Package acide-amine.sty
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- Patience Lang
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1 Package acide-amine.sty This package provide commands who draw an amino acid. You will nd below the list of amino acids available. Molecules were initialy drawn by Florian Hollandt, see : My contribution was only to do all commands. I give the standard three letters code for each commands who draw amino acid. For arginine, the three letters code is arg which has been ever dened in another command. Thus I gave to it he name aarg. The general syntax for an amino acid with the name aaa is : \aaa{ scale } scale is a number between 0 and 1 which control the size of the picture. The following table gives all amino acids. Each molecule is drew by the command in the command column. amino acid command result command result command result command result valine isoleucine leucine \leu{0.5} \leub{0.5} methionine \met{0.5} S phénilalanine \phe{0.5}
2 Alanine \ala{0.5} N Proline \pro{0.5} Tryptophane \trp{0.5} Glycine \gly{0.5} H tyrosine \tyr{0.5} H sérine \ser{0.5} H \serb{0.5} H thréonine \thr{0.5} H cystéine \cys{0.5} SH
3 2 asparagine \asn{0.5} Glutamine \gln{0.5} 2 Arginine \aarg{0.5} 2 lysine \lys{0.5} 2 histidine \hised{0.5} N δ N ɛ \hip{0.5} HN + \hid{0.5} HN N \hie{0.5} N note : commands hie and his give the same result. H acide aspartique \asp{0.5}
4 acide glutamique \glu{0.5} H Here is the package source code : acide-amine.sty % Package acide - amine. sty % Germain Vallverdu - mai 2009 % germain _ vallverdu@ yahoo. fr % http :// germain. salvato - vallverdu. perso. sfr. fr % All molecules were only slightly modified from the picture RNA codons % Author : Florian Hollandt % see : http :// www. texample. net / tikz / examples / author / florian - hollandt / % needs tikz package and the following library \ usepackage { tikz } \ usetikzlibrary { decorations. pathmorphing } % to _x and from _x styles % denote bonds terminating or starting in labeled nodes. % x denotes the number of letters in the node label. \ tikzstyle { to _1} =[ shorten >=5 pt ] \ tikzstyle { to _1 i} =[ shorten >=6 pt ] \ tikzstyle { to _2} =[ shorten >=7 pt ] \ tikzstyle { to _3} =[ shorten >=8 pt ] \ tikzstyle { from _1} =[ shorten <=5 pt ] \ tikzstyle { from _1 i }=[ shorten <=6 pt ] \ tikzstyle { from _2} =[ shorten <=8 pt ] \ tikzstyle { link } =[ decorate, decoration ={ snake, amplitude =1.5 pt, segment length =4 pt }] Lysine \ newcommand {\ lys }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { };
5 \ draw [ to _3] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(270:1) node ( Cd ) {} -- ++(210:1) node ( Ce ) {} -- ++(150:1) node ( Cf ) { $_{\ mbox {2}}$}; Asparagine \ newcommand {\ asn }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _2] ( zero. center ) -- ++(270:1) node ( Cb ){} -- +(30:1) node ( Cd ) { $_{\ mbox {2}}$}; \ draw [ to _1 i] ( Cc. center ) -- +(270:1) node () {}; \ draw [ to _1] ( Cc.210) -- (.150); \ path (. center ) node { }; Arginine \ newcommand {\ aarg }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _2] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(270:1) node ( Cd ) {} -- ++(330:1) node ( 1) { }; \ draw [ from _2, to _3] ( 1. center ) -- ++(30:1) node ( Ce ) {} -- ++(330:1) node { $_{\ mbox {2}}$};
6 \ draw [ to _1 i] ( Ce. center ) -- ++(90:1) node (N 2) {}; \ draw [ to _1] ( Ce.150) -- (N 2.210); \ path (N 2) node [ xshift =1.5 mm ] { }; Serine \ newcommand {\ ser }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _2] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(210:1) node ( Cc ) { H }; Serine bis \ newcommand {\ serb }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _2] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(330:1) node ( Cc ) { H }; Threonine \ newcommand {\ thr }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1);
7 \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _2] ( zero. center ) -- ++(270:1) node ( Cb ){} ( Cb. center ) -- +(210:1) node { H }; Methionine \ newcommand {\ met }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _1] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(30:1) node ( Cd ) {S }; \ draw [ from _1] ( Cd. center ) -- +(330:1); Isoleucine \ newcommand {\ ile }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- +(30:1) node ( Cd ) {} ( Cb. center ) -- +(210:1) node ( Ce ) {};
8 Glutamic acid \ newcommand {\ glu }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _1 i] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(270:1) node ( Cd ) {} -- ++(330:1) node ( ) { H }; \ draw [ to _1] ( Cd. center ) -- +(210:1) node () {}; \ draw [ to _1 i] ( Cd.270) -- (.300); \ path (. center ) node { }; Aspartic acid \ newcommand {\ asp }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _2] ( zero. center ) -- ++(270:1) node ( Cb ){} -- +(30:1) node ( Cd ) { H }; \ draw [ to _1 i] ( Cc. center ) -- +(270:1) node () {}; \ draw [ to _1] ( Cc.210) -- (.150); \ path (. center ) node { }; Glycine \ newcommand {\ gly }[1]{{\ footnotesize
9 \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _1] ( zero. center ) -- ++(270:1) node {H }; Alanine \ newcommand {\ ala }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; ; Valine \ newcommand {\ val }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; ; Glutamine
10 \ newcommand {\ gln }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _3] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(270:1) node ( Cd ) {} -- ++(330:1) node ( ) { $_{\ mbox {2}}$}; \ draw [ to _1] ( Cd. center ) -- +(210:1) node () {}; \ draw [ to _1 i] ( Cd.270) -- (.300); \ path (. center ) node { }; Histidine = HIE \ newcommand {\ his }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- ++(330:1) node ( Cc ){}; \ draw [ to _2] ( Cc. center ) -- ++(108-1*72:1) node ( Cd ) {} -- ++(108-2*72:1) node ( Ce ) { }; \ draw [ from _1, to _1] ( Ce. center ) -- ++(108-3*72:1) node ( Cf ) {} -- ++(108-4*72:1) node ( Cg ) {}; \ draw [ from _1] ( Cg. center ) -- ( Cc. center ); \ draw ( Cc.198+2*72) -- ( Cd.198+1*72); \ draw [ from _1] ( Cg.72) -- ( Cf.198+4*72); \ draw ( Cg. center ) node {N }; \ newcommand {\ hie }[1]{\ his {#1}}
11 Histidine = HID \ newcommand {\ hid }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- ++(330:1) node ( Cc ){}; \ draw [ to _2] ( Cc. center ) -- ++(108-1*72:1) node ( Cd ) {} -- ++(108-2*72:1) node ( Ce ) {} node [ xshift = -0.5 mm ] {N }; \ draw [ from _1, to _1] ( Ce. center ) -- ++(108-3*72:1) node ( Cf ) {} -- ++(108-4*72:1) node ( Cg ) {}; \ draw [ from _1] ( Cg. center ) -- ( Cc. center ); \ draw ( Cc.198+2*72) -- ( Cd.198+1*72); \ draw [ from _1] ( Cg.72) -- ( Cf.198+4*72); \ draw ( Cg. center ) node [ xshift = -0.5 mm ] { HN }; Histidine = HIP \ newcommand {\ hip }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- ++(330:1) node ( Cc ){}; \ draw [ to _2] ( Cc. center ) -- ++(108-1*72:1) node ( Cd ) {} -- ++(108-2*72:1) node ( Ce ) { }; \ draw [ from _1, to _1] ( Ce. center ) -- ++(108-3*72:1) node ( Cf ) {} -- ++(108-4*72:1) node ( Cg ) {}; \ draw [ from _1] ( Cg. center ) -- ( Cc. center ); \ draw ( Cc.198+2*72) -- ( Cd.198+1*72); \ draw [ from _1] ( Cg.72) -- ( Cf.198+4*72); \ draw ( Cg. center ) node [ xshift = -0.5 mm ] { HN }; \ path ( Cc. center ) ++(340:0.75) node [ circle, draw, thin, scale =0.4] {{\ textbf \ small $+$}};
12 Histidine with delta epsilon \ newcommand {\ hised }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- ++(330:1) node ( Cc ){}; \ draw [ to _2] ( Cc. center ) -- ++(108-1*72:1) node ( Cd ) {} -- ++(108-2*72:1) node ( Ce ) {N $_{\ epsilon }$}; \ draw [ from _1, to _1] ( Ce. center ) -- ++(108-3*72:1) node ( Cf ) {} -- ++(108-4*72:1) node ( Cg ) {}; \ draw [ from _1] ( Cg. center ) -- ( Cc. center ); \ draw ( Cc.198+2*72) -- ( Cd.198+1*72); \ draw [ from _1] ( Cg.72) -- ( Cf.198+4*72); \ draw ( Cg. center ) node {N $_{\ delta }$}; Proline \ newcommand {\ pro }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node ( nh ) {N }; \ draw [ link ] ( nh. north ) -- ++(90:1); ; \ path ( Cb. center ) -- +(150:1) node (x) {}; \ path (x. center ) +(170:1) node ( Cd ) {}; \ path (x. center ) +(250:1) node ( Cc ) {}; \ draw [ to _1] ( Cb. center ) -- ( Cc. center ) -- ( Cd. center ) -- ( nh. center );
13 Leucine \ newcommand {\ leu }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- +(30:1) node ( Cd ) {} ( Cc. center ) -- +(270:1) node ( Ce ) {}; Leucine bis \ newcommand {\ leub }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- ++(210:1) node ( Cc ) {} -- +(150:1) node ( Cd ) {} ( Cc. center ) -- +(270:1) node ( Ce ) {}; Tyrosine \ newcommand {\ tyr }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {};
14 \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; ; \ draw ( Cb. center ) -- ++(30:1) node ( Cd ) {} -- ++(330:1) node ( Ce ) {} -- ++(270:1) node ( Cf ) {} -- ++(210:1) node ( Cg ) {} -- ++(150:1) node ( Ch ) {} -- ++(90:1); \ draw ( Cc.330) -- ( Cd.270); \ draw ( Ce.210) -- ( Cf.150); \ draw ( Cg.90) -- ( Ch.30); \ draw [ to _1 i] ( Cf. center ) -- +(330:1) node ( H ) { H }; Tryptophane \ newcommand {\ trp }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; -- ++(330:1) node ( Cc ){}; \ draw [ to _2] ( Cc. center ) -- ++(108-1*72:1) node ( Cd ) {} -- ++(108-2*72:1) node ( Ce ) { }; \ draw [ from _1]( Ce. center ) -- ++(108-3*72:1) node ( Cf ) {} -- ++(108-4*72:1) node ( Cg ) {}; \ draw ( Cg. center ) -- ( Cc. center ); \ draw ( Cc.198+2*72) -- ( Cd.198+1*72); \ draw ( Cg.72) -- ( Cf.198+4*72); \ draw ( Cg. center ) -- ++(240:1) node ( Ch ) {} -- ++(300:1) node ( Ci ) {} -- ++(0:1) node ( Cj ) {} -- ++(60:1) node ( Ck ) {} -- ++(120:1) node ( Cl ) {};
15 \ draw ( Ch.0) -- ( Ci.60); \ draw ( Cj.120) -- ( Ck.180); Cysteine \ newcommand {\ cys }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; \ draw [ to _2] ( zero. center ) -- ++(270:1) node ( Cb ){} -- ++(210:1) node ( Cc ) { SH }; Phenylalanine \ newcommand {\ phe }[1]{{\ footnotesize \ draw ( zero. center ) -- ++(30:1) node ( C ) {}; \ draw [ link ] ( C. center ) -- ++(330:1); \ draw [ to _1] ( C. center ) -- +(90:1) node ( d ) {} node [ xshift =0.5 mm ] { }; \ draw [ to _1 i] ( C.30) -- +(90:1); \ draw [ to _1] ( zero. center ) -- ++(150:1) node (N) { }; ; \ draw ( Cb. center ) -- ++(210:1) node ( Cc ) {} -- ++(150:1) node ( Cd ) {} -- ++(210:1) node ( Ce ) {} -- ++(270:1) node ( Cf ) {} -- ++(330:1) node ( Cg ) {} -- ++(30:1) node ( Ch ) {} -- ++(90:1); \ draw ( Cc.210) -- ( Cd.270); \ draw ( Ce.330) -- ( Cf.30); \ draw ( Cg.90) -- ( Ch.150);
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