diff options
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 179 |
1 files changed, 87 insertions, 92 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index 8ae6c12536..aaf2017799 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2020.01.26 +% Molecular Coding Format manual by Akira Yamaji 2020.07.07 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} %%%%\documentclass[a4paper,twoside]{article} @@ -138,7 +138,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. real number plus (+): Counterclockwize real number minus(-): Clockwize - <10,-30,45,-45,30,-30,60 + <-10,-30,45,-45,30,-30,60 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -147,8 +147,8 @@ pk font,PNG,SVG,EPS or MDL MOL file. current angle and enviroment !6 : !,!,!,!,!,! - <30,!,!,!,!,!,! - <30,!6 + <-30,!,!,!,!,!,! + <-30,!6 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -157,14 +157,14 @@ pk font,PNG,SVG,EPS or MDL MOL file. n:@ : Jump to An ** An: atom number(-999<=n<=4095) - <30,!6,3:@,0,!,5:@,-30 + <-30,!6,3:@,0,!,5:@,-30 \end{verbatim} \MCFgraph %------------------------------------ \begin{verbatim} 3:\ : 3:@,0 - <30,!6,3:\,! + <-30,!6,3:\,! \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -182,7 +182,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. \MCFgraph %----------------------------------------------------------------------------- \begin{verbatim} - <-30,!6, + <30,!6, 2:\~dr,!, : 2:@,0~dr,! 4:\`1.5,-90, : 4:@,0`1.5,-90 6:\^15,-60 : 6:@,0^15,-60 @@ -194,7 +194,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. n:# : Connect to An n1@#n2 : n1:@,n2:# - <30,!6,3:\,!3,6:#~bd,9@#4~bz + <-30,!6,3:\,!3,6:#~bd,9@#4~bz \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -225,8 +225,8 @@ pk font,PNG,SVG,EPS or MDL MOL file. tm : triple !! : !~db / !!! : !~tm - <30,!~dm,!,!~dl,!,!~dr,!~db,!~db,!,!~tm - <30,!~dm,!,!~dl,!,!~dr,!! ,!! ,!,!!! + <-30,!~dm,!,!~dl,!,!~dr,!~db,!~db,!,!~tm + <-30,!~dm,!,!~dl,!,!~dr,!! ,!! ,!,!!! \end{verbatim} \MCFgraph \vspace{-3mm}% @@ -240,7 +240,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. zf : wedge dotted zb : wedge dotted backward - <30,!~wf,!,!~wb,!,!~zf,!,!~zb + <-30,!~wf,!,!~wb,!,!~zf,!,!~zb \end{verbatim} \MCFgraph \vspace{-3mm}% @@ -252,7 +252,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. \begin{verbatim} vf:vector forward / vb:vector backward - <30,!~vf,!,!~vb + <-30,!~vf,!,!~vb \end{verbatim} \MCFgraph \vspace{-3mm}% @@ -266,7 +266,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. dt : dotted / wv : wave bd : broad / bz : broad dotted - <30,!7,1=dt,3=wv,5=bd,7=bz + <-30,!7,1=dt,3=wv,5=bd,7=bz \end{verbatim} \MCFgraph \vspace{-3mm}% @@ -289,7 +289,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. wb_ : wedge backward over line bd_ : broad over line - <-30,!8,!,60,90`8, + <30,!8,!,60,90`8, {2~si_,4~wf_,6~wb_,8~bd_}:/_`2 \end{verbatim} \MCFgraph @@ -299,7 +299,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. \begin{verbatim} (!,!n)`length : change length of !,!n - <30,!2,!2`1.2,!2 + <-30,!2,!2`1.2,!2 ** !2`1.2 : '`1.2,!2 \end{verbatim} @@ -308,7 +308,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. \begin{verbatim} ``length : change all bond length after - <30,!2,``1.2,!4 + <-30,!2,``1.2,!4 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -325,7 +325,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. \begin{verbatim} Insert hetero atom - <30,!2,O,!2,N,!2 + <-30,!2,O,!2,N,!2 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -474,7 +474,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. \subsubsection{Insert group} \begin{verbatim} / : single - <30,!,/Me,!,/Et,!3,/Pr,!,/iPr, + <-30,!,/Me,!,/Et,!3,/Pr,!,/iPr, !3,/tBu,!,/Ph^-30,! ** Me:methyl(/_) Et:ethyl(/!) @@ -505,14 +505,14 @@ pk font,PNG,SVG,EPS or MDL MOL file. ` : change length > : change enviroment - <30,``1,!, + <-30,``1,!, /_`2^30,!2,/!2>lr,!2,/!2>rl,!) \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Add group} \begin{verbatim} - <-30,!17,2:/_,4:/!,6:/!2, + <30,!17,2:/_,4:/!,6:/!2, 10:/iPr,14:/tBu,16:/Ph^-60 \end{verbatim} \MCFgraph @@ -521,7 +521,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. \begin{verbatim} ~,^,` : change type,angle,length - <-30,!6, + <30,!6, {2~wf,4~zf,6^-30}:/_ \end{verbatim} \MCFgraph @@ -530,7 +530,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. ^,`,> : change angle,length,environment - <30,!7`1, + <-30,!7`1, 3:/_`2^30,5:/!2>lr,7:/!2>rl \end{verbatim} \MCFgraph @@ -551,7 +551,7 @@ pk font,PNG,SVG,EPS or MDL MOL file. >lr : left-right enviroment >rl : right-left enviroment - <30,!6, + <-30,!6, {3^-30,3,3^30}:/'(!3,"{lr}")>lr, {5^-30,5,5^30}:/'(!3,"{rl}")>rl \end{verbatim} @@ -562,20 +562,20 @@ pk font,PNG,SVG,EPS or MDL MOL file. >45 : fixed angle enviroment >'(-90,90,-90) : multi angle enviroment - <-30,!6,2>45:/'(!3,"{45}"), + <30,!6,2>45:/'(!3,"{45}"), {6>'(-90,90,-90)}:/'(!3,"{(-90,90,-90)}") \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- \subsection{Miscellaneous} %----------------------------------------------------------------------------- -\subsubsection{Change atom and Group} +\subsubsection{Change atom and add group} \begin{verbatim} NH,SO,SOO : inset hetero atom and group simultaneously - <30,!2,NH,!,SO,!,SOO,! + <-30,!2,NH,!,SO,!,SOO,! \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -602,21 +602,8 @@ pk font,PNG,SVG,EPS or MDL MOL file. >| : end brock |=n, bond length=n ,=| - <30,!2,|<,``1.2,!2,>|,!2 - <30,!2,|=1.2,!2,=|,!2 -\end{verbatim} -\MCFgraph -%----------------------------------------------------------------------------- -\subsubsection{Chain start multiple characters} -\begin{verbatim} - if chain start multi charactor string, - use !0 instead of ! - - MC(<30,COOH,!0,!3,COOH) -\end{verbatim} -\MCFgraph -\begin{verbatim} - MC(<30,COOH,!4,COOH) + <-30,!2,|<,``1.2,!2,>|,!2 + <-30,!2,|=1.2,!2,=|,!2 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- @@ -959,7 +946,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) \subsubsection{Atom frame} \begin{verbatim} sw_aframe=1 ** default: sw_aframe=0 - MC(<30,COOH,!0,COOH) + MC(<30,COOH,!,COOH) \end{verbatim} \MCFgraph \newpage @@ -1095,6 +1082,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) beginfont() fsize:=(60mm,20mm); msize:=(1,0.85); + %--------------------------------------- MCat(0,0)(<30,Ph,3=dl,4:/NH2) add( labeloffset:=.7aw; @@ -1104,6 +1092,7 @@ beginfont() drawarrow B3m..A3+B2up**1.5aw ..{A3down}A3; ) + %--------------------------------------- MCat(1,0)(<30,?6,{1,5}=dl,4://NH2) add( labeloffset:=.7aw; @@ -1112,6 +1101,7 @@ beginfont() label(lonepair A3ang,A3+A3up**.7aw); ) ext(drawdblarrow (.4w,.4h)..(.55w,.4h);) + %--------------------------------------- endfont \end{verbatim} \MCFgraph @@ -1134,12 +1124,11 @@ endfont h[m]: molecular height ratio_thickness_char: pen thickness / char width - -%======================================== -ext(label(inf_EN,(.5w,0));) => all font -%======================================== +%---------------------------------------- beginfont() - fsize:=(70mm,30mm;); blength:=0.065; + fsize:=(70mm,30mm;); + blength:=0.065; + %--------------------------------------- MCat(0.1,0.5) (<-210,60`1,60`1,60`1,{1,3}=dl, 1:/R1,4:/R2^-60) @@ -1151,6 +1140,7 @@ beginfont() label.bot("Dienophile",p0+(.5w,0));) MCat(0.9,0.5) (<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1) + %--------------------------------------- ext( drawarrow (.52w,.5h)..(.6w,.5h); defaultscale:=0.7; @@ -1164,39 +1154,60 @@ endfont \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- -\newpage -\section{MCF example} -%----------------------------------------------------------------------------- -\subsection{Acetamiprid} +\subsection{Local ext() setting} \begin{verbatim} - <30,Ph,2:N,1:/Cl, - 4:\,!,N,/_,!,/_,!!,N,!,CN +beginfont("EN:?3") + fsize:=(12mm,15mm); + MCat(0.5,1)(<30,?3) +endfont +beginfont("EN:?4") + fsize:=(12mm,15mm); + MCat(0.5,1)(?4) + %------------------------------- + ext(label.top(inf_EN,(0.5w,0));) + %------------------------------- +endfont +beginfont("EN:?5") + fsize:=(12mm,15mm); + MCat(0.5,1)(?5) +endfont +beginfont("EN:?5") + fsize:=(12mm,15mm); + MCat(0.5,1)(?6) +endfont \end{verbatim} -\MCFgraph -%----------------------------------------------------------------------------- -\subsection{Fenitrothion} +\MCFgraph\MCFgraph\MCFgraph\MCFgraph +\subsection{Global ext() setting} \begin{verbatim} - <30,!,O,!,P,//S,/O!^160,!,O,!, - |,Ph,3:/_,4:/NO2 +ext_clear: reset global ext() + +beginfont("EN:?3") + fsize:=(12mm,15mm); + MCat(0.5,1)(<30,?3) +endfont +%------------------------------- +ext(label.top(inf_EN,(0.5w,0));) +%------------------------------- +beginfont("EN:?4") + fsize:=(12mm,15mm); + MCat(0.5,1)(?4) +endfont +beginfont("EN:?5") + fsize:=(12mm,15mm); + MCat(0.5,1)(?5) +endfont +%--------- +ext_clear; +%--------- +beginfont("EN:?6") + fsize:=(12mm,15mm); + MCat(0.5,1)(?6) +endfont \end{verbatim} -\MCFgraph +\MCFgraph\MCFgraph\MCFgraph\MCFgraph %----------------------------------------------------------------------------- -\subsection{Permethrin} -\begin{verbatim} - <-30,?3,2^-35:*/_,2^35:/*_, - 1:\,!!,/Cl,!,Cl, - 3:\,//O,!,O,!2,Ph, - -4:\,O,-60,Ph -\end{verbatim} -\MCFgraph %----------------------------------------------------------------------------- -\subsection{Endosulfan} -\begin{verbatim} - <26,?7,7=?6[13],11:@,208~wf`1.45,8~wb:#, - 10=d,{3,5}:O,4:S,4://O, - {8,9,10,11,12^-210,12^-150}:/Cl -\end{verbatim} -\MCFgraph +\section{MCF example} %----------------------------------------------------------------------------- \subsection{Luciferin} \begin{verbatim} @@ -1206,14 +1217,6 @@ endfont \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- -\subsection{Warfarin} -\begin{verbatim} - <30,Ph,3=?6,8=dl, - 10:O,7:/OH,9://O, - 8:\,/Ph`1,60,!,//O,! -\end{verbatim} -\MCFgraph -%----------------------------------------------------------------------------- \subsection{Limonin} \begin{verbatim} <30,?6,{-3,-4}=?6,-5=?3, @@ -1278,7 +1281,7 @@ endfont \subsection{Atoropin} \begin{verbatim} <-30,O,!,//O,!,!,Ph, - $1:@,-120~zb, + $1:@,-60~zb, |,?7,6:*\^190`1.02,N,/_,3~wb:#, $3:*\*,!,OH \end{verbatim} @@ -1301,14 +1304,6 @@ endfont \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- -\subsection{Validamycin} -\begin{verbatim} - <30,?6,{5,6}:/OH,3:/!OH>rl, - $4:\,O,-60,|,?6,2:O,{3,4,5}:/OH,6:/!OH, - $1:\,NH,!,|,?6,2=dl,{4,5,6}:/OH,3:/!OH -\end{verbatim} -\MCFgraph -%----------------------------------------------------------------------------- \subsection{Paclitaxel} \begin{verbatim} ?6,5=d,3:@,|=1,36,45,45,45,45,=|,$5:#, @@ -1329,7 +1324,7 @@ endfont %------------------------------------------------------------------------- input mcf2graph.mf; % input macro %------------------------------------------------------------------------- -sw_aux_out:=1; % aux(information) file output on > Gloval setting +sw_aux_out:=1; % aux(information) file output on > Global setting fsize:=(60mm,40mm); % (font width,font height) > var3:="cal_MW"; tag3:="cMW"; > AUX file table var4:="cal_FM"; tag4:="cFM"; > |