From d4bcdd471d32a18a14ce486284c593d3cb90f7a1 Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Mon, 10 Oct 2016 21:14:36 +0000 Subject: mcf2graph (10oct16) git-svn-id: svn://tug.org/texlive/trunk@42248 c570f23f-e606-0410-a88d-b1316a301751 --- .../doc/metapost/mcf2graph/mcf_manual.tex | 1499 ++++++++------------ 1 file changed, 586 insertions(+), 913 deletions(-) (limited to 'Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex') diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex index 7a2bf1d9fc7..265c66c9d8a 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex @@ -1,11 +1,14 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2016.08.21 +% Molecular Coding Format manual by Akira Yamaji 2016.10.10 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} -\usepackage{graphicx} -%%%%\usepackage[dvipdfmx]{graphicx} +%%%%\usepackage{graphicx} +\usepackage[dvipdfm]{graphicx} %%%%\usepackage[pdftex]{graphicx} %%%%\usepackage{epstopdf} +\usepackage[dvipdfmx]{hyperref} +%%%%\usepackage[pdftex]{hyperref} +\hypersetup{colorlinks=true,linkcolor=blue} \topmargin=-18mm \textheight=254mm \textwidth=168mm @@ -16,23 +19,17 @@ \newcount \fontnum% \newcount \tempnum% \newdimen \htman% -\newdimen \gpman% -\htman=47mm% -\gpman=4mm% -\fontnum=0% +\newdimen \wdman% +\newdimen \htmans% +\htman=45mm% +\wdman=94mm% +\htmans=42mm% +\fontnum=20% \tempnum=1% %---------------------------------------------------------------------------- \font\@strufont=mcf_man_soc\relax% %---------------------------------------------------------------------------- -\def\MCFtitle#1{\framebox{\sf No.\the\tempnum}\hspace{2mm}\bf #1} -%---------------------------------------------------------------------------- -\def\MCFstru{% - \rlap{\makebox(72,4)[t]{\makebox(68,48){\@strufont\char\fontnum}}}% - \advance\fontnum\@ne\relax}% -\def\MCFstructure{% - \makebox(72,4)[t]{\frame{\ - \makebox(68,48){\@strufont\char\fontnum}}}% - \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax}% +\def\MCFstructure{\hspace{5mm}{\@strufont\char\fontnum}\advance\fontnum\@ne\relax}% %-------------------------------------------------------------------- \def\@F{F}\def\@C{C}\def\@EN{EN}\def\@NO{NO}\def\@cMW{cMW}\def\@cFM{cFM}% \def\@fst#1:#2;{#1}\def\@sec#1:#2;{#2}% @@ -48,1164 +45,763 @@ \ifx\@tag\@cFM\edef\CALfm{\@var}\fi \fi}% \def\put@char{% - \begin{picture}(84,50)% - \put(0,45){\bf [\MOLnum]\MOLnameE}% - \put(5,40){\small\tt FM:\CALfm{ }MW:\CALmw}% - \put(10,0){\font\@strufont=\MOLfile\relax% + \begin{picture}(84,30)% + \put(0,25){\bf [\MOLnum]\MOLnameE}% + \put(5,20){\small\tt FM:\CALfm{ }MW:\CALmw}% + \put(5,0){\font\@strufont=\MOLfile\relax% \hbox{\@strufont\char\MOLchar}}% \end{picture}% } %---------------------------------------------------------------------------- \def\INFO#1{\@for\@temp:=#1\do{\mol@sel\@temp}\put@char}% %---------------------------------------------------------------------------- +\def\figex#1#2#3#4{% +\makebox[5mm]{}%% +\makebox[#1]{\tt #2}% +\makebox[#1]{\tt #3}% +\makebox[#1]{\tt #4}}% +%---------------------------------------------------------------------------- \begin{document} -\begin{center} - {\LARGE\bf Molecular Coding Format manual}\vspace{3mm}\\ - Author : Akira Yamaji \quad Date : \today\\ - Located at : http://www.ctan.org/pkg/mcf2graph\vspace{3mm}\\ -\begin{minipage}{148mm} -\quad Molecular Coding Format(MCF) is new linear notation represent chemical - structure diagrams. This 'Coding' is named from coding(programing) technique - like adressing,grouping,macro,etc. There are no Meta language commands in MCF. - mcf2graph.mf(metapost/metafont macro) convert MCF file to graphics file - pk font,PNG,SVG,EPS or MDL MOL file(V2000). \\ -\end{minipage}\\ -\end{center} +\title{\Huge\sf Molecular Coding Format manual} +\author{Akira Yamaji} +\date{\today} +\maketitle +\begin{center} Located at http://www.ctan.org/pkg/mcf2graph \end{center} +%----------------------------------------------------------------------------- +\vspace{10mm} +{\@strufont% +\makebox[10mm]{}\char0\raisebox{10mm}{\char1}\char2\raisebox{10mm}{\char3}\\ +\makebox[10mm]{}\char4\raisebox{10mm}{\char5}\char6\raisebox{10mm}{\char7}\\ +\makebox[10mm]{}\char8\raisebox{10mm}{\char9}\char10\raisebox{10mm}{\char11}\\ +\makebox[10mm]{}\char12\raisebox{10mm}{\char13}\char14\raisebox{10mm}{\char15}\\ +\makebox[10mm]{}\char16\raisebox{10mm}{\char17}\char18\raisebox{10mm}{\char19}\\} +%----------------------------------------------------------------------------- +\twocolumn +\tableofcontents +%----------------------------------------------------------------------------- \linethickness{0.08mm}% -\noindent% %---------------------------------------------------------------------------- -{\bf (Molecular definition file)} -\begin{verbatim} -%------------------------------------------------------------------------- -input mcf2graph.mf; % input macro -%------------------------------------------------------------------------- -sw_auxout:=1; % aux(information) file output on > Gloval setting -sw_numberA:=0; % numbering atom off > -sw_numberB:=0; % numbering bond off > -sw_expand:=0; % substituent expand mode off > -sw_start_vector:=0; % start vector output off > -sw_font_frame:=0; % font frame off > -font_wd#:=60mm#; % font width > -font_ht#:=40mm#; % font height > -var3:="cal_MW"; tag3:="cMW"; > AUX file table -var4:="cal_FM"; tag4:="cFM"; > -outputformat:="png"; hppp:=vppp:=0.1; > PNG output -outputtemplate:="%j-%3c.png"; > -%------------------------------------------------------------------------- -beginfont("NO:1","EN:Ampicillin") > begin font(information) - MCf(<45,?4,2:N,2=?5,-1:S, > begin MCF (1) - @(3^45,4^-45)/*H,1://O^15,5:/*COOH^-18, > - @(6^35,6^-35)/Me, > - 4\^75,NH,!,//O,!,/*NH,!,Ph) > end MCF -endfont > end font -%------------------------------------------------------------------------ -beginfont("NO:2","EN:Cholesterol") > begin font(information) - MCf(<30,?6,$(-4,-2)?6,-4=?5,7=dl, > begin MCF (2) - 1:*/OH,@(4,12)*/Me^60,9:*/H^60, > - 10:/*H^180,@(11,-1)/*H^-60, > - -1\^17,/*Me,!4,/Me,!) > end MCF -endfont > end font -%------------------------------------------------------------------------ -bye - -\end{verbatim} -%------------------------------------------------------------------------ -{\bf (Molecular structure output)}\vspace{5mm}\\ -\INFO{F:mcf_man_soc,C:90,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:91,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% \newpage -%------------------------------------------------------------------------ -\noindent% -{\bf (Molecular information output)}\vspace{2mm}\\ -'filename'-info.aux : for use in \TeX, it takes over filename, -char number, molecular information,etc. -\begin{verbatim} -(sw_auxfix=0) -F:mcf_man_soc;C:90;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin -F:mcf_man_soc;C:91;cMW:386.6532;cFM:C27H46O;EN:Cholesterol - ..................................................... - ..................................................... - -(sw_auxfix=1) -F;C;cMW;cFM;EN -mcf_man_soc;90;349.40462;C16H19N3O4S;Ampicillin -mcf_man_soc;91;386.6532;C27H46O;Cholesterol - ...................................... - ...................................... - -( tag : variable ) -F : filename C : char number NO : serial number EN : english name -cMW : molecular weight calculated cFM : molecular formula calculated -MW : molecular weight from literature data - -\end{verbatim} -%---------------------------------------------------------------------------- -{\bf (LaTeX file example)} -%############################################################################ -\begin{verbatim} -%---------------------------------------------------------------------------- -\documentclass[a4paper]{article} -\usepackage{graphicx} -\pagestyle{empty} -\makeatletter% -%-------------------------------------------------------------------- -\def\@F{F}\def\@C{C}\def\@EN{EN}\def\@NO{NO}\def\@MW{MW}\def\@FMc{FMc}% -\def\@fst@param#1:#2;{#1}\def\@sec@param#1:#2;{#2}% -\def\mol@sel#1{% -\if#1\empty\relax\else% - \edef\@tag{\expandafter\@fst@param#1;}% - \edef\@var{\expandafter\@sec@param#1;}% - \ifx\@tag\@F\edef\MOLfile{\@var}\fi% - \ifx\@tag\@C\edef\MOLchar{\@var}\fi% - \ifx\@tag\@EN\edef\MOLnameE{\@var}\fi% - \ifx\@tag\@NO\edef\MOLnum{\@var}\fi - \ifx\@tag\@MW\edef\CALmw{\@var}\fi - \ifx\@tag\@FMc\edef\CALfm{\@var}\fi -\fi}% -\def\put@char{% - \begin{picture}(84,42)% - \put(0,38){\bf [\MOLnum]\MOLnameE{ }\small\tt/FM:\CALfm/MW:\CALmw}% - \put(10,0){\font\@strufont=\MOLfile\relax% - \hbox{\@strufont\char\MOLchar}}% - \end{picture}% -\def\INFO#1{\@for\@temp:=#1\do{\mol@sel\@temp}\put@char}% -\makeatother -%-------------------------------------------------------------------- -\begin{document} -\unitlength=1mm% -\INFO{F:mcf_man_soc,C:90,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:91,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% -\end{document} -%-------------------------------------------------------------------- -\end{verbatim}\vspace{5mm}% -%############################################################################ -%---------------------------------------------------------------------------- -\noindent +\section{Introduction} +Molecular Coding Format(MCF) is new linear notation + represent chemical structure diagrams. +This 'Coding' is named from coding(programing) technique +like adressing,grouping,macro,etc. +There are no Meta language commands in MCF. +mcf2graph.m convert MCF file to graphics file +pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Chain(1)} +\section{MCF syntax} +\subsection{Make bond} +\subsubsection{Chain} \begin{verbatim} -real number plus (+): anticlockwize -real number minus(-): clockwize - -<30,-60,60,-90,120,-90,60 + real number plus (+): anticlockwize + real number minus(-): clockwize + <30,-60,60,-90,120,-90,60 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Chain(2)} \begin{verbatim} -! : take value 60 or -60 depend on + ! : take value 60 or -60 depend on current angle and enviroment -!6 : !,!,!,!,!,! + !6 : !,!,!,!,!,! <30,!,!,!,!,!,! <30,!6 - \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Jump to atom and branch bond} +\subsubsection{Jump and branch bond} \begin{verbatim} -n* : Jump to An - + n* : Jump to An + ** An: atom number(-999<=n<=4095) + <30,!6,3*,0,!,5*,-30 +\end{verbatim} +\MCFstructure +%------------------------------------ +\begin{verbatim} + 3\ : 3*,0 -** An(-999<=n<=4095): atom number + <30,!6,3\,! \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Jump to atom and branch bond} +\subsubsection{Branch bond} \begin{verbatim} -3\ : 3*,0 + 2\ : 2*,0 + 4*\ : 4*,0~wf + 6\* : 6*,0~zf + 8\\ : 8*,0~dm - <30,!6,3\,! + <30,!8,2\,!,4*\,!,6\*,!,8\\,! +\end{verbatim} +\MCFstructure +%----------------------------------------------------------------------------- +\begin{verbatim} + 2\~dr : 2*,0~dr + 4\`1.5 : 4*,0`1.5 + 6\^15 : 6*,0^15 + <-30,!6, + 2\~dr,!, + 4\`1.5,!, + 6\^15,-60 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Connect atom} +\subsubsection{Connect atom} \begin{verbatim} -&n : Connect to An + &n : Connect to An <30,!6,3\,!,&5 - \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ring} +\subsubsection{Ring} \begin{verbatim} -?n : n membered ring - - ?6 - - ** ?6 : <-120,60,60,60,60,60,&1 - ** ?n(3<=n<=20) - ** bold arrow is default angle and position + ?n : n membered ring(3<=n<=20) + ?6 : <-120,60,60,60,60,60,&1 + ?6 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Rotate current angle} +\subsubsection{Rotate current angle} \begin{verbatim} - : change enviroment -** Me:methyl Et:ethyl - Pr:propyl iPr:isopropyl - tBu:tertial buthyl Ph:phenyl + <30,``1,!,/Me~zf`2^30,!,/Me~zf`2^30, + !2,*/Pr>lr,!2,*/Pr>rl,!) \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Insert substituent(2)} +\subsubsection{Add substituent} \begin{verbatim} -/ : single -// : double -*/ : wedge forward -/* : wedge dotted forward -** : direct - -MCf(<30,!,//O,!,/*H,!,*/H,!,/?3,!,**?3,!) + <-30,!17,2:/Me,4:/Et,6:/Pr, + 10:/iPr,14:/tBu,16:/Ph^-30 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Insert substituent(3)} +\subsubsection{Add modified substituent} \begin{verbatim} -~ : change type -^ : change angle -` : change length -> : change enviroment + ~,^,` : change type,angle,length -MCf(<30,``1, - !,/Me~zf`2^30,!,/Me~zf`2^30, - !2,*/Pr>lr,!2,*/Pr>rl,!) -\end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ -%----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Add substituent(1)} -\begin{verbatim} -sw_numberA:=1; numberA_end:=12; -MCf(<30,!11, - 2:/Me,3:/Et,6:/Pr,7:/iPr, - 10:/tBu,11:/Ph^-30) + <-30,!6,@(2~wf,4~zf,6^-30)/H \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Add substituent(2)} \begin{verbatim} -~,^,` : change type,angle,length - of substituent + ^,`,> : change angle,length,environment -MCf(<30,?6, - @(3`2^30,3~wf,4~zf,6~wf^-30,6~zf^30)/H) + <30,!7`1,@(3)/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Add substituent(3)} +\subsection{Chain environment} +\subsubsection{Horizontal,vertical} \begin{verbatim} -~,^,`,> : change type,angle,length, - environment of substituent + >hz : horizontal enviroment (default) + >vt : vertical enviroment -MCF(<30,!7`1, -@(2,3)/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl) + ?4,@(3^-90,3^-30,3^90)/'(!3,"{hz}")>hz, + @(1^-60,1`2,1^60)/'(!2,"{vt}")>vt \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Chain strech direction environment (1)} +\subsubsection{Left-right,right-left} \begin{verbatim} ->hz : horizontal enviroment (default) ->vt : vertical enviroment - - ?4, - @(3^-90,3^-30,3^90)/'(!3,"{hz}")>hz, - @(1^-60,1`2,1^60)/'(!2,"{vt}")>vt - -\end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ -%----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Chain strech direction environment (2)} -\begin{verbatim} ->lr : left-right enviroment ->rl : right-left enviroment + >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{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Chain strech direction environment (3)} +\subsubsection{Fixed angle,multi angle} \begin{verbatim} - >45 : fixed angle enviroment - >'(-90,90,-90) : multi angle enviroment + >45 : fixed angle enviroment + >'(-90,90,-90) : multi angle enviroment <-30,!6,@(2>45)/'(!3,"{45}"), @(6>'(-90,90,-90))/'(!3,"{(-90,90,-90)}") \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Change atom and Substituent} +\subsection{Miscellaneous} +%----------------------------------------------------------------------------- +\subsubsection{Change atom and Substituent} \begin{verbatim} -NH,SO,SOO : inset hetero atom and substituent - simultaneously + NH,SO,SOO : + inset hetero atom and substituent + simultaneously <30,!2,NH,!,SO,!,SOO,!3 - \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Change color} +\subsubsection{Change color} \begin{verbatim} -@(5)green : change color of A5 green -$(3)red : change color of B3 red + @(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 + <30,Ph,@(2,5)N,2:red,5:blue,3=green -** METAFONT ignore color command + ** METAFONT ignore color command \end{verbatim} -\end{minipage} %%%%\MCFstructure % for Metafont -\makebox(72,3.5)[t]{\frame{\makebox(68,42.3)% -{\includegraphics{mcf_man_soc-042.eps}}}}% for dvipdfmx -%%%%{\includegraphics[width=30mm]{mcf_man_soc-042.png}}}}% for pdfLaTeX +\includegraphics{mcf_man_soc-060.eps}% for dvipdfmx \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax% -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Chain start multiple characters} +\subsubsection{Make block} +\begin{verbatim} + { : start brock + } : end brock + + <30,!2,{,``1.2,!2,},!2 +\end{verbatim} +\MCFstructure +%----------------------------------------------------------------------------- +\subsubsection{Chain start multiple characters} \begin{verbatim} -if chain start multi charactor string, -use !0 instead of ! + if chain start multi charactor string, + use !0 instead of ! MCd( 1,1)(0 ,0.9)(<30,COOH,!0,!3,COOH) MCd(.8,1)(0.3,0.1)(<30,COOH,!4,COOH) \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{User definition} +\subsubsection{User definition} \begin{verbatim} -iBuOH : user defined substructure + iBuOH : user defined substructure iBuOH:='(!,/Me,!,OH) MCf(<30,?6,@(4,6)/iBuOH) - \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Inline definition} +\subsubsection{Inline definition} \begin{verbatim} -Insert user defined substructure + Insert user defined substructure <30,!3,/'(!,/Me,!,OH),!3 - \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ -%----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Font size} +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\newpage +\section{Option parameter} +%------------------------------------------------------------------------------ +\subsection{Size parameter} +\subsubsection{Font size} \begin{verbatim} beginfont("EN:Caffeine") font_wd#:=30mm#; %<==font width font_ht#:=20mm#; %<==font height - sw_font_frame:=1; MCf(<30,?6,-4=?5,$(3,8)dl,@(2,6,7,9)N, - @(2,6,9)/Me,@(1,5)//O) - endfont + @(2,6,9)/Me,@(1,5)//O) endfont \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Max ratio bond/width length} +\subsubsection{Margin left and right} \begin{verbatim} - max_bond_width:=0.10; - MCd(1,1)( 0, .5)(<30,Ph) - max_bond_width:=0.15; - MCd(1,1)(.33,.5)(<30,Ph) - max_bond_width:=0.25; - MCd(1,1)( 1, .5)(<30,Ph) - -** default: max_bond_width=0.15 + default: margin_left_right=0.4mm \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ +\begin{picture}(12,20) +\put(1,14){\makebox(10,6)[r]{\tt 0mm}} +\put(1, 7){\makebox(10,6)[r]{\tt 0.4mm}} +\put(1, 0){\makebox(10,6)[r]{\tt 5mm}} +\end{picture} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio thickness/bond length} +\subsubsection{Margin top and bottom} \begin{verbatim} -ratio_thickness_bond:= 0.005; -MCd(1,.6)(0, .5)(<30,Ph) -ratio_thickness_bond:= 0.015; -MCd(1,.6)(.5,.5)(<30,Ph) -ratio_thickness_bond:= 0.030; -MCd(1,.6)(1, .5)(<30,Ph) - -** default: ratio_thickness_bond=0.015 + default: margin_top_bottom=0.4mm \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0mm}{0.4mm}{5mm} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Offset thickness of bond} +\subsubsection{Offset thickness of bond} \begin{verbatim} -beginfont() offset_thickness#:=0pt#; -MCd(1,.3)(0, .5)(<30,Ph) endfont -beginfont() offset_thickness#:=0.2pt#; -MCd(1,.3)(.5,.5)(<30,Ph) endfont -beginfont() offset_thickness#:=0.5pt#; -MCd(1,.3)(1, .5)(<30,Ph) endfont - -** default: offset_thickness#=0.2pt# + default: offset_thickness#=0.2pt# \end{verbatim} -\end{minipage} -\MCFstru\MCFstru\MCFstructure% -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0pt}{0.2pt}{0.5pt} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio char/bond thickness} +\subsubsection{Offset of doublebond gap} \begin{verbatim} -ratio_char_bond:=1.0; -MCd(1,.6)(0, .5)(<30,?6,5:O,2:NH) -ratio_char_bond:=1.5; -MCd(1,.6)(.5,.5)(<30,?6,5:O,2:NH) -ratio_char_bond:=2.0; -MCd(1,.6)(1, .5)(<30,?6,5:O,2:NH) - -** default: ratio_char_bond=1.5 + default: offset_bond_gap#=0.3pt# \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.0pt}{0.3pt}{1.0pt} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio bondgap/bond length} +\subsubsection{Offset of atom width} \begin{verbatim} -ratio_bondgap_bond:= 0.10; -MCd(1,.6)(0, .5)(<30,Ph) -ratio_bondgap_bond:= 0.15; -MCd(1,.6)(.5,.5)(<30,Ph) -ratio_bondgap_bond:= 0.20; -MCd(1,.6)(1, .5)(<30,Ph) - -** default: ratio_bondgap_bond=0.15 + default: offset_atom#=0.8pt# \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.0pt}{0.8pt}{2.0pt} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Offset of doublebond gap} +\subsubsection{Offset of wedge width} \begin{verbatim} -beginfont() offset_bond_gap#:=0.0pt#; -MCd(1,.3)(0, .5)(<30,Ph) endfont -beginfont() offset_bond_gap#:=0.3pt#; -MCd(1,.3)(.5,.5)(<30,Ph) endfont -beginfont() offset_bond_gap#:=1.0pt#; -MCd(1,.3)(1, .5)(<30,Ph) endfont - -** default: offset_bond_gap#=0.3pt# + default: offset_wedge#=0.4pt# \end{verbatim} -\end{minipage} -\MCFstru\MCFstru\MCFstructure% -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.0pt}{0.4pt}{1.0pt} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio atom/bond length} +\subsubsection{Max bond length} \begin{verbatim} -ratio_atom_bond:= 0.25; -MCd(1,.6)(0, .5)(<30,?6,@(2,5)O) -ratio_atom_bond:= 0.36; -MCd(1,.6)(.5,.5)(<30,?6,@(2,5)O) -ratio_atom_bond:= 0.45; -MCd(1,.6)(1, .5)(<30,?6,@(2,5)O) - -** default: ratio_atom_bond=0.36 + default: max_bond_length#=10mm# \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{18mm}{6mm}{8mm}{20mm} +%----------------------------------------------------------------------------- +\subsection{Ratio parameter} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Offset of atom width} +\subsubsection{Thickness/bond length} \begin{verbatim} -beginfont() offset_atom#:=0.0pt#; -MCd(1,.3)(0, .5)(<30,Ph,@(2,4,6)N) endfont -beginfont() offset_atom#:=0.8pt#; -MCd(1,.3)(.5,.5)(<30,Ph,@(2,4,6)N) endfont -beginfont() offset_atom#:=2.0pt#; -MCd(1,.3)(1, .5)(<30,Ph,@(2,4,6)N) endfont - -** default: offset_atom#=0.8pt# + default: ratio_thickness_bond=0.015 \end{verbatim} -\end{minipage} -\MCFstru\MCFstru\MCFstructure% -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.005}{0.015}{0.030} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio wedge/bond length} +\subsubsection{Char/bond thickness} \begin{verbatim} -ratio_wedge_bond:=0.10; -MCd(1,.6)(0, .5)(<30,?6,5:*/Me) -ratio_wedge_bond:=0.12; -MCd(1,.6)(.5,.5)(<30,?6,5:*/Me) -ratio_wedge_bond:=0.20;; -MCd(1,.6)(1, .5)(<30,?6,5:*/Me) - -** default: ratio_wedge_bond=0.12 + default: ratio_char_bond=1.5 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{1.0}{1.5}{2.0} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Offset of wedge width} +\subsubsection{Bondgap/bond length} \begin{verbatim} -beginfont() offset_wedge#:=0.0pt#; -MCd(1,.3)(0, .5)(<30,?6,5:*/Me) endfont -beginfont() offset_wedge#:=0.4pt#; -MCd(1,.3)(.5,.5)(<30,?6,5:*/Me) endfont -beginfont() offset_wedge#:=1.0pt#; -MCd(1,.3)(1, .5)(<30,?6,5:*/Me) endfont - -** default: offset_wedge#=0.4pt# + default: ratio_bondgap_bond= 0.15 \end{verbatim} -\end{minipage} -\MCFstru\MCFstru\MCFstructure% -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.10}{0.15}{0.20} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio font atom gap/atom length} +\subsubsection{Atom/bond length} \begin{verbatim} -ratio_atomgap_atom:=0.0; -MCd(1,.6)(0, .5)(<30,?6,@(2,5)O) -ratio_atomgap_atom:=0.050; -MCd(1,.6)(.5,.5)(<30,?6,@(2,5)O) -ratio_atomgap_atom:=0.12; -MCd(1,.6)(1, .5)(<30,?6,@(2,5)O) - -** default: ratio_atomgap_atom=0.050 + default: ratio_atom_bond= 0.36 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.25}{0.36}{0.46} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio chain/ring length} +\subsubsection{Wedge/bond length} \begin{verbatim} -ratio_chain_ring:= 0.4; -MCd(1,.6)(0, .5)(<30,?6,5:/Et) -ratio_chain_ring:= 0.66; -MCd(1,.6)(.5,.5)(<30,?6,5:/Et) -ratio_chain_ring:= 1.0; -MCd(1,.6)(1, .5)(<30,?6,5:/Et) - -** default: ratio_chain_ring=0.66 + default: ratio_wedge_bond=0.12 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.10}{0.12}{0.20} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Ratio zebra gap/bond length} +\subsubsection{Font atom gap/atom length} \begin{verbatim} -ratio_zebragap_bond:=0.06; -MCd(1,.6)(0, .5)(<30,Ph,5:/*Me`1) -ratio_zebragap_bond:=0.12; -MCd(1,.6)(.5,.5)(<30,Ph,5:/*Me`1) -ratio_zebragap_bond:=0.20; -MCd(1,.6)(1, .5)(<30,Ph,5:/*Me`1) - -** default: ratio_zebragap_bond=0.12 + default: ratio_atomgap_atom= 0.050 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.0}{0.050}{0.12} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Margin left and right} +\subsubsection{Chain/ring length} \begin{verbatim} -margin_left_right:=0mm; -MCd(1,1)(0.5,0.9)(<30,CH3,!0,!17,CH3) -margin_left_right:=0.4mm; -MCd(1,1)(0.5,0.5)(<30,CH3,!0,!17,CH3) -margin_left_right:=5mm; -MCd(1,1)(0.5,0.1)(<30,CH3,!0,!17,CH3) - -** default: margin_left_right=0.4mm + default: ratio_chain_ring= 0.66 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.4}{0.65}{1.0} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Margin top and bottom} +\subsubsection{Zebra gap/bond length} \begin{verbatim} -margin_top_bottom:=0mm; -MCd(1,1)(0.1,0.5)(<30,Ph,2:/OH,5:/NH2) -margin_top_bottom:=0.4mm; -MCd(1,1)(0.5,0.5)(<30,Ph,2:/OH,5:/NH2) -margin_top_bottom:=5mm; -MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2) - -** default: margin_top_bottom=0.4mm + default: ratio_zebragap_bond=0.12 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\figex{20mm}{0.06}{0.12}{0.20} +%----------------------------------------------------------------------------- +\subsection{Drawing mode} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch numbering atom} +\subsubsection{Numbering atom} \begin{verbatim} numberA_start:=3; numberA_end:=8; - - sw_numberA:=1; MCd(1,1)(.5,.9)(<30,!9) - sw_numberA:=2; MCd(1,1)(.5,.5)(<30,!9) - sw_numberA:=3; MCd(1,1)(.5,.1)(<30,!9) - - ** default: numberA_start=1 numberA_end=4095 + default: sw_numberA=0 : + numberA_start=1 numberA_end=4095 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ +\begin{picture}(5,20) +\put(0,14){\makebox[5mm]{\tt 1}} +\put(0, 8){\makebox[5mm]{\tt 2}} +\put(0, 2){\makebox[5mm]{\tt 3}} +\end{picture} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch numbering bond} +\subsubsection{Numbering bond} \begin{verbatim} numberB_start:=3; numberB_end:=8; - - sw_numberB:=1; MCd(1,1)(.5,.9)(<30,!9) - sw_numberB:=2; MCd(1,1)(.5,.5)(<30,!9) - sw_numberB:=3; MCd(1,1)(.5,.1)(<30,!9) - - ** default: numberB_start=1 numberB_end=4095 + default: sw_numberB=0 : + numberB_start=1 numberB_end=4095 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ +\begin{picture}(5,20) +\put(0,14){\makebox[5mm]{\tt 1}} +\put(0, 8){\makebox[5mm]{\tt 2}} +\put(0, 2){\makebox[5mm]{\tt 3}} +\end{picture} +%----------------------------------------------------------------------------- +\subsubsection{Solid mode} +\begin{verbatim} + MCd(1,1)(0,.5)(Ph,4:/Me) + sw_solid:=1; + bond_len#:=6mm#; + MCd(1,1)(1,.5)(Ph,4:/Me) +\end{verbatim} +\MCFstructure\\ +\makebox[5mm]{}% +\makebox[30mm]{\tt 0 :default}% +\makebox[30mm]{\tt 1}% %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch substituent off} +\subsubsection{Expand mode} +\begin{verbatim} + MCd(1,.5)(0,0.5)(<30,Ph,4:/COOH,3:/NH2) + sw_expand:=1; + MCd(1,.5)(1,0.5)(<30,Ph,4:/COOH,3:/NH2) +\end{verbatim} +\MCFstructure\\ +\makebox[5mm]{}% +\makebox[30mm]{\tt 0 :default}% +\makebox[30mm]{\tt 1}% +%----------------------------------------------------------------------------- +\subsubsection{Substituent off mode} \begin{verbatim} MCd(1,.5)( 0,0.5)(<30,Ph,4:/Cl,3:/F) - sw_subst_off:=1; MCd(1,.5)( 1,0.5)(<30,Ph,4:/Cl,3:/F) - - ** default: sw_subst_off=0 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\makebox[5mm]{}% +\makebox[30mm]{\tt 0 :default}% +\makebox[30mm]{\tt 1}% %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch all bond single} +\subsubsection{Single bond mode} \begin{verbatim} MCd(1,.5)( 0,0.5)(<30,Ph,4:/Cl,3:/F) - sw_bond_single:=1; MCd(1,.5)( 1,0.5)(<30,Ph,4:/Cl,3:/F) - - ** default: sw_bond_single=0 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\makebox[5mm]{}% +\makebox[30mm]{\tt 0 :default}% +\makebox[30mm]{\tt 1}% +%----------------------------------------------------------------------------- +\subsection{Frame,vector} %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch start vector} +\subsubsection{Start vector} \begin{verbatim} + MCf(<30,Ph,4:/Cl,3:/F) sw_start_vector:=1; MCf(<30,Ph,4:/Cl,3:/F) - - ** default: sw_start_vector=0 \end{verbatim} -\end{minipage} -\MCFstructure -\vspace{\gpman}\\ +\MCFstructure\\ +\makebox[5mm]{}% +\makebox[30mm]{\tt 0 :default}% +\makebox[30mm]{\tt 1}% %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch font frame} +\subsubsection{Font frame} \begin{verbatim} -sw_font_frame=0 : no frame **default -sw_font_frame=1 : draw frame of font -sw_font_frame=2 : draw frame inside margin -sw_font_frame=3 : draw both + sw_font_frame=0 : no frame **default + sw_font_frame=1 : draw frame of font + sw_font_frame=2 : draw frame inside margin + sw_font_frame=3 : draw both -sw_font_frame:=3; -margin_left_right:=5mm; margin_top_bottom:=2mm; -MCf(<30,Ph,4:/Cl,3:/F) + sw_font_frame:=3; + margin_left_right:=5mm; + margin_top_bottom:=2mm; + MCf(<30,Ph,4:/Cl,3:/F) \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch molecular frame} +\subsubsection{Molecular frame} \begin{verbatim} - MCd(1,.5)(0,0.5)(<30,Ph,4:/Cl,3:/F) - sw_mol_frame:=1; MCd(1,.5)(1,0.5)(<30,Ph,4:/Cl,3:/F) - - ** default: sw_mol_frame=0 + ** default: sw_mol_frame=0 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch atom frame} +\subsubsection{Atom frame} \begin{verbatim} - sw_atom_frame:=1; MCf(<30,Ph,4:/COOH,3:/OH) - - ** default: sw_atom_frame=0 + ** default: sw_atom_frame=0 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch solid mode} +\subsection{Clipping font} \begin{verbatim} - MCd(1,.8)( 0,0.5)(<30,Ph,4:/Cl,3:/F) - - sw_solid:=1; - ratio_bond_width:=0.08; - MCd(1,.8)( 1,0.5)(<30,Ph,4:/Cl,3:/F) - - ** default: sw_solid=0 + beginfont() + sw_clip:=0; + MCf(<30,Ph,4:/Cl,3:/F) endfont + ** default: sw_clip=0 \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ -%----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Switch Expand} \begin{verbatim} - MCd(1,.5)(0,0.5)(<30,Ph,4:/COOH,3:/NH2) - - sw_expand:=1; - MCd(1,.5)(1,0.5)(<30,Ph,4:/COOH,3:/NH2) - - ** default: sw_expand=0 + beginfont() + sw_clip:=1; + MCf(<30,Ph,4:/Cl,3:/F) endfont \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ -%----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Function MCd (draw)} +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\newpage +\section{MCF draw function} +\subsection{Function MCd (draw)} \begin{verbatim} MCd(a,b)(c,d)(...) a: ratio molecular width/font width @@ -1213,72 +809,57 @@ MCf(<30,Ph,4:/Cl,3:/F) c: x axis position d: y axis position - MCd(1,0.8)(0.2,0.9)(<30,Ph,2:/OH,5:/NH2) - MCd(1,0.8)(0.8,0.1)(<30,Ph,2:/OH,5:/NH2) + MCd(1,0.8)(0.2,0.9)(<30,Ph,3:/F,4:/Cl) + MCd(1,0.8)(0.8,0.1)(<30,Ph,3:/F,4:/Cl) \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Function MCf (fit draw)} +\subsection{Function MCf (fit draw)} \begin{verbatim} MCf(...) : MCd(1,1)(0.5,0.5)(...) sw_font_frame:=1; sw_mol_frame:=1; - MCf(<30,Ph,2:/OH,5:/NH2) + MCf(<30,Ph,3:/F,4:/Cl) \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Local setting} +\subsection{Local setting} \begin{verbatim} -beginfont() - sw_mol_frame:=1; % <<== Local setting - MCd(1,.4)( 0,.5)(Ph) -endfont -beginfont() MCd(1,.4)(.5,.5)(Ph) endfont -beginfont() MCd(1,.4)( 1,.5)(Ph) endfont + beginfont() MCd(1,.4)(0,.5)(Ph) endfont + beginfont() + ratio_thickness_bond:=0.05; + MCd(1,.4)(0.5,.5)(Ph) + endfont + beginfont() MCd(1,.4)(1,.5)(Ph) endfont \end{verbatim} -\end{minipage} -\MCFstru\MCFstru\MCFstructure% -\vspace{\gpman}\\ +\MCFstructure %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Global setting} +\subsection{Global setting} \begin{verbatim} -sw_mol_frame:=1; % <<== Global setting -beginfont() MCd(1,.4)( 0,.5)(Ph) endfont -beginfont() MCd(1,.4)(.5,.5)(Ph) endfont -beginfont() MCd(1,.4)( 1,.5)(Ph) endfont + ratio_thickness_bond:=0.05; + beginfont() MCd(1,.4)( 0,.5)(Ph) endfont + beginfont() MCd(1,.4)(.5,.5)(Ph) endfont + beginfont() MCd(1,.4)( 1,.5)(Ph) endfont \end{verbatim} -\end{minipage} -\MCFstru\MCFstru\MCFstructure% -\vspace{\gpman}\\ +\MCFstructure %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Output molecular information} +\subsection{Output molecular information} \begin{verbatim} var3:="calc_weight"; tag3:="cMW"; var4:="calc_formula"; tag4:="cFM"; %% Output to mcf_man_soc-info.aux %% -F:mcf_man_soc;C:85;cMW:194.19174;cFM:C8H10N4O2 +..... ;C:85;cMW:194.19174;cFM:C8H10N4O2 cMW:calculated molecular weight cFM:calculated molecular formula \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Output additional information} +\subsection{Output additional information} \begin{verbatim} beginfont("EN:Tocopherol","CAS:59-02-9") -MCf(...) endfont + MCf(...) endfont %% Output to mcf_man_soc-info.aux %% F:mcf_man_soc;C:86;EN:Tocopherol;CAS:59-02-9 @@ -1286,56 +867,46 @@ F:mcf_man_soc;C:86;EN:Tocopherol;CAS:59-02-9 *F:filename *C:char number EN:molecular name CAS:CAS number *:default output \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Change aux information delimiter} +\subsection{Change aux information delimiter} \begin{verbatim} aux_delimiter:="/"; beginfont("EN:Ampicillin","CAS:69-53-4") -MCf(...) endfont + MCf(...) endfont %% Output to mcf_man_soc-info.aux %% F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4 -**default aux_delimiter=";" - + **default aux_delimiter=";" \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Fixed aux information} +\subsection{Fixed aux information} \begin{verbatim} -tag3:="NO"; var3:="inf_NO"; -tag4:="EN"; var4:="inf_EN"; -sw_auxfix:=1; auxtag_out; -beginfont("EN:Cholesterol","NO:1") ... endfont + tag3:="NO"; var3:="inf_NO"; + tag4:="EN"; var4:="inf_EN"; + sw_auxfix:=1; auxtag_out; + beginfont("EN:Cholesterol","NO:1") + ..... endfont -%% Output to mcf_man_soc-info.aux %% -F;C;NO;EN -mcf_man_soc;91;1;Ampicillin + %% Output to mcf_man_soc-info.aux %% + F;C;NO;EN + mcf_man_soc;91;1;Ampicillin \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(1) Warfarin} +\newpage +\section{MCF example} +\subsection{Warfarin} \begin{verbatim} <30,Ph,3=?6,8=dl, 10:O,7:/OH,9://O, 8\,/Ph`1,60,!,//O,! \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(2) Limonin} +\subsection{Limonin} \begin{verbatim} <30,?6,$(-3,-4)?6,-5=?3, -2=wf,-1=wb,6=?5,-4=?6,-5=wf, @@ -1344,34 +915,27 @@ mcf_man_soc;91;1;Ampicillin @(1^60,5^180,16^60)/*H, 14\*,|,?5,$(1,4)dl,3:O \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(3) Sesamine} +\subsection{Sesamine} \begin{verbatim} - <54,?5,1=?5,@(4,7)O,@(1^-54,2^54)*/H, + <54,?5,1=?5, + @(4,7)O,@(1^-54,2^54)*/H, #5*\^-12,Ph,|,-3=?5,@(-1,-3)O, #8*\^-12,Ph,|,-3=?5,@(-1,-3)O \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(4) Colchicine} +\subsection{Colchicine} \begin{verbatim} - <30,Ph,@(1,2,6)/OMe,-4=?7,-5=?7, + <30,Ph,@(1,2,6)/OMe, + -4=?7,-5=?7, $(-1,-4,-6)dl,-2://O,-3:/OH, 9\,NH,!,//O,! \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(5) Lycorine} +\subsection{Lycorine} \begin{verbatim} <30,Ph, -4=?6,-2=?6,6=?5,(9,12)=?5[3], @@ -1380,12 +944,9 @@ mcf_man_soc;91;1;Ampicillin 9:/*H^180,10:*/H^60, 13:*/OH,14:/*OH \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(6) Gibberellin} +\subsection{Gibberellin} \begin{verbatim} <18,?5,3=?7,5=?6[12], 8*,160`1.3,&3, @@ -1394,12 +955,9 @@ mcf_man_soc;91;1;Ampicillin 2:/COOH,7://Me,13:*/OH,8:/*OH, 14:*/Me,@(1^60,4^60)*/H \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(7) Quinine} +\subsection{Quinine} \begin{verbatim} <30,Ph,3=Ph,7:N,6:/OMe, 10\,*/OH,/H~zf^-60,!, @@ -1407,35 +965,43 @@ mcf_man_soc;91;1;Ampicillin 4*\,!~dr, 2*,165~zf,60,&5~zb \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(8) Atoropin} +\subsection{Atoropin} \begin{verbatim} <-30,O,!,//O,!,!,Ph, #1\~zb^-120, |,?7,6*\^190`1.02,N,/Me,&3~wb, #3\~wv,!,OH \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(9) Validamycin} +\subsection{Rotenone} +\begin{verbatim} + <-60,?5,$(-3,-2,-3,-4)?6, + $(7,9,-2,-4)dl,$(3,17)dr, + @(2,13,16)O,10://O,@(11^-60,12^60)*/H, + @(-2,-3)/OMe,1*\,/Me,!~dl +\end{verbatim} +\MCFstructure +%----------------------------------------------------------------------------- +\subsection{Pyrethrin I} +\begin{verbatim} + <30,?3,@(3^35~wf,3^-35~zf)/Me, + 1*\,!~dl,iPr,2\*,//O,!,O,-36~zb,|, + ?5,-2=d,-1:/Me,-3://O,-2\,!4,$(-1,-3)dl +\end{verbatim} +\MCFstructure +%----------------------------------------------------------------------------- +\subsection{Validamycin} \begin{verbatim} <30,?6,@(5,6)/OH,3\,-60,OH, #4\,O,-60,|,?6,2:O,@(3,4,5,6)/OH, #1\,NH,!,|,?6,2=d,@(4,5,6)/OH,-4\,!,OH \end{verbatim} -\end{minipage} \MCFstructure -\vspace{\gpman}\\ %----------------------------------------------------------------------------- -\begin{minipage}[t][\htman]{90mm} -\MCFtitle{Example(10) Paclitaxel} +\subsection{Paclitaxel} \begin{verbatim} ?6,5=d,3*,{,``1,36,45,45,45,45,},, -4=?6,-4=?4,-1=wb,-3=wf,-1:O,||, @@ -1446,7 +1012,114 @@ mcf_man_soc;91;1;Ampicillin 7\*,O,-45,//O,60,Ph,11*\,O,-60,//O,60, 12\*^-15,O,60,//O,-60 \end{verbatim} -\end{minipage} \MCFstructure %----------------------------------------------------------------------------- +\onecolumn% +\section{Example to use mcf2graph} +\subsection{Molecular definition file example} +\begin{verbatim} +%------------------------------------------------------------------------- +input mcf2graph.mf; % input macro +%------------------------------------------------------------------------- +sw_auxout:=1; % aux(information) file output on > Gloval setting +font_wd#:=60mm#; % font width > +font_ht#:=40mm#; % font height > +var3:="cal_MW"; tag3:="cMW"; > AUX file table +var4:="cal_FM"; tag4:="cFM"; > +%%%% var5:="cal_MW"; tag5:="cMW"; > +%%%% var6:="cal_FM"; tag6:="cFM"; > +%%%% var7:="inf_USE"; tag7:="USE"; > +%%%% var8:="inf_EXA"; tag8:="EXA"; > +%%%% var9:="inf_EXB"; tag9:="EXB"; > +%%%% auxtag_out; > +%%%% sw_checklist:=1; > +%%%% sw_MOLout:=1; > +outputformat:="png"; hppp:=vppp:=0.1; > PNG output +outputtemplate:="%j-%3c.png"; > +%------------------------------------------------------------------------- +beginfont("NO:1","EN:Ampicillin") > begin font(information) + MCf(<45,?4,2:N,2=?5,-1:S, > begin MCF (1) + @(3^45,4^-45)/*H,1://O^15,5:/*COOH^-18, > + @(6^35,6^-35)/Me, > + 4\^75,NH,!,//O,!,/*NH,!,Ph) > end MCF +endfont > end font +%------------------------------------------------------------------------ +beginfont("NO:2","EN:Cholesterol") > begin font(information) + MCf(<30,?6,$(-4,-2)?6,-4=?5,7=dl, > begin MCF (2) + 1:*/OH,@(4,12)*/Me^60,9:*/H^60, > + 10:/*H^180,@(11,-1)/*H^-60, > + -1\^17,/*Me,!4,/Me,!) > end MCF +endfont > end font +%------------------------------------------------------------------------ +bye +\end{verbatim} +%------------------------------------------------------------------------ +\subsection{Molecular structure output example} +\INFO{F:mcf_man_soc,C:100,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% +\INFO{F:mcf_man_soc,C:101,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% +\newpage +%------------------------------------------------------------------------ +\noindent% +\subsection{Molecular information output example} +'filename'-info.aux : for use in \TeX, it takes over filename, +char number, molecular information,etc. +\begin{verbatim} +(sw_auxfix=0) +F:mcf_man_soc;C:109;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin +F:mcf_man_soc;C:110;cMW:386.6532;cFM:C27H46O;EN:Cholesterol + ..................................................... + ..................................................... + +(sw_auxfix=1) +F;C;cMW;cFM;EN +mcf_man_soc;90;349.40462;C16H19N3O4S;Ampicillin +mcf_man_soc;91;386.6532;C27H46O;Cholesterol + ...................................... + ...................................... + +( tag : variable ) +F : filename C : char number NO : serial number EN : english name +cMW : molecular weight calculated cFM : molecular formula calculated +MW : molecular weight from literature data +\end{verbatim} +%---------------------------------------------------------------------------- +\subsection{LaTeX file example} +%############################################################################ +\begin{verbatim} +%-------------------------------------------------------------------- +\documentclass[a4paper]{article} +\usepackage{graphicx} +\pagestyle{empty} +\makeatletter% +%-------------------------------------------------------------------- +\def\@F{F}\def\@C{C}\def\@EN{EN}\def\@NO{NO}\def\@MW{MW}\def\@FMc{FMc}% +\def\@fst@param#1:#2;{#1}\def\@sec@param#1:#2;{#2}% +\def\mol@sel#1{% +\if#1\empty\relax\else% + \edef\@tag{\expandafter\@fst@param#1;}% + \edef\@var{\expandafter\@sec@param#1;}% + \ifx\@tag\@F\edef\MOLfile{\@var}\fi% + \ifx\@tag\@C\edef\MOLchar{\@var}\fi% + \ifx\@tag\@EN\edef\MOLnameE{\@var}\fi% + \ifx\@tag\@NO\edef\MOLnum{\@var}\fi + \ifx\@tag\@MW\edef\CALmw{\@var}\fi + \ifx\@tag\@FMc\edef\CALfm{\@var}\fi +\fi}% +\def\put@char{% + \begin{picture}(84,42)% + \put(0,38){\bf [\MOLnum]\MOLnameE{ }\small\tt/FM:\CALfm/MW:\CALmw}% + \put(10,0){\font\@strufont=\MOLfile\relax% + \hbox{\@strufont\char\MOLchar}}% + \end{picture}% +\def\INFO#1{\@for\@temp:=#1\do{\mol@sel\@temp}\put@char}% +\makeatother +%-------------------------------------------------------------------- +\begin{document} +\unitlength=1mm% +\INFO{F:mcf_man_soc,C:100,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% +\INFO{F:mcf_man_soc,C:101,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% +\end{document} +%-------------------------------------------------------------------- +\end{verbatim}% +%############################################################################ \end{document} -- cgit v1.2.3