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diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex new file mode 100644 index 00000000000..2b0c4e507c6 --- /dev/null +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex @@ -0,0 +1,572 @@ +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% Molecular Coding Format manual by Akira Yamaji 2015.7 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\documentclass[a4paper]{article} +\usepackage{graphicx} +\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% +}% +%---------------------------------------------------------------------------- +\def\MCFstructureEPS{% + \makebox(75,0)[t]% + {\frame{\makebox(70,35){% + \ifnum\fontnum<10\includegraphics{mcf_man_soc-00\the\fontnum}% + \else\ifnum\fontnum<100\includegraphics{mcf_man_soc-0\the\fontnum}\fi\fi}}}% + \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax% +}% +%---------------------------------------------------------------------------- +\begin{document} +\noindent% +\begin{picture}(180,0) + \put(50,12){{\LARGE Molecular coding format manual}\hspace{20mm} + by Akira Yamaji 2015.7} +\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 + dm:double,dl:double(left),dr:double(right), + wf:wedge forward,wb:wedge backward, + zf:wedge dotted,zb:wedge dotted backward + + ^^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,!3,!`1.2,!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,!3,``1.2,!3 +\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,$(3,3,3)??6 NG + ?6,$(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 (2)} +\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 (3)} +\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,$(3,9)??6,(4,11)=??6[4], + (16,17)=??6[3],(20,5)=??4[2] + +\end{verbatim} +\end{minipage} +\MCFstructure +\vspace{6mm}\\ +%----------------------------------------------------------------------------- +\begin{minipage}[t][38mm]{100mm} +\MCFtitle{Fused ring (4)} +\begin{verbatim} +(20,5)=??5[3] : fuse 3/5 ring to B20..B5 +(16,17)=??5[2] : fuse 2/5 ring to B16..B17 + + ^^30,?6,$(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,{,``1,!7,}, + @(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,?6,@(2,5)N, + 2:red,5:green,3=red + +\end{verbatim} +\end{minipage} +\MCFstructureEPS +\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}\\ +%----------------------------------------------------------------------------- +\end{document} |