which draws the pentane molecule. An alias ``\verb/xy/'' was defined beforehand for the code \verb/CH_2/:
\exemple{Pentane}|\definesubmol{xy}{CH_2}
	\chemfig{H_3C-!{xy}-!{xy}-!{xy}-CH_3}|

In this case the technique is not very interesting because ``\verb/!{xy}/'' is just as long to type as the code it replaces.

But in certain cases, this feature saves a lot of space in the code of the molecule and increases readability. In the following example, we draw the complete structural diagram of butane. We will define an alias with the control sequence ``\verb/\xx/'' for the sub-molecule $\mathrm{CH_2}$. If we use only relative angles, it is possible to rotate the entire molecule to any given angle by using the optional global angle parameter which specifies the default bond angle of the main molecule. It is set to 15\degres{} here:
\exemple{Butane}|\definesubmol\xx{C(-[::+90]H)(-[::-90]H)}
\chemfig{[:15]H-!\xx-!\xx-!\xx-!\xx-H}|

\begingroup\color{gray}% !!! Nouveau
\nouveau La commande \verb-\definesubmol- admet un argument optionnel et sa syntaxe complète est la suivante :
\centerverb/\definesubmol{<nom>}[<code1>]{code2}/
\medskip

Dans la cas où l'argument optionnel est présent, l'alias ``\verb-!<nom>-'' sera remplacé par \verb'<code1>' si la liaison qui arrive sur l'alias vient de droite, c'est à dire si l'angle que fait la liaison arrivant est compris entre 90\degres{} et 270\degres{}, ces valeurs étant non comprises. Pour tous les autres cas où la liaison arrive de gauche ou verticalement, l'alias sera remplacé par \verb-<code2>-.

On va définir une séquence de contrôle \verb-\Me- pour ``méthyl'' de telle sorte que l'alias ``\verb-!\Me-'' soit remplacé par ``\verb-H_3C-'' lorsque la liaison arrive de droite et par ``\verb-CH_3-'' lorsqu'elle arrive de droite. Avec cet alias, on peut observer sur l'exemple que l'on n'a plus à s'occuper de l'angle (que dans certaines molécules complexes on ne connait même pas) :
\exemple{Alias dual}/\definesubmol\Me[H_3C]{CH_3}
\chemfig{*6((-!\Me)=(-!\Me)-(-!\Me)=(-!\Me)-(-!\Me)=(-!\Me)-)}/
\endgroup% !!! fin

\section{Decorations}
\subsection{Lewis diagrams}\label{lewis}
The macro \verb+\lewis+ allows placement of pairs of electrons, of single electrons, or of empty slots. This syntax is used:
\centerverb|\lewis{<n1><n2>...<ni>,<atom>}|
\smallskip

where the \verb-<n1>-\dots\verb-<ni>- represent the desired positions (in multiples of 45\degres) around the \verb-<atom>-. These whole numbers must be between 0 and 7.

This command can also be used inside the argument of \verb-\chemfig-:
\exemple{The \string\lewis\ macro}|\lewis{0246,A}\par\medskip
	\lewis{1357,B}\par\medskip
	\chemfig{H-\lewis{26,O}-S(=[2]\lewis{13,O})
		(=[6]\lewis{57,O})-\lewis{26,O}-H}|

If one wishes to draw two electrons instead of a line, follow the integer with a ``\verb-:-''. If one wishes to draw a single electron, follow it with a ``\verb-.-''. To draw a lacuna, follow it with a ``\verb-|-'':
\exemple{Lewis diagrams}*\lewis{0:2:4:6:,C}\qquad\lewis{1:3:5:7:,C}\par\bigskip
	\lewis{0.2.4.6.,C}\qquad\lewis{1.3.5.7.,C}\par\bigskip
	\lewis{0:2.4|,X}\par\bigskip
	Hydronium ion: \chemfig{H-\lewis{5|7,O^+}(-[2]H)-H}*

All the decorations drawn by \verb-\lewis- are not included in the bounding box of the atom; they are drawn afterwards. A consequence of this is seen in the two examples above, where the frame does not appear to be properly fitted to the drawing of the molecule, which extends downward slightly. This will be seen more often in this the ``Decorations'' chapter, which presents commands which do not change the bounding box.

This can be seen more clearly by drawing an \verb-\fbox- around decorated atoms:
\exemple{Bounding box and the \string\lewis\ macro}*\fboxsep0pt
	\fbox{\lewis{0.2.4.6.,A}}\par\medskip
	\fbox{\lewis{13,B}}*

\label{setlewis}Several parameters can be set with the help of the macro
\centerverb|\setlewis{<dim1>}{<dim2>}{<tikz code>}|
\smallskip

If an argument is empty, it takes its default value.
\begin{itemize}
	\item \verb-<dim1>- is the distance between the bounding box and the decoration. It is 0.2ex by default;
	\item \verb-<dim2>- is the length of the line segment representing a pair of electrons. It is 1.5ex by default;
	\item \verb-<code tikz>- is code which is passed directly to \TIKZ. This code is empty by default.
\end{itemize}

\exemple{Parameters for the \string\lewis\ macro}*\setlewis{4pt}{1.5em}{red}
	\chemfig{A-\lewis{26,B}-C}\par\bigskip
	\setlewis{}{}{line width=0.4pt}
	\chemfig{A-\lewis{2|,B}-C}*

\subsection{Stacking characters}
The macros\label{chemabove}
\centerverb|\chemabove[<dim>]{<code>}{<stuff>}|
and
\centerverb|\chembelow[<dim>]{<code>}{<stuff>}|
\smallskip

place the \verb-<stuff>- above and below the \verb-<code>- respectively at a vertical distance \verb-<dim>-, without changing the bounding box of \verb-<code>-. The length \verb-<dim>- is 1.5pt by default.

These commands are independent of the macro \verb-\chemfig- and can be used either inside or outside its argument.

They are especially useful in rings, if care is taken to put braces around the letters A, B, C and D in order to prevent \CF from starting a new atom on these letters:
\exemple{Staking in rings}|\chemfig{*5(-\chembelow{A}{B}--\chemabove{C}{D}--)}|

They are sometimes useful for placing pseudo-exponents which do not change the bounding box of the atoms, so that the bonds do not end up being too short:
\exemple{Hydronium ion}*\chemfig{H-\chemabove{\lewis{5|7,O}}{\quad\scriptstyle+}(-[2]H)-H}*

\subsection{Chemical reactions}
To write chemical reactions, \CF provides a command for the signs and a command for the arrows.

\label{chemsign}The command \verb-\chemsign[<dim>]<sign>- typesets the \verb-<sign>-, which is surrounded on both sides by an unbreakable horizontal space \verb-<dim>- defaulting to 0.5em.

\label{chemrel}The command \verb-\chemrel[<arg1>][<arg2>]{<arrow code>}- draws an arrow where the optional arguments \verb-<arg1>- and \verb-<arg2>- are placed above and below the arrow respectively, without modifying its bounding box. The \verb-<arrow code>- is passed directly to \TIKZ except when it involves ``\verb/<>/'', which allows two arrows to be drawn one above the other.
\exemple{Types of arrows}*A\chemrel{->}B\par
A\chemrel{<-}B\par
A\chemrel{<->}B\par
A\chemrel{<>}B\par
A\chemrel{->,red,thick}B*

\label{setchemrel}The command \verb-\setchemrel{<dim1>}{<dim2>}{<dim3>}- allows settings of the dimensions used in drawing the arrow:
\begin{itemize}
	\item \verb-<dim1>- is the vertical spacing between the arrow and the optional text above and/or below it. If the argument is empty, it defaults to 2pt;
	\item \verb-<dim2>- is the unbreakable horizontal space inserted before and after the arrow. If the argument is empty, it defaults to 0.7em;
	\item \verb-<dim3>- is the length of the arrow. If the argument is empty, if defaults to 4em.
\end{itemize}

\exemple{Text above arrows}*\setchemrel{1pt}{}{6em}
A\chemrel[\footnotesize above][\tiny below]{<->}B*

Here is an example of a chemical reaction:
\exemple*{Chemical reaction}|\setchemrel{0pt}{1.2em}{6em}
\chemfig{**6(------)}\chemsign+\chemfig{H_3C-Cl}
\chemrel[\itshape\footnotesize Catalyst]{->}
\chemfig{**6(---(-)---)}\chemsign+\chemfig{H-Cl}|

And another:
\exemple*{Synthesis of phenylacetylene}/\chemfig{*6(-=*6(-(-Br)-(-Br))-=-=)}
\chemrel[\chemfig{NaNH_2}][\chemfig{NH_3}]{->}
\chemfig{*6(-=(-~)-=-=)}/

\section{Using {\ttfamily\textbackslash chemfig} in the {\ttfamily tikzpicture} environment}
It is possible to call the \verb-\chemfig- inside a \verb-tikzpicture- environment:
\exemple{\textbackslash chemfig inside tikzpicture}|\begin{tikzpicture}[help lines/.style={thin,draw=black!50}]
		\draw[help lines] (0,0) grid (4,4);
		\draw(0,0) -- (2,1);
		\draw(2,2) circle (0.5);
		\node at (1,3) {\chemfig{A=B-[:30]C}};
		\node[draw,red,anchor=base] at(3,2){\chemfig{X>[2,,,,blue]Y}};
	\end{tikzpicture}|

\section{Beyond chemistry}\label{style.noeuds}
At heart \CF is a tool for drawing graphs, and this tool has been programmed to adapt it for chemistry. In some ways it is possible to return \CF to its roots to draw organization charts or other diagrams represented by graphs.

Each atom is contained in a \TIKZ node. By default these nodes have an ``inner sep'' and an ``outer sep'' equal to 0pt. They are rectangular as seen on page~\pageref{longueur.liaison}. These defaults can be overwritten with the macro \verb-\setnodestyle-, the argument of which is passed to \TIKZ and specifies the style of the nodes containing the atoms.

In this example we specify only ``draw,inner sep=2pt'', which has the effect of drawing the outline of the nodes and separating the outline and node contents by 2pt. We also specify \verb-\setbondoffset{0pt}- so that the bonds touch the edges of the nodes. The interatomic spacing is increased to 75pt. Finally, the command \verb-\printatom- is made as simple as possible so that math mode is no longer used and spaces are thus preserved.
\exemple*{An organization chart}/\setnodestyle{draw,inner sep=2pt}
\setbondoffset{0pt}
\setatomsep{75pt}
\renewcommand\printatom[1]{##1}
\chemfig{The boss-[6]Me(-[4]Them(-[6]The others)(-[7,2]Group 1))-You(-[:-120,0.5]Him)(-[:-60,0.5]Her)}/

Here is another organization chart where the nodes are circular and coloured cyan:
\exemple*{Family diagram}/\setnodestyle{draw,circle,fill=cyan,minimum size=30pt}
\setbondoffset{0pt}
\setatomsep{80pt}
\renewcommand\printatom[1]{\textsf{##1}}
\chemfig{Me(-[:-50,1.2]Brother)(-[:-10]Brother(-[:15]Niece)(-[:-35]Niece))
(-[:-155,0.8]Sister-[:-80]Nephew)(-[:95,1.25]Father(-[:-25,0.8]Uncle)(-[:-65,0.8]Aunt))
(-[:135]Mother-[:-95,0.5]Uncle)}/

\section{Annotated examples}\label{exemples.commentes}
In this chapter, several molecules will be drawn, putting into use the methods previously described. The aim here is to show a logical order for putting together a molecule so that the user unfamiliar with \CF will learn how to construct complex molecules. The construction steps will be shown to help with this learning process.

In addition, several possibilities --- some intuitive and others less so --- will be shown which give the same graphical results, with the objective being to show that \CF allows some flexibility in encoding molecules. One can see how each is put together and adopt the methods with which one is most comfortable.

\subsection{Ethanal}
Here we will draw the ethanal (or acetaldehyde) molecule: \chemfig{H-C(-[2]H)(-[6]H)-C(-[7]H)=[1]O}

The best method for non-cyclic molecules is to select the longest chain. Here one could take ``\verb|H-C-C=0|'' for example. The bond \verb|C=O| is tilted to 45\degres{} by using the predefined angle ``\verb-[1]-''. This give a ``backbone'' of the molecule to which the branches merely have to be added:
\exemple{Backbone of ethanal}|\chemfig{H-C-C=[1]O}|

The three hydrogen atoms still have to placed at the correct orientation with the help of predefined angles. The first is at 90\degres{} with the branch ``\verb/(-[2]H)/'', the second at 270\degres{} with ``\verb/(-[6H])/'', and the one on the right at 315\degres{} with ``\verb/(-[7]H)/'':
\exemple{Ethanal}|\chemfig{H-C(-[2]H)(-[6]H)-C(-[7]H)=[1]O}|

\subsection{2-amino-4-oxohexanoic acid}
Here is the molecule to be drawn: \chemfig{-[::+30]-[::-60](=[:-90]O)-[::+60]-[::-60](-[:-90]NH_2)-[::+60](=[:90]O)-[::-60]OH}

As is often the case for most molecules, there are several methods and for each several different ways of getting the result. Here we will look at four different methods.

\subsubsection{Absolute angles}
We will first of all draw the central chain with absolute angles. We set the default angle to $+30\degres$ with the optional argument, and so only the descending bonds need to have their absolute angle set to $-30\degres$:
\exemple{Backbone (absolute angles)}|\chemfig{[:30]--[:-30]--[:-30]--[:-30]OH}|

The branches ``\verb/(=[6]O)/'', ``\verb/(-[6]NH_2)/'' and ``\verb/(=[2]O)/'' still have to be added to the correct vertices:
\exemple{Molecule (absolute angles)}|\chemfig{[:30]--[:-30](=[6]O)--[:-30](-[6]NH_2)-(=[2]O)-[:-30]OH}|

\subsubsection{Relative angles}
A more general approach uses only relative angles, in this way:
\exemple{Structure (relative angles)}|\chemfig{[:30]--[::-60]--[::-60]--[::-60]OH}|

then
\exemple{Molecule (relative angles)}|\chemfig{[:30]--[::-60](=[::-60]O)--[::-60](-[::-60]NH_2)
-(=[::60]O)-[::-60]OH}|

\subsubsection{Ring}
Since the angles between the bonds are 120\degres{}, it is possible to use a 6-ring, although this method is less natural. Here we take advantage of the fact that a ring can be left unfinished. The ring must be rotated 120\degres{} so that the first vertex is to the south-east of the ring:
\exemple{Backbone (ring)}|\chemfig{[:120]NH_2*6(---=O)}|

Now the branches must be added to the right vertices:
\exemple{Molecule (ring)}|\chemfig{[:120]NH_2*6(-(-(=[::60]O)-[::-60]OH)--(--[::60])=O)}|

\subsubsection{Nested rings}
Delving deeper into the ring method, we can also consider nesting incomplete 6-rings. We could start with this backbone:
\exemple{Backbone (nested rings)}|\chemfig{*6(--*6(--=O))}|

And then add the bonds which leave the vertices of these rings. There are no angles to worry about because the bonds leaving the rings are the bisectors of the sides of the ring, exactly what we want here:
\exemple{Molecule (nested rings)}|\chemfig{*6((-)-(=O)-*6(-(-NH_2)-(-OH)=O))}|

A close look shows that the second line segment of the double bond to the oxygen atom is \emph{inside} the incomplete 6-ring\footnote{This was also true for the preceding method with one ring.} Despite its brevity, this code does not give a perfect drawing. This can of course be corrected by adding a little to the code:
\exemple{Molecule (corrected nested rings)}|\chemfig{*6((-)-(=O)-*6(-(-NH_2)-(-OH)(=[::60]O)))}|

\subsection{Glucose}
The goal here is to represent the glucose molecule according to several different conventions.

\subsubsection{Skeleton diagram}
The code here looks like that of 2-amino-4-oxohexanoic acid. This gives almost the same structure with absolute angles, except here the default angle is $-30\degres$:
\exemple[60]{Backbone}|\chemfig{[:-30]HO--[:30]--[:30]--[:30]-H}|

Adding the branches is no problem. We use predefined absolute angles:
\exemple[60]{Glucose, skeleton diagram}|\chemfig{[:-30]HO--[:30](<[2]OH)-(<:[6]OH)
-[:30](<:[2]OH)-(<:[6]OH)-[:30](=[2]O)-H}|

\subsubsection{Fisher projection}
The goal is to get the molecule below:
\begin{center}
	\definesubmol{x}{(-[4]H)(-[0]OH)}
	\definesubmol{y}{(-[0]H)(-[4]OH)}
	\chemfig{[2]OH-[3]-!x-!x-!y-!x-=[1]O}
\end{center}
The idea is to begin to draw the longest chain vertically by giving a default angle of ``\verb-[2]-''. Here is the skeleton, where we have added lower case letters at the end of each vertical bond:
\exemple{Skeleton}|\chemfig{[2]OH-[3]-a-b-c-d-=[1]O}|

Next we define two aliases for the horizontal bonds and the atoms at their ends. Lets choose ``\verb-x-'' which we will put in place of the lower case a, c and d, and ``\verb-y-'' which will replace the letter c. Since these alias are just one character, we do not need braces and can write ``\verb-!x-'' instead of ``\verb-!{x}-'':
\exemple{Glucose (Fisher projection)}|\definesubmol{x}{(-[4]H)(-[0]OH)}
\definesubmol{y}{(-[0]H)(-[4]OH)}
\chemfig{[2]OH-[3]-!x-!x-!y-!x-=[1]O}|

\subsubsection{``Chair'' representation}
We will depict the $\alpha$-D-glucose molecule:
\chemfig{?(-[:190]OH)-[:-50](-[:170]OH)-[:10](-[:-55,0.7]OH)-[:-10](-[6,0.7]OH)-[:130]O-[:190]?(-[:150,0.7]-[2,0.7]OH)}

To do this, we will first of all draw five sides of the chair and link the first vertex to the last with a hook ``\verb-?-''. We will use the following absolute angles, running counterclockwise: $-50\degres$, $10\degres$, $-10\degres$, $130\degres$, $190\degres$.
\exemple{Structure}|
\chemfig{?-[:-50]-[:10]-[:-10]-[:130]O-[:190]?}|

Now we simply add the branches inside parentheses. The angles are chosen to give the best impression of presentive, and some bonds are shortened by a factor of 0.7:
\exemple{Chair representation}|\chemfig{?(-[:190]OH)-[:-50](-[:170]OH)-[:10](-[:-55,0.7]OH)
-[:-10](-[6,0.7]OH)-[:130]O-[:190]?(-[:150,0.7]-[2,0.7]OH)}|

\subsubsection{Haworth projection}
The goal is to depict this D-glucopyranose molecule:
{\setcrambond{2pt}{}{}
\chemfig{HO-[2,0.5,2]?<[7,0.7](-[2,0.5]OH)-[,,,,line width=2pt](-[6,0.5]OH)>[1,0.7](-[6,0.5]OH)-[3,0.7]O-[4]?(-[2,0.3]-[3,0.5]OH)}}

First of all we will choose the longest chain, which starts at the ``HO'' group on the left and continues through fives sides of the ring. The ring will be closed with a hook. For the vertical bond which leaves from the first ``HO'' group, we need to specify that it will leave from the second atom using the optional argument. Furthermore, it will be shortened with a coefficient of 0.5. Its optional argument will thus be ``\verb/[2,0.5,2]/''.

Next, to give the impression of perspective to the ring, the diagonal bonds will be shortened by a coefficient of 0.7. For the bold diagonal lines we will use Cram bonds, having redefined the base of the triangles to be 2pt. The bold horizontal bond needs to be drawn with a thickness of 2pt, and so its optional argument will be ``\verb/[0,,,,line width=2pt]/''. Here is the skeleton of the molecule:
\exemple{Structure}|\setcrambond{2pt}{}{}
\chemfig{HO-[2,0.5,2]?<[7,0.7]-[,,,,
line width=2pt]>[1,0.7]-[3,0.7]O-[4]?}|

All that needs to be done now is to add the branches at the correct places, giving the right absolute angles and sometimes reducing the length to better give the illusion of prespective:
\exemple{Projection de Haworth}|\setcrambond{2pt}{}{}
\chemfig{HO-[2,0.5,2]?<[7,0.7](-[2,0.5]OH)-[,,,,
line width=2pt](-[6,0.5]OH)>[1,0.7](-[6,0.5]OH)-[3,0.7]
O-[4]?(-[2,0.3]-[3,0.5]OH)}|

\subsection{Adrenaline}
We want to draw the adrenaline molecule:
\chemfig{*6((-HO)-=-(-(<[::60]OH)-[::-60]-[::-60,,,2]HN-[::+60]CH_3)=-(-HO)=)}

We are going to use two different methods.

\subsubsection{Using one ring}
First of all, we start with a 6-ring and we draw the start of the branches which leave it:
\exemple[60]{Skeleton of adrenaline}|\chemfig{*6((-HO)-=-(-)=-(-HO)=)}|

The branch on the right still needs to be completed using, for example, relative angles:
\exemple[60]{Adrenaline, step two}|\chemfig{*6((-HO)-=-(--[::-60]-[::-60]
HN-[::+60]CH_3)=-(-HO)=)}|

Then we need to add a Cram-bonded \verb-OH- and indicate that the bond which arrives at ``\verb-HN-'' does so on the second atom, i.e., ``N''. We use the fourth optional argument of the bond:
\exemple[60]{Adrenaline}|\chemfig{*6((-HO)-=-(-(<[::60]OH)-[::-60]-[::-60,,,2]
HN-[::+60]CH_3)=-(-HO)=)}|

\subsubsection{Using two rings}
This method is less natural, but the goal is to show here how to make a bond invisible.

We could improve this code by considering that the drawing of the adrenaline molecule is made of two 6-rings adjacent to each other:
\exemple[60]{Adrenaline, two-ring skeleton}|\chemfig{*6((-HO)-=*6(--HN---)-=-(-HO)=)}|

Now the first two bonds of the ring on the right need to be made invisible. To do this we use the argument that is passed to \TIKZ, specifying ``\verb-draw=none-''. These bonds will thus have this code: ``\verb/-[,,,,,draw=none]/''. To keep the code readable, we define an alias named ``\verb-&-'' for these bonds:
\exemple[60]{Adrenaline, step two}|\definesubmol{&}{-[,,,,draw=none]}
\chemfig{*6((-HO)-=*6(!&!&HN---)-=-(-HO)=)}|

The rest becomes easy; just add the branches to the right vertices:
\exemple[60]{Adrenaline, step three}|\definesubmol{&}{-[,,,,draw=none]}
\chemfig{*6((-HO)-=*6(!&!&HN(-CH_3)--(<OH)-)-=-(-HO)=)}|

To finish, we specify that the bonds that \emph{arrive at and leave from} ``\verb-HN-'' must do so at the second atom. We therefore define another alias for the invisible bond which arrives at ``\verb-HN-'':
\exemple[60]{Adrenaline}|\definesubmol{&}{-[,,,,draw=none]}
\definesubmol{&&}{-[,,,2,draw=none]}
\chemfig{*6((-HO)-=*6(!&!{&&}HN(-CH_3)-[,,2]-(<OH)-)-=-(-HO)=)}|

\subsection{Guanine}
We will draw the guanine molecule:
\chemfig{*6((-H_2N)=N-*6(-\chembelow{N}{H}-=N?)=?-(=O)-HN-[,,2])}\medskip

First of all, let's begin by drawing the nested rings, putting just the nitrogen atoms at the vertices:
\exemple{Guanine, skeleton}|\chemfig{*6(=N-*6(-N-=N)=--N-)}|

Then we can draw the horizontal bond in the right ring with a hook. We will also place a hydrogen atom under the nitrogen atom of the 5-ring with the command \verb-\chembelow{N}{H}-. We also need to write ``\verb-HN-'' instead of ``\verb-N-'' at the vertex at the upper left of the molecule:
\exemple{Guanine, step two}|\chemfig{*6(=N-*6(-\chembelow{N}{H}-=N?)=?--HN-)}|

We note that one bond leaves from the wrong atom\footnote{This seems illogical because the angle of the bond from the \texttt{HN} group toward the first vertes lies between $-90\degres$ and $90\degres$; \CF should therefore leave from the second atom. To explain this contradiction, one must know that in rings, the last bond always links the last vertex to the first, ignoring the \emph{calculated theoretical} angle of this bond (which here is $-90\degres$). \CF uses this theoretical angle to determine the departure and arrival atoms, but does not use it to draw the bond because the two ends are already defined. The departure atom for the last bond is thus the first atom.}! The automatic calculation mechanism must be corrected so that the bond leaves from the second atom ``\verb-N-'' instead of the first. To do this we give an optional argument for the last bond of the first 6-ring ``\verb-[,,2]-'':
\exemple{Guanine, step three}|\chemfig{*6(=N-*6(-\chembelow{N}{H}-=N?)=?--HN-[,,2])}|

Simply add the branches to the right vertices. Note especially the branch leaving the first vertex of the first 6-ring ``\verb/(-N_2N)/'':
\exemple{Guanine}|\chemfig{*6((-H_2N)=N-*6(-\chembelow{N}{H}-=N?)=?-(=O)-HN-[,,2])}|

We could also draw the same molecule with a regular 5-ring, as is sometimes done:
\exemple{Guanine with 5-ring}|\chemfig{*6((-H_2N)=N-*5(-\chembelow{N}{H}-=N-)=-(=O)-HN-[,,2])}|

\section{List of commands}
The commands created by \CF are:
\begin{center}
\begin{tabular}{>\footnotesize l>\footnotesize p{9cm}}\\\hline
\hfill\normalsize Commands\hfill\null &\hfill\normalsize Description\hfill\null\\\hline
\verb-\chemfig<code>-& draws the molecule whose design is described by the \verb-<code>-\\
\verb-\printatom- & displays the atoms within the molecules. It can be redefined to customize the ouput. See page~\pageref{perso.affichage}\\
\verb-\setnodestyle{<style tikz>}-& using \TIKZ syntax, this macro defines the style of nodes containing the atoms. See page~\pageref{style.noeuds}\\
\verb-\definesubmol{<nom>}[code1]{<code2>}- & créé un alias \verb-!<nom>- que l'on peut placer dans le code des molécules à dessiner qui remplace le \verb-<code1>- ou le \verb-<code2>- selon l'inclinaison de la dernière liaison. Voir page~\pageref{definesubmol}\\
\verb-\chemskipalign- & Ignore le groupe d'atomes en cours pour le mécanisme d'alignement vertical. Voir page~\pageref{chemskipalign}.\\
\verb-\redefinesubmol{<name>}{<code>}- & replaces a pre-existing alias \verb-!<name>- with the new \verb-<code>-. See page~\pageref{redefinesubmol}\\[2ex]\hline
&\\
\verb-\setcrambond{<dim1>}{<dim2>}{<dim3>}- & sets the dimensions of the triangles representing Cram bonds: \verb-<dim1>- is the size of the base, \verb-<dim2>- is the spacing between the dashes and \verb-<dim3>- is the side of the dashes. See page~\pageref{setcrambond}\\
\verb-\setatomsep{<dim>}>- & sets the interatomic distance. See page~\pageref{setatomsep}\\
\verb-\setbondoffset{<dim>}- & sets the space between bonded atoms and the bond. See page~\pageref{setbondoffset}\\
\verb-\setdoublesep{<dim>}- & sets the spacing between the two lines of a double bond. See page~\pageref{setdoublesep}\\[2ex]\hline
&\\
\verb-\lewis{<codes>,<atom>}- & displays the \verb-<atom>- and places Lewis dot decorations as specified in the \verb-<code>-. The dots drawn do not change the bounding box. See page~\pageref{lewis}\\
\verb-\setlewis{<dim1>}{<dim2>}{<tikz code>}- & sets the Lewis dot parameters; \verb-<dim1>- is the distance between the atoms and the decoration, \verb-<dim2>- is the length of the line representing the pair of electrons and \verb-<tikz code>- is code which is passed directly to \TIKZ. See page~\pageref{setlewis}\\[2ex]\hline
&\\
\verb-\chemmove[<options tikz>]<code tikz>- & Ouvre un environnement \verb-tikzpicture- en y ajoutant à celles qui existent déjà les \verb-<options tikz>-, et relie avec le \verb-<code tikz>- les nœuds posés dans les molécules à l'aide du caractère ``\verb-@-''. Voir page~\pageref{mecanismes-reactionnels}.\\
\verb-\chemsign[<dim>]<sign>- & draws the \verb-<sign>-, placing before and after it an unbreakable space of length \verb-<dim>-. See page~\pageref{chemsign}\\
\verb-\chemrel[<txt1>][<txt2>]{<arrow code>}- & draws an arrow described by its \verb-<arrow code>- and places the optional text \verb-<txt1>- and \verb-<txt2>- above and below the arrow respectively. See page~\pageref{chemrel}\\
\verb-\setchemrel{<dim1>}{<dim2>}{<dim3>}- & sets the dimensions of the arrow drawn with the command \verb-\chemrel-: \verb-<dim1>- is the vertical space between the arrow and the optional text, \verb-<dim2>- is the unbreakable horizontal space inserted before and after the arrow  and \verb-<dim3>- is the length of the arrow. See page~\pageref{setchemrel}\\[2ex]\hline
&\\
\verb-\chemabove[<dim>]{<txt1>}{txt2}- & writes \verb-<txt1>- and places \verb-<txt2>- above, leaving \verb-<dim>- of vertical space. This command does not change the bounding box of \verb-<txt1>-. See page~\pageref{chemabove}\\
\verb-\chembelow[<dim>]{<txt1>}{txt2}- & writes \verb-{txt1}- and places \verb-<txt2>- below, leaving \verb-<dim>- of vertical space. This command does not change the bounding box of \verb-<txt1>-. See page~\pageref{chemabove}\\
\verb-\chemname[<dim>]{<molécule>}{<nom>}- & Affiche le \verb-<nom>- sous la \verb-<molécule>-\\
\verb-\chemnameinit- & Initialise la plus grande profondeur des molécules rencontrées pour avoir un alignement correct de leurs noms\\\hline
\end{tabular}
\end{center}
\newpage

\part{Gallery}
This manual concludes with drawings of molecules of varying complexity.

The curious user can look at the \verb-<code>- of each molecule, though it does become less attractive the more complex the molecule gets. Indeed, beyond a certain level of complexity, though it it is fairly easy to write \verb-<code>-, it becomes much harder to read the \verb-<code>- to analyse it afterwards. We quickly reached the limits of immediate readability of the code of a complex drawing.

Anyway, I hope that this package will help all \LaTeX{} users wishing to draw molecules. Given the newness of this package, I hope that you will be forgiving with bugs you encounter and send me an \href{mailto:unbonpetit@gmail.com}{\texttt{\textbf{email}}} to let me know of any malfunctions or suggestions for improvement.\nobreak 

\hfill Christian \textsc{Tellechea}
\bigskip

\begin{center}
\parskip0pt
$\star$\par
$\star\quad\star$
\end{center}
\bigskip

\exemple*{2-methylpentane}/\chemfig{[7]H_3C-CH(-[6]CH_3)-[1]CH_2-CH_2-[1]CH_3}/

\exemple*{3-ethyl-2-methylhexane}/\chemfig{H_3C-[7]CH(-[6]CH_3)-[1]CH(-[7]C_3H_7)-[2]CH_2-[3]H_3C}/

\exemple*{Stearine, condensed structural diagram}/\definesubmol{@}{([0,2]-O-[0,1]C(=[2,1]O)-C_{17}H_{33})}
\chemfig{[2,2]CH_2!@-CH_{\phantom 2}!@-CH_2!@}/

\exemple*{Stearine, skeleton diagram}/\definesubmol{x}{-[:+30,.6]-[:-30,.6]}
\definesubmol{y}{-O-(=[2,.6]O)-!x!x!x!x!x!x!x!x}
\chemfig{[2](!y)-[,1.5](!y)-[,1.5](!y)}/

\exemple*{Methyl 2-methylpropanoate}/\chemfig{H_3C-CH_2(-[2]CH_3)-C(=[1]O)-[7]O-CH_3}/

\exemple*{Vanillin}/\chemfig{HC*6(-C(-OH)=C(-O-[::-60]CH_3)-CH=C(-[,,,2]HC=[::-60]O)-HC=[,,2])} \quad or \quad
\chemfig{*6(-(-OH)=(-OCH_3)-=(-=[::-60]O)-=)}/

\exemple*{Caffeine}/\chemfig{*6((=O)-N(-CH_3)-*5(-N=-N(-CH_3)-=)--(=O)-N(-H_3C)-)}/

\exemple*{Aspirin}/\chemfig{*6(-=-(-O-[::-60](=[::-60]O)-[::+60])=(-(=[::+60])-[::-60]OH)-=)}/Aspirin is a registered trademark of Bayer in many countries.

\exemple*{Phthalic anhydride}/\chemfig{*6(=*5(-(=O)-O-(=O)-)-=-=-)}/

\exemple*{Camphor}/\chemfig{*6(-(<:[::120](-[::-100,0.7])(-[::100,0.7]))--(=O)-(-)(<:[::120])--)}
\quad ou \quad
\setcrambond{3pt}{}{}
\chemfig{<[:10](>[:85,1.8]?(-[:160,0.6])-[:20,0.6])
>[:-10]-[:60](=[:30,0.6]O)-[:170]?(-[:30,0.6])-[:190]-[:240]}/

\exemple*{Triphenylmethane}/\chemfig{*6(-=-*6(-(-*6(=-=-=-))-*6(=-=-=-))=-=)}
\quad ou \quad
\definesubmol{@}{*6(=-=-=-)}
\chemfig{(-[:-30]!@)(-[:90]!@)(-[:210]!@)}/

\exemple*{Amygdalin}/\setcrambond{2pt}{}{}
\definesubmol{c1}{-[:200]-[:120]O-[:190]}
\definesubmol{c2}{-[:170](-[:200,0.7]HO)<[:300](-[:170,0.6]HO)
-[:10,,,,line width=2pt](-[:-40,0.6]OH)>[:-10]}
\definesubmol{csub}{-[:155,0.65]-[:90,0.65]}
\chemfig{O(!{c1}(!{csub}O(!{c1}(!{csub}OH)!{c2}))!{c2})-[:-30](-[:-90]CN)-[:30]*6(=-=-=-)}/

\exemple*{Adenosine triphosphate}/\setcrambond{3pt}{}{}
\definesubmol{a}{-P(=[::-90,0.75]O)(-[::90,0.75]HO)-}
\chemfig{[:-54]*5((--[::60]O([::-60]!aO([::-60]!aO([::60]!aHO))))<(-OH)
-[,,,,line width=2pt](-OH)>(-N*5(-=N-*6(-(-NH_2)=N-=N-)=_-))-O-)}/

\exemple*{Viagra}/\chemfig{N*6((-H_3C)---N(-S(=[::+120]O)(=[::+0]O)-[::-60]*6(-=-(-O-[::-60]-[::+60]CH_3)
=(-*6(=N-*5(-(--[::-60]-[::+60]CH_3)=N-N(-CH_3)-=)--(=O)-N(-H)-))-=))---)}/

\exemple*{Cholesterol ester}/\chemfig{[:30]R-(=[::+60]O)-[::-60]O-*6(--*6(=--*6(-*5(---(-(-[::+60]Me)
-[::-60]-[::-60]-[::+60]-[::-60](-[::-60]Me)-[::+60]Me)-)-(-[::+0]Me)---)--)-(-[::+0]Me)---)}/

\exemple*{Porphyrin}/\chemfig{?=[::+72]*5(-N=(-=[::-72]*5(-[,,,2]HN-[,,2](=-[::-36]*5(=N-(=-[::-72]*5(-NH-[,,1]?=-=))
-=-))-=-))-=-)}/

\exemple*{Manganese 5,10,15,20-tetra(N-ethyl-3-carbazolyl) porphyrin}/\definesubmol{A}{*6(=-*5(-*6(-=-=-)--N(--[::-60])-)=-=-)}
\chemfig{([::+180]-!A)=[::+72]*5(-N=(-(-[::+54]!A)=[::-72]*5(-N(-[::-33,1.5,,,draw=none]Mn)
-(=(-[::+72]!A)-[::-36]*5(=N-(=(-[::+54]!A)-[::-72]*5(-N-(-)=-=))-=-))-=-))-=-)}/

\exemple*{Penicillin}/\chemfig{[:-90]HN(-[::-45](-[::-45]R)=[::+45]O)>[::+45]*4(-(=O)-N*5(-(<:(=[::-60]O)
-[::+60]OH)-(<[::+0])(<:[::-108])-S>)--)}/

\exemple*{LSD}/\chemfig{[:150]?*6(=*6(--*6(-N(-CH_3)--(<(=[::+60]O)-[::-60]N(-[::+60]-[::-60])
-[::-60]-[::+60])-=)([::-120]<H)---)-*6(-=-=-(-[::-30,1.155]\chembelow{N}{H}?)=))}/

\exemple*{Strychnine}/\chemfig{*6(=-*6(-N*6(-(=O)--([::-120]<:H)*7(-O--=?[0]([::-25.714]-[,2]?[1]))
-*6(-?[0,{>}]--(<N?[1]?[2])-(<[::-90]-[::-60]?[2]))(<:[::+0]H)-([::+120]<H))--?)=?-=-)}/

\exemple*{Codeine}/\chemfig{[:-30]**6(-(-OH)-?-*6(-(-[3]-[2,2]-[0,.5])*6(-(<:[:-150,1.155]O?)
-(<:OH)-=-)-(<:[1]H)-(-[2]NCH_3)--)---)}/

\exemple*{A dye (red)}/\chemfig{**6(--*6(-(-NO_2)=-(-\lewis{26,O}-[0]H)=(-\lewis{4,N}=[0]\lewis{2,N}-[0]Ar)-)----)}/

\exemple*{Menthone}/\chemfig{CH_3-?(-[2]H)(-[::-30,2]-[::+60](=[1]\lewis{20,O})
-[::-150,1.5](-[:20]CH(-[1]CH_3)(-[7]CH_3))(-[6]H)-[::-90,2]-[::+60]?)}/

\exemple*{Fischer indole synthesis}/\chemfig{*6(=-*6(-\chembelow{N}{H}-NH_2)=-=-)}
\chemsign+
\chemfig{(=[:-150]O)(-[:-30]R_2)-[2]-[:150]R_1}
\chemrel[$\mathrm{H^+}$]{-stealth}
\chemfig{*6(-=*5(-\chembelow{N}{H}-(-R_2)=(-R_1)-)-=-=)}/

\exemple*{Mécanisme réactionnel : groupement carbonyle}/
\chemfig{C([3]-)([5]-)=[@{db,.5}]@{atoo}\lewis{06,O}}
\chemrel{<>}
\chemfig{\chemabove{C}{\scriptstyle\oplus}([3]-)([5]-)-\chemabove
    {\lewis{026,O}}{\hspace{5mm}\scriptstyle\ominus}}
\chemmove{\draw[->,shorten <=2pt, shorten >=2pt](db) ..controls +(up:5mm) and +(up:5mm)..(atoo);}/

\exemple*{Mécanismes réactionnels : dérivés nitrés}/
\chemfig{R-\chembelow{N}{\hspace{-5mm}\scriptstyle\oplus}([1]=[@{db}]@{atoo1}O)([7]-[@{sb}]@{atoo2}
    \chemabove{\lewis{157,O}}{\hspace{7mm}\scriptstyle\ominus})}
\chemrel{<->}
\chemfig{R-\chemabove{N}{\hspace{-5mm}\scriptstyle\oplus}([1]-\chemabove{O}{\scriptstyle\ominus})([7]=O)}
\chemmove{
    \draw[->,shorten <=2pt, shorten >=2pt](db) ..controls +(120:5mm) and +(120:5mm)..(atoo1);
    \draw[->,shorten <=3pt, shorten >=2pt](atoo2) ..controls +(225:10mm) and +(225:10mm)..(sb);
}/

\exemple*{Addition nucléophile. Amines primaires}/\chemfig{R-@{aton}\lewis{2,N}H_2}
\chemsign{+}
\chemfig{@{atoc}C([3]-CH_3)([5]-CH_3)=[@{atoo1}]O}
\hspace{1cm}
\chemfig{@{atoo2}\chemabove{H}{\scriptstyle\oplus}}
\chemmove[-stealth,shorten <=3pt,dash pattern= on 1pt off 1pt,thin]{
    \draw[shorten >=2pt](aton) ..controls +(up:10mm) and +(left:5mm)..(atoc);
    \draw[shorten >=8pt](atoo1) ..controls +(up:10mm) and +(north west:10mm)..(atoo2);}
\chemrel[\tiny addition]{<>}
\chemfig{R-@{aton}\chembelow{N}{\scriptstyle\oplus}H([2]-[@{sb}]H)-C(-[2]CH_3)(-[6]CH_3)-OH}
\par
\chemmove{
    \draw[-stealth,dash pattern= on 1pt off 1pt,shorten <=3pt, shorten >=2pt]
    (sb)..controls +(left:5mm) and +(135:2mm)..(aton);}
\chemrel{<>}
\chemfig{R-@{aton}\lewis{2,N}([6]-[@{sbh}]H)-[@{sb}]C(-[2]CH_3)(-[6]CH_3)-[@{sbo}]@{atoo}
\chemabove{O}{\scriptstyle\oplus}(-[1]H)(-[7]H)}
\chemmove[-stealth,shorten <=3pt,shorten >=2pt,dash pattern= on 1pt off 1pt,thin]{
    \draw(aton) ..controls +(up:5mm) and +(up:5mm)..(sb);
    \draw(sbh) ..controls +(left:5mm) and +(south west:5mm)..(aton);
    \draw(sbo) ..controls +(up:5mm) and +(north west:5mm)..(atoo);}
\chemrel[\tiny élimination]{<>}
\chemfig{R-N=C(-[1]CH_3)(-[7]CH_3)}
\chemsign{+}
\chemfig{H_3\chemabove{O}{\scriptstyle\oplus}}/

\exemple*{Mécanismes réactionnels de la chloration}/\scriptsize
\setbondoffset{1pt}\setatomsep{2em}
\chemfig{Cl-[4]@{a0}(=[@{a1}:120]@{a2}O)-[:-120](=[:-60]O)-[4]Cl}
\chemsign{+}
\chemfig{*6(-=-=(-@{oh1}OH)-=)}
\chemrel{-stealth}
\chemfig{*6((-O-[:150](-[@{o0}:150]@{o1}\lewis{6.,O})(-[@{cl0}:60]@{cl1}Cl)-[:240](-[4]Cl)=[6]O)=-=-=-)}
\chemrel{-stealth}
\chemfig{*6((-O-[:150](=[2]O)-[:-150](=[6]O)-[:150]Cl)=-=-=-)}
\chemsign{+}
\chemfig{HCl}
\par
\chemfig{*6(-=*6(-O-*6(-@{o2}(=[@{o3}]@{o4}O)-Cl)=)-=-=)}
\chemsign{+}
\chemfig{*6(-=-=(-@{oh2}OH)-=)}
\chemrel{-stealth}
\chemfig{*6(-=*6(-O-(-(-[@{cl2}:60]@{cl3}Cl)(-[@{o5}:-120]@{o6}\lewis{6.,O})-O-[::-40]*6(=-=-=-))=)-=-=)}
\kern-3em \chemrel{-stealth}
\chemfig{[:30]*6(=-(-O-[:-60](=O)-[:-120](=[4]O)-[:-60]O-*6(=-=-=-))=-=-)}
\kern-3em \chemsign{+}
\chemfig{HCl}
\chemmove[line width=0.2pt,-stealth,dash pattern = on 2pt off 1pt]{
    \draw[shorten <=2pt](a1)..controls+(200:5mm)and+(200:5mm)..(a2);
    \draw[shorten >=2pt](oh1.west)..controls+(180:15mm)and+(60:5mm)..(a0);
    \draw[shorten <=6pt,shorten >=2pt](o1)..controls+(270:5mm)and+(270:5mm)..(o0);
    \draw[shorten <=2pt](cl0)..controls+(150:5mm)and+(150:5mm)..(cl1.150);
    \draw[shorten <=2pt](o3)..controls +(30:3mm) and +(30:5mm)..(o4.east);
    \draw[shorten >=2pt](oh2.135).. controls +(150:10mm) and +(90:10mm).. (o2);
    \draw[shorten >=2pt,shorten <=5pt]([xshift=-1.5mm]o6.315)..controls +(315:5mm) and +(315:5mm)..(o5);
    \draw[shorten <=2pt](cl2)..controls +(135:5mm) and +(135:5mm)..(cl3.north west);}/

\exemple*{Cannizzaro}/\chemfig{[:-30]*6(=-=(-@{atoc}C([6]=[@{db}]@{atoo1}O)-H)-=-)}
\chemrel[\chemfig{@{atoo2}\chemabove{O}{\scriptstyle\ominus}}H]{-stealth}
\chemmove[-stealth,shorten >=2pt,dash pattern=on 1pt off 1pt,thin]{
        \draw[shorten <=8pt](atoo2) ..controls +(up:10mm) and +(up:10mm)..(atoc);
        \draw[shorten <=2pt](db) ..controls +(left:5mm) and +(west:5mm)..(atoo1);}
\chemfig{[:-30]*6(=-=(-C([6]-[@{sb1}]@{atoo1}\chembelow{O}{\scriptstyle\ominus})([2]-OH)-[@{sb2}]H)-=-)}
\hspace{1cm}
\chemfig{[:-30]*6((-@{atoc}C([6]=[@{db}]@{atoo2}O)-[2]H)-=-=-=)}
\chemmove[-stealth,shorten <=2pt,shorten >=2pt,dash pattern=on 1pt off 1pt,thin]{
        \draw([yshift=-4pt]atoo1.270) ..controls +(0:5mm) and +(right:10mm)..(sb1);
        \draw(sb2) ..controls +(up:10mm) and +(north west:10mm)..(atoc);
        \draw(db) ..controls +(right:5mm) and +(east:5mm)..(atoo2);}
\vspace{1cm}
\par
\chemrel{-stealth}
\chemfig{[:-30]*6(=-=(-C([1]-@{atoo2}O-[@{sb}0]@{atoh}H)([6]=O))-=-)} \hspace{1cm}
\chemfig{[:-30]*6((-C(-[5]H)(-[7]H)-[2]@{atoo1}\chemabove{O}{\scriptstyle\ominus})-=-=-=)}
\chemmove[-stealth,shorten >=2pt,dash pattern=on 1pt off 1pt,thin]{
        \draw[shorten <=7pt](atoo1.90) ..controls +(+90:8mm) and +(up:10mm)..(atoh);
        \draw[shorten <=2pt](sb) ..controls +(up:5mm) and +(up:5mm)..(atoo2);}/

\begingroup
\catcode`;=12
\exemple*{Réarrangement de Beckmann}/
\setbondoffset{1pt}
\setatomsep{2.5em}
\chemfig{(-[:-150]R')(-[:-30]R)=[2]N-[:30]OH}
\kern-1em
\chemrel[\chemfig{\chemabove{H}{\kern10pt\scriptstyle\oplus}}]{<>}
\kern-0.5em
\chemfig{(-[@{a0}:-150]R')(-[:-30]R)=[2]@{a1}N-[@{b0}:30]@{b1}\chemabove{O}{\scriptstyle\oplus}H_2}
\chemmove[red,-stealth,red,shorten <=2pt]{
    \draw(a0)..controls +(135:2mm) and +(215:4mm).. (a1);
    \draw(b0)..controls +(120:2mm) and +(180:3mm).. ([yshift=7pt]b1.180);
}
\kern-1.5em
\chemrel[\chemfig{{-}H_2O}]{<>}
$\left[\begin{tabular}{c}
    \chemfig{R'-\lewis{2:,N}=@{a1}\chemabove{C}{\scriptstyle\oplus}-R}\\
    \tikz\draw[stealth-stealth](0,3mm)--(0,-3mm);\\
    \chemfig{R'-\chemabove{N}{\scriptstyle\oplus}~C-R}
\end{tabular}\right]$
\chemrel[\chemfig{H_2@{a0}\lewis{0:2:,O}}]{<>}\par
\chemmove[red,-stealth,red,shorten <=3pt]{
    \draw(a0)..controls+(90:10mm)and+(45:10mm)..([yshift=6pt]a1.45);
}
\chemfig{*6(R\rlap{$'$}-N=(-R)-\chemabove{O}{\scriptstyle\oplus} H_2)}
\chemrel[\chemfig{{-}\chemabove{H}{\kern10pt\scriptstyle\oplus}}]{<>}
\chemfig{*6(R\rlap{$'$}-N=(-R)-OH)}
\chemrel{-stealth}
\chemfig{*6(R\rlap{$'$}-\chembelow{N}{H}-(-R)(=[2]O))}
/
\endgroup

\exemple*{Sulfonation de la naphtalène}/\newcommand\putchemnode[1]{\begin{tikzpicture}[remember picture]\node(##1){};\end{tikzpicture}}
\definesubmol\cycleoplus{-[,0.25,,,draw=none]\oplus}
\definesubmol{so2oh}{S(=[::90]O)(=[::-90]O)-OH}
\footnotesize
\setatomsep{2.5em}
\begin{tabular}{ll}
&\putchemnode{l1}\chemname{\chemfig{*6(=-*6(-=-(!\cycleoplus)-(-SO_3H)-)=-=-)}}{Ion 1-arenium}
\chemrel{-stealth}
\chemname{\chemfig{*6(=-*6(-=-=(-!{so2oh})-)=-=-)}}{Acide 1-naphthalenesulfonique}\\
\chemname{\chemfig{*6(=-*6(-=-=-)=-=-)}}{Naphtalène}
\chemsign{+}
\chemfig{H_2SO_4}\putchemnode{a}\kern1cm&\\[-5ex]
&\putchemnode{l2}\chemname{\chemfig{*6(=-*6(-=-(-SO_3H)-(!\cycleoplus)-)=-=-)}}{Ion 2-arenium}\kern-3em
\chemrel{-stealth}
\chemname{\chemfig{*6(=-*6(-=-(-!{so2oh})=-)=-=-)}}{Acide 2-naphthalenesulfonique}
\end{tabular}
\chemmove[-stealth,yshift=1cm]{
    \draw(a)--node[sloped,above]{80\degres C}(l1);\draw(a)--node[sloped,above]{160\degres C}(l2);}/

\begingroup\catcode`;12
\exemple*{Schéma explicatif}/\parbox{0.8\linewidth}{
\hspace{10em}
\tikz[remember picture]\node(n0){\chemname{}{Attaques\\nucléophiles}};\par
\vspace{2ex}\hspace{15em}
\chemfig{R^2-(-[:-60]@{m3}H)-[:60]@{m0}(-[:120]R^1)(-[1,0.25,,,draw=none]\scriptstyle\color{red}\delta+)
    =[@{m1}]@{m2}\lewis{1:7:,O}-[1,0.5,,,draw=none]\scriptstyle\color{red}\delta{-}}
\hspace{5em}
\chemname[-15ex]{}{\tikz[remember picture]\node(n1){};Réactions d'addition}\kern1em
\chemname{}{\tikz[remember picture]\node(n2){};Propriétés basiques}\par
\vspace{6ex}\hspace{8em}
\chemname{}{Propriétés acides des atomes\tikz[remember picture]\node(n3){};
    \\d'hydrogène en position $\alpha$}
\chemmove[-stealth,line width=0.8pt,green!60!black!70]{
    \draw[shorten >=2pt](n0)..controls+(270:4em)and+(180:2em)..(m0);
    \draw[shorten >=8pt](n1)..controls+(180:2em)and+(60:2em)..(m1);
    \draw[shorten >=5pt](n2)..controls+(180:2em)and+(270:2em)..([xshift=3pt]m2.315);
    \draw[shorten >=2pt](n3)..controls+(0:2em)and+(270:2em)..(m3);
}}/
\endgroup

\exemple*{Cristallography}/\newcommand\disk{\tikz\draw[fill=black,overlay](0,0)circle(2pt);}
\setatomsep{20pt}
\renewcommand\printatom[1]{##1}
\setbondoffset{2pt}
\definesubmol{hat}{-[:40,1.5]\disk-[::-30,2]\disk-[::-30,2]\disk-[::-120,2]\disk-[::-30,2]\disk}
\definesubmol{motif}{-[:40,1.5]\disk(-[2,3])-[::-30,2]\disk
(-[2,3])-[::-30,2]\disk(-[2,3])-[::-120,2]\disk(-[2,3])-[::-30,2]\disk}
\chemfig{\disk?[a](-[2,3]\disk?[b](-[2,3]\disk?[c]!{hat}?[c])!{motif}?[b](-[2,3]))!{motif}?[a](-[2,3])}
\qquad
\redefinesubmol{motif}{\disk(-[2,3])(-[:42,3.6,,,draw=none]\disk)-[:30,2.6]\disk
(-[2,3])-[0,3]\disk(-[2,3])-[:-150,2.6]\disk(-[4,3])-[2,3]-[4,3]}
\redefinesubmol{hat}{\disk-[:30,2.6]\disk-[0,3]\disk-[:-150,2.6]\disk-[4,3]}
\chemfig{!{motif}!{motif}!{hat}}
\qquad
\redefinesubmol{motif}{(-[2,3])(-[:25,2.75,,,white]-[2,1.5,,,white]\disk)-[:50,3]\disk
(-[2,3])-[::-50,3]\disk(-[2,3])-[::-130,3]\disk-[2,3]-[4,3]\disk}
\redefinesubmol{hat}{-[:50,3]\disk-[::-50,3]\disk-[::-130,3]\disk}
\chemfig{-[4,3]\disk!{motif}(-[:25,2.75,,,draw=none]\disk?[uat]?[dat](-[::0,2.75]?[uat1]?[dat1]
-[::-90,1.3]\disk?[uat2]?[dat2])-[::-90,1.3]-[:25,2.75])!{hat}?[uat3]?[dat3]-[:50,1.5]
(-[6,1.5,,,draw=none]\disk?[dat,,,blue]?[dat1,,,blue]?[dat2,,,blue]?[dat3,,,blue])
-[2,1.5,,,draw=none]\disk?[uat,,,red]?[uat1,,,red]?[uat2,,,red]?[uat3,,,red]}/

\exemple*{Taxotere}/\chemfig{-[::-30](-[5])(-[7])-[::+60]-[::-60]O-[::+60](=[::-45]O)-[::+90]HN>:[::-60](-[::+60]**6(------))
-[::-30](<:[2]OH)-[::-60](=[6]O)-[::+60]O>:[::-60]*7(---?(<[::-120]OH)-(<|[1]CH_3)(<:[::-90]CH_3)
-(-[1](<[::+80]HO)-[0](=[::+60]O)-[7](<|[::+130]CH_3)(-[::+75](<|[2]OH)-[::-60]-[::-60](<[::+30]O-[::-90])
-[::-60](<[::+90])(<:[::+30]O-[7](-[6]CH_3)=[0]O)-[::-60])-[6]-[5,1.3]?(<:[7]O-[5](=[::-60]O)
-[6]**6(------)))=(-[2]CH_3)-)}/
\end{document}