%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Molecular Coding Format manual by Akira Yamaji 2015.7.25 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage[dvipdfmx]{graphicx} %%%%\usepackage[pdftex]{graphicx} %%%%\usepackage{epstopdf} \pagestyle{empty} \topmargin=-17mm \textheight=27.5cm \textwidth=18cm \oddsidemargin=-9mm \parindent=0mm \unitlength=1mm% \makeatletter %---------------------------------------------------------------------------- \newcount \fontnum% \newcount \tempnum% \fontnum=0% \tempnum=1% %---------------------------------------------------------------------------- \font\@strufont=mcf_man_soc\relax% %---------------------------------------------------------------------------- \def\MCFtitle#1{\framebox{\bf No.\the\tempnum}\hspace{2mm}#1} %---------------------------------------------------------------------------- \def\MCFstructure{% \makebox(75,0)[t]{\frame{\makebox(70,35){\@strufont\char\fontnum}}} \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax% }% %---------------------------------------------------------------------------- \begin{document} \noindent% \begin{picture}(180,0) \put(35,12){{\LARGE Molecular Coding Format manual}\hspace{10mm} by Akira Yamaji 2015.7.25} \end{picture}\vspace{-6mm}\\ %---------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Chain (1)} \begin{verbatim} plus(+):anticlockwize,minus(-)clockwize bold arrow is default angle and position ^^30,-60,60,-60,60,-60,60 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %1---------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Chain (2)} \begin{verbatim} !,!!: take 60 or -60 depend on current angle and enviroment !6 (!!6) ** !!6: !,!,!,!,!,! !6: {,!!6,} \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Ring} \begin{verbatim} six membered ring ?6 (??6) ** ??6 :^^-120,60,60,60,60,60,&(-5) ?6 : {,??6,} \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{rotate} \begin{verbatim} ^^angle:rotate current angle ^^30,!4,^^30,?6 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change bond (1)} \begin{verbatim} ~bond change bond dm:double,dl:double(left),dr:double(right), wf:wedge forward,wb:wedge backward, zf:wedge dotted,zb:wedge dotted backward ^^30,!~dm,!~dl,!~dr,!~wf,!~wb,!~zf,!~zb \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change bond (2)} \begin{verbatim} Bn=bond : change bond vf:vector forward, vb:vector backward, tm:triple, wv:waved, bd:broad single, ov:over line ^^30,!9,1=vf,2=vb,3=tm,4=dt,5=wv, @(7~bd^-45`2,9~ov^45`2)/Me \end{verbatim} \end{minipage} \MCFstructure \newpage %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change bond length (1)} \begin{verbatim} B`length : change bond length of B ^^30,!2,!2`1.2,! \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change bond length (2)} \begin{verbatim} ``length : change all bond length after ^^30,!2,``1.2,!2,! \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change chain length (3)} \begin{verbatim} ?n`length : change ring length ^^30,?6,3\,?6`1.2,4=??6 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change atom (1)} \begin{verbatim} Insert hetero atom ^^30,!2,O,!2 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change atom (2)} \begin{verbatim} 2:O : change A2 C to O @(3,5)N : change A3,A5 C to N ^^30,!6,2:O,@(3,5)N \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change atom (3)} \begin{verbatim} 2:N : change A2(brock ahead) C to N ?6,4\,?6,2:N \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change atom (4)} \begin{verbatim} 2:N : change A2(brock ahead) C to N ??6 is not brock ?6,4\,??6,2:N \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change atom (5)} \begin{verbatim} #2:N : change A#2 C to N ?6,4\,?6,#2:N \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change atom (6)} \begin{verbatim} -2:N : change A(-2) C to N ?6,4\,?6,-2:N \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Fused ring (1)} \begin{verbatim} ?6,3=?6 : fuse ?6 at B3 ?6,3=?6 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Fused ring (2)} \begin{verbatim} ?6,$(3,3,3)??6 NG ?6,$(3,9,14)??6 OK ?6,$(-4,-3,-3)??6 OK ?6,$(#3,#9,#14)??6 OK \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Fused ring (3)} \begin{verbatim} ?6,$(3,3,3)?6 OK ?6,$(3,9,14)?6 NG ?6,$(-4,-3,-3)?6 OK ?6,$(#3,#9,#14)?6 OK \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Fused ring (4)} \begin{verbatim} (4,11)=??6[4] : fuse 4/6 ring to B4 ..B11 (16,17)=??6[3] : fuse 3/6 ring to B16..B17 (20,5)=??4[2] : fuse 2/4 ring to B20.. B5 ^^30,?6,$(3,9)??6,(4,11)=??6[4], (16,17)=??6[3],(20,5)=??4[2] \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Fused ring (5)} \begin{verbatim} (20,5)=??5[3] : fuse 3/5 ring to B20..B5 (16,17)=??5[2] : fuse 2/5 ring to B16..B17 ^^30,?6,$(3,9)??6,(4,11)=??6[4], (20,5)=??5[3],(16,17)=??5[2] \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Spiro ring} \begin{verbatim} 4*,?5 : add ?5(5 membered ring) to A4 ^^30,!6,4*,?5 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Branch (1)} \begin{verbatim} / : branch bond / : process at last ^^30,!3,/!2,!3 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Branch (2)} \begin{verbatim} 4\ : branch bond at A4 ^^30,!6,4\,!2 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Substituent (1)} \begin{verbatim} / : single // : double */ : wedge forward /* : wedge backward ** : direct ^^30,!,//O,!,/*H,!,*/H,!,/?3,!,**?3,! \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Substituent (2)} \begin{verbatim} Insert substituent ^^30,!,/Me,!,/Et,!3,/Pr,!,/iPr,!3,/tBu,! \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Substituent (3)} \begin{verbatim} Add substituent ^^30,!10,2:/Me,3:/Et,6:/Pr,7:/iPr,10:/tBu \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Substituent (4)} \begin{verbatim} ~,^,`,> : change type,angle,length,enviroment of substituent ^^30,?6, @(3`2^30,3~wf,4~zf,6~wf^-30,6~zf^30)/H \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Substituent (5)} \begin{verbatim} ~,^,`,> : change type,angle,length,enviroment of substituent ^^30,!7`1, @(2,3)/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change atom and Substituent} \begin{verbatim} NH,SOO : inset hetero atom and substituent simultaneously ^^30,!3,NH,!,SOO,!3 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Chain strech direction environment (1)} \begin{verbatim} >hz : horizontal enviroment (default) >vt : vertical enviroment ?4, @(3^-90,3^-30,3^90)/'(!3,"{>hz}")>hz, @(1^-60,1`1.5,1^60)/'(!2,"{>vt}")>vt \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Chain strech direction environment (2)} \begin{verbatim} >lr : left-right enviroment >rl : right-left enviroment ^^30,!6, @(3^-30,3,3^30)/'(!3,"{>lr}")>lr, @(5^-30,5,5^30)/'(!3,"{>rl}")>rl \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Chain strech direction environment (3)} \begin{verbatim} >45 : fixed angle enviroment >'(-90,90,-90) : multi angle enviroment ^^-30,!6,@(2>45)/'(!3,"{>45}"), @(6>'(-90,90,-90))/'(!2,"{>(-90,90,-90)}") \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Change color} \begin{verbatim} @(5)green : change color of A5 green $(3)red : change color of B3 red ^^30,Ph,@(2,5)N, 2:red,5:blue,3=green \end{verbatim} \end{minipage} %%%%\MCFstructure % for Metafont \makebox(75,0)[t]{\frame{\makebox(70,35)% {\includegraphics{mcf_man_soc-032.eps}}}}% for dvipdfmx %%%%{\includegraphics[width=30mm]{mcf_man_soc-030.png}}}}% for pdfLaTeX \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax% \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Chain start multiple characters} \begin{verbatim} Use !0 instead of !, if begin with multi charactor string ^^30,COOH,!0,!,/OH^-30,/COOH^30,!2,COOH \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{User definition} \begin{verbatim} iBuOH : user defined substructure iBuOH:='(!,/Me,!,OH) MCf(^^30,?6,@(4,6)/iBuOH) \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Inline definition} \begin{verbatim} Insert user defined substructure ^^30,!3,/'(!,/Me,!,OH),!3 \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Switch Start Vector} \begin{verbatim} MCd(.8,.8)( 0, 0)(^^30,Ph,4:/Cl,3:/F) sw_start_vector:=1; MCd(.8,.8)( 1, 1)(^^30,Ph,4:/Cl,3:/F) \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Switch NumberingA} \begin{verbatim} sw_numberA:=1; MCf(^^30, Ph,-4=Ph1,-3\,!,Ph,10:/Et) \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Switch NumberingB} \begin{verbatim} sw_numberB:=1; MCf(^^30, Ph,-4=Ph1,-3\,!,Ph,10:/Et) \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Switch Frame} \begin{verbatim} MCd(.8,.8)(0,0)(^^30,Ph,4:/Cl,3:/F) sw_frame:=1; MCd(.8,.8)(1,1)(^^30,Ph,4:/Cl,3:/F) \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Switch Solid ratio} \begin{verbatim} MCd(.8,.8)( 0, 0)(^^30,Ph,4:/Cl,3:/F) sw_solid:=1; ratio_bond_width:=0.08; MCd(.8,.8)( 1, 1)(^^30,Ph,4:/Cl,3:/F) \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Switch Expand} \begin{verbatim} MCd(.6,.6)(0,0)(^^30,Ph,4:/COOH,3:/NH2) sw_expand:=1; MCd(.6,.6)(1,1)(^^30,Ph,4:/COOH,3:/NH2) \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Example(1) Ampicillin} \begin{verbatim} ^^45, ?4,2:N,2=??5,-1:S, @(3^45,4^-45)/*H,1://O^15, 5:/*COOH^-18,@(6^35,6^-35)/Me, 4\^75,NH,!,//O,!,NH,!,Ph \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Example(2) Cholesterol} \begin{verbatim} ^^30, ?6,$(-4,-2)??6,-4=??5,7=dl, 1:*/OH,@(4,12)*/Me^60,9:*/H^60, 10:/*H^180,@(11,-1)/*H^-60, -1\^17,/*Me,!4,/Me,!, \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Example(3) alfa-Tocopherol} \begin{verbatim} ^^30, Ph,3=??6, 7:O,@(1,2,5)/Me,8:/*Me^60,6:/OH, 8\,!12,@(4,8)/*Me,12:/Me \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Example(4) Caffeine} \begin{verbatim} ^^30, ?6,-4=??5,$(3,8)dl,@(2,6,7,9)N, @(2,6,9)/Me,@(1,5)//O \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Example(5) Lycorine} \begin{verbatim} ^^30, Ph,-4=??6,-2=??6,6=??5,(9,12)=??5[3], 13=dl,8:N,@(15,17)O, 9:/*H^180,10:*/H^60,13:*/OH,14:/*OH \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][38mm]{100mm} \MCFtitle{Example(6) Gibberellin} \begin{verbatim} ^^12, ?6`1.3,3=??5,9=??7,12\^160`1.6,&8, 4\^155~zf`-1.2,O,55,//O^180`1,&2~zb, 3=dr,11=wf,13=wb,7:/COOH,11://Me,1:*/OH, 12:/*OH,2:*/Me,@(3^-60,9^60)*/H \end{verbatim} \end{minipage} \MCFstructure \vspace{6mm}\\ %----------------------------------------------------------------------------- \end{document}