%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Molecular Coding Format manual by Akira Yamaji 2018.04.16 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} %%%%\documentclass[a4paper,twoside]{article} %%%%\usepackage{graphicx} \usepackage[dvipdfmx]{graphicx} %%%%\usepackage[pdftex]{graphicx} %%%%\usepackage{epstopdf} \usepackage[dvipdfmx]{hyperref} %%%%\usepackage[pdftex]{hyperref} \hypersetup{colorlinks=true,linkcolor=blue} \topmargin=-18mm \textheight=254mm \textwidth=168mm \oddsidemargin=0mm %%%%\oddsidemargin=7mm %%%%\evensidemargin=-7mm \unitlength=1mm% \makeatletter %---------------------------------------------------------------------------- \newcount \fontnum% \newcount \tempnum% \newdimen \htman% \newdimen \wdman% \newdimen \htmans% \htman=45mm% \wdman=94mm% \htmans=42mm% \fontnum=21% \tempnum=1% %---------------------------------------------------------------------------- \font\@strufont=mcf_man_soc\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}% \def\mol@sel#1{% \if#1\empty\relax\else% \edef\@tag{\expandafter\@fst#1;}% \edef\@var{\expandafter\@sec#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\@cMW\edef\CALmw{\@var}\fi \ifx\@tag\@cFM\edef\CALfm{\@var}\fi \fi}% \def\put@char{% \begin{picture}(84,28)% \put(0,23){\bf [\MOLnum]\MOLnameE}% \put(5,18){\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}% %---------------------------------------------------------------------------- \begin{document} \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} \begin{center} Suggestion or request mail to: mcf2graph@gmail.com \end{center} %----------------------------------------------------------------------------- \thispagestyle{empty} \vspace{3mm}% \begin{center} {\@strufont% \char1 \raisebox{10mm}{\char2 }\char3 \raisebox{10mm}{\char4}\\ \char5 \raisebox{10mm}{\char6 }\char7 \raisebox{10mm}{\char8}\\ \char9 \raisebox{10mm}{\char10}\char11\raisebox{10mm}{\char12}\\ \char13\raisebox{10mm}{\char14}\char15\raisebox{10mm}{\char16}\\ \char17\raisebox{10mm}{\char18}\char19\raisebox{10mm}{\char20}\\ }% \end{center} %----------------------------------------------------------------------------- \twocolumn \thispagestyle{empty} \tableofcontents %----------------------------------------------------------------------------- \linethickness{0.08mm}% %---------------------------------------------------------------------------- \newpage \setcounter{page}{1} \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 convert MCF file to graphics file pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ %----------------------------------------------------------------------------- \section{MCF syntax} \subsection{Make bond} \subsubsection{Chain} \begin{verbatim} real number plus (+): Counterclockwize real number minus(-): Clockwize <10,-30,45,-45,30,-30,60 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \begin{verbatim} ! : take value 60 or -60 depend on current angle and enviroment !6 : !,!,!,!,!,! <30,!,!,!,!,!,! <30,!6 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Jump and branch bond} \begin{verbatim} n:@ : Jump to An ** An: atom number(-999<=n<=4095) <30,!6,3:@,0,!,5:@,-30 \end{verbatim} \MCFstructure %------------------------------------ \begin{verbatim} 3:\ : 3:@,0 <30,!6,3:\,! \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Branch bond} \begin{verbatim} 2:\ : 2:@,0 4:*\ : 4:@,0~wf 6:\* : 6:@,0~zf 8:\\ : 8:@,0~dm 10:*\* : 10:@,0~wv <30,!8, 2:\,!,4:*\,!,6:\*,!,8:\\,!,10:*\*,! \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \begin{verbatim} <-30,!6, 2:\~dr,!, : 2:@,0~dr,! 4:\`1.5,-90, : 4:@,0`1.5,-90 6:\^15,-60 : 6:@,0^15,-60 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Connect atom} \begin{verbatim} n:& : Connect to An <30,!6,3:\,!,5~bd:& \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Ring} \begin{verbatim} ?n : n membered ring(3<=n<=20) ?6 : <-120,60,60,60,60,60,1:& ?6 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Rotate current angle} \begin{verbatim} : change enviroment <30,``1,!, /_`2^30,!2,/!2>lr,!2,/!2>rl,!) \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Add substituent} \begin{verbatim} <-30,!17,2:/_,4:/!,6:/!2, 10:/iPr,14:/tBu,16:/Ph^-60 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Add modified substituent} \begin{verbatim} ~,^,` : change type,angle,length <-30,!6, {2~wf,4~zf,6^-30}:/_ \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \begin{verbatim} ^,`,> : change angle,length,environment <30,!7`1, 3:/_`2^30,5:/!2>lr,7:/!2>rl \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Chain environment} \subsubsection{Horizontal,vertical} \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} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Left-right,right-left} \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} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Fixed angle,multi angle} \begin{verbatim} >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} \MCFstructure %----------------------------------------------------------------------------- \subsection{Miscellaneous} %----------------------------------------------------------------------------- \subsubsection{Change atom and Substituent} \begin{verbatim} NH,SO,SOO : inset hetero atom and substituent simultaneously <30,!2,NH,!,SO,!,SOO,! \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Change color, atom font} \begin{verbatim} 1=green : change color of B1 green 3:red : change color of A3 red atomfont:="cmr8" : use cmr8 for atom font defaultfont:="uhvr8r"; defaultsize:=8bp; MCa(0,0.5)(<30,Ph,{1,5}:N,3:/COOH,4:/NO2, 1:red,5:blue,3=green) ext(label.urt("(draw)",p0+(0,h));) atomfont:="cmr8"; % default:"draw" atomfontsize:=8bp; % default:8bp MCa(1,0.5)(<30,Ph,{1,5}:N,3:/COOH,4:/NO2) ext(label.urt("(cmr8)",p0+(0,h));) \end{verbatim} \hspace{5mm}\includegraphics{mcf_man_soc-064.eps}% for dvipdfmx %%%%\hspace{5mm}\includegraphics[width=7cm]{mcf_man_soc-064.png}% for dvipdfmx %%%%\MCFstructure % for Metafont \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax% %----------------------------------------------------------------------------- \subsubsection{Make block} \begin{verbatim} |< : start brock >| : end brock |<=n : |<,``n <30,!2,|<,``1.2,!2,>|,!2 <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 ! MCf(<30,COOH,!0,!3,COOH) \end{verbatim} \MCFstructure \begin{verbatim} MCf(<30,COOH,!4,COOH) \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{User definition} \begin{verbatim} user defined substructure iBuOH:='(!,/_,!,OH) <30,?6,{4,6}:/iBuOH \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \begin{verbatim} Insert user defined substructure <30,!3,/'(!,/_,!,OH),!3 \end{verbatim} \MCFstructure %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \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 MCf(<30,?6,-4=?5,{3,8}=dl,{2,6,7,9}:N, {2,6,9}:/_,{1,5}://O) endfont \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Margin left and right} \begin{verbatim} default: margin_left_right=0.4mm \end{verbatim} \MCFstructure \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} %----------------------------------------------------------------------------- \subsubsection{Margin top and bottom} \begin{verbatim} default: margin_top_bottom=0.4mm \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0mm 0.4mm 5mm \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Offset thickness of bond} \begin{verbatim} default: offset_thickness=0.2pt \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0pt 0.2pt 0.5pt \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Offset of doublebond gap} \begin{verbatim} default: offset_bond_gap=0.3pt \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.0pt 0.3pt 1.0pt \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Offset of atom width} \begin{verbatim} default: offset_atom=0.8pt \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.0pt 0.8pt 2.0pt \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Offset of wedge width} \begin{verbatim} default: offset_wedge=0.4pt \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.0pt 0.4pt 1.0pt \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Max bond length} \begin{verbatim} default: max_bond_length=10mm \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 6mm 8mm 20mm \end{verbatim} %----------------------------------------------------------------------------- \subsection{Ratio parameter} %----------------------------------------------------------------------------- \subsubsection{Thickness/bond length} \begin{verbatim} default: ratio_thickness_bond=0.015 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.005 0.015 0.030 \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Char/bond thickness} \begin{verbatim} default: ratio_char_bond=1.5 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 1.0 1.5 2.0 \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Bondgap/bond length} \begin{verbatim} default: ratio_bondgap_bond= 0.15 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.10 0.15 0.20 \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Atom/bond length} \begin{verbatim} default: ratio_atom_bond= 0.36 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.25 0.36 0.46 \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Wedge/bond length} \begin{verbatim} default: ratio_wedge_bond=0.12 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.10 0.12 0.20 \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Font atom gap/atom length} \begin{verbatim} default: ratio_atomgap_atom= 0.050 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.0 0.050 0.12 \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Chain/ring length} \begin{verbatim} default: ratio_chain_ring= 0.66 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.4 0.65 1.0 \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Zebra gap/bond length} \begin{verbatim} default: ratio_zebragap_bond=0.12 \end{verbatim} \MCFstructure \vspace{-3mm}% \begin{verbatim} 0.06 0.12 0.20 \end{verbatim} %----------------------------------------------------------------------------- \subsection{Drawing mode} %----------------------------------------------------------------------------- \subsubsection{Numbering atom} \begin{verbatim} numberA_start:=3; numberA_end:=8; default: sw_numberA=0 : numberA_start=1 numberA_end=4095 \end{verbatim} \MCFstructure \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{Numbering bond} \begin{verbatim} numberB_start:=3; numberB_end:=8; default: sw_numberB=0 : numberB_start=1 numberB_end=4095 \end{verbatim} \MCFstructure \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{Clipping mode} \begin{verbatim} sw_clip:=0; MCd(1,0.7)(0.2,0.3)(Ph) MCd(1,0.7)(0.8,0.7)(Ph) ** default: sw_clip=0 \end{verbatim} \MCFstructure \begin{verbatim} sw_clip:=1; MCd(1,0.7)(0.2,0.3)(Ph) MCd(1,0.7)(0.8,0.7)(Ph) \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Solid mode} \begin{verbatim} (fit to font size) sw_solid=0 ** default \end{verbatim} \MCFstructure %----------------------------------------- \begin{verbatim} (solid ratio bond/font width) sw_solid:=1; ratio_bond_width=0.1 font_width=60mm (bond_len=60mm*0.1=6mm) ** ignore bond_len \end{verbatim} \MCFstructure %----------------------------------------- \begin{verbatim} (solid bond length) sw_solid:=2; bond_len=10mm ** ignore ratio_bond_width \end{verbatim} \MCFstructure %----------------------------------------- \begin{verbatim} (solid bond length and clip) sw_solid:=2; sw_clip:=1; bond_len=10mm \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Expand mode} \begin{verbatim} default: sw_expand=0 \end{verbatim} \MCFstructure\\ \makebox[5mm]{}% \makebox[30mm]{\tt 0 :default}% \makebox[30mm]{\tt 1}% %----------------------------------------------------------------------------- \subsubsection{Substituent off mode} \begin{verbatim} default: sw_subst_off=0 \end{verbatim} \MCFstructure\\ \makebox[5mm]{}% \makebox[30mm]{\tt 0 :default}% \makebox[30mm]{\tt 1}% %----------------------------------------------------------------------------- \subsubsection{Single bond mode} \begin{verbatim} default: sw_bond_single=0 \end{verbatim} \MCFstructure\\ \makebox[5mm]{}% \makebox[30mm]{\tt 0 :default}% \makebox[30mm]{\tt 1}% %----------------------------------------------------------------------------- \subsection{Frame} %----------------------------------------------------------------------------- \subsubsection{Font frame} \begin{verbatim} (Draw font frame) margin_left_right:=5mm; margin_top_bottom:=2mm; sw_font_frame:=1; MCf(<30,Ph,4:/Cl,3:/F) \end{verbatim} \MCFstructure \begin{verbatim} (Draw frame inside margin) sw_font_frame=2 \end{verbatim} \MCFstructure \begin{verbatim} (Draw both frame) sw_font_frame=3 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Molecular frame} \begin{verbatim} sw_mol_frame:=1; MCd(1,.5)(1,0.5)(<30,Ph,4:/Cl,3:/F) ** default: sw_mol_frame=0 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Atom frame} \begin{verbatim} sw_atom_frame:=1; MCf(<30,COOH,!0,COOH) ** default: sw_atom_frame=0 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Local parameter setting} \begin{verbatim} beginfont() MCf(Ph) endfont beginfont() %-------------------------- ratio_thickness_bond:=0.05; %-------------------------- MCf(Ph) endfont beginfont() MCf(Ph) endfont \end{verbatim} \MCFstructure\MCFstructure\MCFstructure %----------------------------------------------------------------------------- \subsection{Global parameter setting} \begin{verbatim} beginfont() MCf(Ph) endfont %-------------------------- ratio_thickness_bond:=0.05; %-------------------------- beginfont() MCf(Ph) endfont beginfont() MCf(Ph) endfont \end{verbatim} \MCFstructure\MCFstructure\MCFstructure %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \newpage \section{Function} \subsection{Function MCd()} \begin{verbatim} (Draw molecule) MCd(a,b)(c,d)(...) a: ratio molecular width/font width b: ratio molecular hight/font hight c: x axis position d: y axis position beginfont() 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) endfont \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Function MCa()} \begin{verbatim} (Draw molecule at (x,y)) MCa(a,b)(...) : MCd(1,1)(a,b)(...) a: x axis position b: y axis position beginfont() MCa(0.2,0.5)(<30,Ph,3:/F,4:/Cl) MCa(0.8,0.5)(<30,Ph,3:/F,4:/Cl) endfont \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Function MCc()} \begin{verbatim} (Draw molecule to center of font) MCc(a,b)(...) : MCd(a,b)(0.5,0.5)(...) a: ratio molecular width/font width b: ratio molecular hight/font hight beginfont() MCc(1 ,1 )(?6) MCc(0.75,0.75)(?6) MCc(0.5 ,0.5 )(?6) endfont \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Function MCf()} \begin{verbatim} (Draw molecule fit to font size) MCf(...) : MCd(1,1)(0.5,0.5)(...) (Draw molecule fit to font height) beginfont() font_wd:=25mm; font_ht:=15mm; MCf(<30,Ph) endfont \end{verbatim} \MCFstructure \begin{verbatim} beginfont() font_wd:=25mm; font_ht:=15mm; MCf(<90,Ph,3:/F,4:/Cl) endfont \end{verbatim} \MCFstructure \begin{verbatim} (Draw molecule fit to font width) beginfont() font_wd:=15mm; font_ht:=25mm; MCf(<30,Ph) endfont \end{verbatim} \MCFstructure \begin{verbatim} beginfont() font_wd:=15mm; font_ht:=25mm; MCf(<30,Ph,3:/F,4:/Cl) endfont \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \newpage \subsection{Function EXT()} \begin{verbatim} (Add extra graphic to font) w: font width h: font height w0: font width-margin_left_right*2 h0: font height-margin_top_bottom*2 aw: atom font size em: label font size p0: x=margin_left_right y=margin_top_bottom n: molecular number p[m]: molecular origin position w[m]: molecular width h[m]: molecular height %---------------------------------------- beginfont() font_wd:=70mm; font_ht:=30mm; ratio_bond_width:=0.065; sw_solid:=1; %--------------------------------------- MCd(1,1)(0.1,0.5) (<-210,60`1,60`1,60`1,{1,3}=dl, 1:/R1,4:/R2^-60) ext( defaultscale:=0.6; label.bot("Diene",p0+(0.5w,0)); ) %--------------------------------------- MCd(1,1)(0.4,0.5) (<-30,-60`1,1=dl,1:/R3,2:/R4^60) ext( defaultscale:=0.6; label.bot("Dienophile",p0+(0.5w,0)); ) %--------------------------------------- MCd(1,1)(0.9,0.5) (<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1) %--------------------------------------- EXT( drawarrow (0.52w,0.5h)..(0.6w,0.5h); defaultscale:=0.7; label("+",(0.25w,0.5h)); label.bot("Diels-Alder Reaction", (0.5w,h)); ) %--------------------------------------- endfont \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \newpage \subsection{Function ext()} \begin{verbatim} (Add extra graphic to molecule) w: molecular width h: molecular height aw: atom font size em: label font size p0: origin of molecular structure l: bond length An: atom number A[m]: atom position A[m]dir: branch direction of A[m] Bn: bond number B[m]s: bond start position B[m]e: bond end position B[m]: bond position(0.5[B[m]s,B[m]e]) B[m]dir: bond direction %---------------------------------------- beginfont() font_wd:=50mm; font_ht:=20mm; %--------------------------------------- MCd(1,0.7)(0,0.5)(<30,?6,3=dl,4:/CH3) ext( label.top("+",A7); drawarrow B3{dir(B3dir-90)}.. {dir(B7dir+90)}0.4[B7s,B7e]; ) %--------------------------------------- MCd(1,0.7)(1,0.5)(<30,?6,4://CH3) ext( labeloffset:=0bp; label.lrt("+",A3); ) %--------------------------------------- EXT( drawdblarrow (0.4w,0.5h)..(0.55w,0.5h); ) %--------------------------------------- endfont \end{verbatim} \MCFstructure \begin{verbatim} label: defaultfont: label font defaultfont="draw": draw font **default defaultfont="draw" drawarrow & drawdblarrow: sw_arrow=0: emulation mode sw_arrow=1: plain.mp mode **default sw_arrow=0 \end{verbatim} %----------------------------------------------------------------------------- \newpage \section{MCF example} %----------------------------------------------------------------------------- \subsection{Acetamiprid} \begin{verbatim} <30,Ph,2:N,1:/Cl, 4:\,!,N,/_,!,/_,!!,N,!,CN \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Fenitrothion} \begin{verbatim} <30,!,O,!,P,//S,/O!^160,!,O,!, |,Ph,3:/_,4:/NO2 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Permethrin} \begin{verbatim} <-30,?3,2^-35:*/_,2^35:/*_, 1:\,!!,/Cl,!,Cl, 3:\,//O,!,O,!2,Ph, -4:\,O,-60,Ph \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \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} \MCFstructure %----------------------------------------------------------------------------- \subsection{Luciferin} \begin{verbatim} <30,Ph,3=?5,8:\,?5,{9,16}=dl, {9,14}:N,{7,11}:S, 1:/OH,-2:*/COOH \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Warfarin} \begin{verbatim} <30,Ph,3=?6,8=dl, 10:O,7:/OH,9://O, 8:\,/Ph`1,60,!,//O,! \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Limonin} \begin{verbatim} <30,?6,{-3,-4}=?6,-5=?3, -2=wf,-1=wb,6=?5,-4=?6,-5=wf, {13,15,17,20}:O,{3,12,21}://O, {4~wf^60,8~zf^60,18^35,18^-35}:/_, {1^60,5^180,16^60}:/*H, 14:\*,|,?5,{1,4}=dl,3:O \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Sesamine} \begin{verbatim} <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} \MCFstructure %----------------------------------------------------------------------------- \subsection{Colchicine} \begin{verbatim} <30,Ph,{1,2,6}:/O!, -4=?7,-5=?7, {-1,-4,-6}=dl,-2://O,-3:/O!, 9:\,NH,!,//O,! \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{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:/*OMe \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Gibberellin} \begin{verbatim} <18,?5,3=?7,5=?6[12], 8:@,160`1.3,3:&, 13=dl,6=wf,8=wb, 5:@,40~zf`1,O,60,//O^180,14~zb:&, 2:/COOH,7://_,13:*/OH,8:/*OH, 14:*/_,{1^60,4^60}:*/H \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Quinine} \begin{verbatim} <30,Ph,3=Ph,7:N,6:/O!, 10:\,*/OH,/H~zf^-60,!, |,?6,2:N,1:*/H^60, 4:*\,!!, 2:@,165~zf,60,5~zb:& \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Atoropin} \begin{verbatim} <-30,O,!,//O,!,!,Ph, $1:@,-120~zb, |,?7,6:*\^190`1.02,N,/_,3~wb:&, $3:*\*,!,OH \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \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}:/O!,1:*\,/_,!! \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsection{Pyrethrin I} \begin{verbatim} <30,?3,{3^35~wf,3^-35~zf}:/_, 1:*\,!!,iPr,2:\*,//O,!,O,-36~zb,|, ?5,-2=d,-1:/_,-3://O,-2\,!4,{-1,-3}=dl \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \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} \MCFstructure %----------------------------------------------------------------------------- \subsection{Paclitaxel} \begin{verbatim} ?6,5=d,3:@,|<=1,36,45,45,45,45,>|,$5:&, -4=?6,-4=?4,-1=wb,-3=wf,-1:O,||, {4^35,4^-35,6}:/_,{3^-60,15}:*/OH, 8:/*H^-60,9:*/_^60,10://O, 1:\,O,!,//O,!,*/OH,!,/Ph, 60~wf,NH,-60,//O,60,Ph, 7:\*,O,-45,//O,60,Ph,11:*\,O,-60,//O,60, 12:\*^-15,O,60,//O,-60 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \onecolumn \section{Example to use mcf2graph} \subsection{Molecular definition file} \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"; > %%%% sw_report:=1; > Report output %%%% sw_MOLout:=1; > MOL file output 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}:/_, > 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}:*/_^60,9:*/H^60, > 10:/*H^180,{11,-1}:/*H^-60, > -1:@,17,/*_,!4,/_,!) > end MCF endfont > end font %------------------------------------------------------------------------ beginfont("NO:3","EN:Limonin") > begin font(information) MCf(<30,?6,{-3,-4}=?6, > begin MCF (3) -5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf, > {13,15,17,20}:O,{3,12,21}://O, > {4~wf^60,8~zf^60,18^35,18^-35}:/_, > {1^60,5^180,16^60}:/*H, > 14:\*,|,?5,{1,4}=dl,3:O) > end MCF endfont > end font %------------------------------------------------------------------------ beginfont("NO:4","EN:beta-carotene) > begin font(information) MCf(<30,?6,3=dl,{3,5^35,5^-35}:/_, > begin MCF (4) 4:\,|,!18,{1,3,5,7,9,11,13,15,17}=dr, > {3,7,12,16}:/_, > |,?6,6=dl,{6,2^35,2^-35}:/_) > end MCF endfont > end font %------------------------------------------------------------------------ beginfont("NO:5","EN:Gibberellin A3"); > begin font(information) MCf(<18,?5,3=?7,5=?6[12], > begin MCF (5) 8:@,160`1.3,3:&,13=dl,6=wf,8=wb, > 5:@,40~zf`1,O,60,//O^180,14~zb:&, > 2:/COOH,7://_,13:*/OH,8:/*OH, > 14:*/_,{1^60,4^60}:*/H) > end MCF endfont; > end font %------------------------------------------------------------------------ bye \end{verbatim} %------------------------------------------------------------------------ \noindent% \newpage \subsection{Information auxfile output} \paragraph{(Insert option parameter setting)} \begin{verbatim} sw_auxout:=1; ** default : sw_auxout=0 \end{verbatim} \paragraph{(Command line)} \begin{verbatim} >mpost -s ahangle=0 FILENAME (molecular definition file) \end{verbatim} \paragraph{(Sourse)} \begin{verbatim} beginfont("EN:Ampicillin")(....) beginfont("EN:Cholesterol")(....) beginfont("EN:Limonin")(....) beginfont("EN:beta-Carotene")(....) beginfont("EN:Gibberellin A3")(....) \end{verbatim} \paragraph{(Setting)} \begin{verbatim} tag1:="F"; var1:="jobname"; * default output tag2:="C"; var2:="char_num"; * default output tag3:="cMW"; var3:="calc_weight"; tag4:="cFM"; var4:="calc_formula"; \end{verbatim} \paragraph{(Output)} \begin{verbatim} (sw_auxfix=0) F:mcf_man_soc;C:1;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin F:mcf_man_soc;C:2;cMW:386.6532;cFM:C27H46O;EN:Cholesterol F:mcf_exa_soc;C:3;cMW:470.5113;cFM:C26H30O8;EN:Limonin F:mcf_exa_soc;C:4;cMW:536.8722;cFM:C40H56;EN:beta-Carotene F:mcf_exa_soc;C:5;cMW:346.3742;cFM:C19H22O6;EN:Gibberellin A3 (sw_auxfix=1) F;C;cMW;cFM;EN mcf_man_soc;1;349.40462;C16H19N3O4S;Ampicillin mcf_man_soc;2;386.6532;C27H46O;Cholesterol mcf_exa_soc;3;470.5113;C26H30O8;Limonin mcf_exa_soc;4;536.8722;C40H56;beta-Carotene mcf_exa_soc;5;346.3742;C19H22O6;Gibberellin A3 (aux_delimiter:="/";) F:mcf_man_soc/C:1/cMW:349.40462/cFM:C16H19N3O4S/EN:Ampicillin F:mcf_man_soc/C:2/cMW:386.6532/cFM:C27H46O/EN:Cholesterol F:mcf_exa_soc/C:3/cMW:470.5113/cFM:C26H30O8/EN:Limonin F:mcf_exa_soc/C:4/cMW:536.8722/cFM:C40H56/EN:beta-Carotene F:mcf_exa_soc/C:5/cMW:346.3742/cFM:C19H22O6/EN:Gibberellin A3 \end{verbatim} \paragraph{(Tag)} \begin{verbatim} F : filename C : char number NO : serial number EN : english name JN : japanese name FM : formula from literature data MW : molecular weight from literature data USE : the use cMW : molecular weight calculated cMI : monoisotopic mass calculated cFM : molecular formula calculated \end{verbatim} %------------------------------------------------------------------------ \newpage \noindent% \subsection{Report output} \paragraph{(Insert option parameter setting)} \begin{verbatim} sw_report:=1; ** default : sw_report=0 \end{verbatim} \paragraph{(Command line)} \begin{verbatim} >mpost -s ahangle=0 -s ahlength=2 FILENAME (molecular definition file) \end{verbatim} \paragraph{(Output)} \begin{verbatim} ------------------------------------------------------------------ Molecular name = Nicotine Warnings = 0 / Expanded command = 40 Width * Height = 49.57332 * 41.37605 Shift width * height = 0 * -9.07253 Bond length = 12.75589 Atom size = 5.38914 Atom count= 12 Bond count= 13 Ring count= 2 Hide H count= 14 ------------------------------------------------------------------ < NO. >( x axis , y axis )< atom >< bond >< hide_H > A1 ( 0 , 0 ) C 3 1 A2 ( 0.866 , -0.5 ) N 3 A3 ( 1.732 , 0 ) C 3 1 A4 ( 1.732 , 1 ) C 4 A5 ( 0.866 , 1.5 ) C 3 1 A6 ( 0 , 1 ) C 3 1 A7 ( 2.304 , 1.33 ) C 3 1 A8 ( 3.217 , 0.923 ) N 3 A9 ( 3.886 , 1.666 ) C 2 2 A10 ( 3.386 , 2.532 ) C 2 2 A11 ( 2.408 , 2.325 ) C 2 2 A12 ( 3.399 , 0.067 ) C 1 3 ------------------------------------------------------------------ < NO. >< bond (sdt)> B1 1 -> 2 ( 2) 330 ( -30) 1 ( 12.76) B2 2 -> 3 ( 1) 30 ( 30) 1 ( 12.76) B3 3 -> 4 ( 2) 90 ( 90) 1 ( 12.76) B4 4 -> 5 ( 1) 150 ( 150) 1 ( 12.76) B5 5 -> 6 ( 2) 210 ( -150) 1 ( 12.76) B6 6 -> 1 ( 1) 270 ( -90) 1 ( 12.76) B7 4 -> 7 ( 1) 30 ( 30) 0.66 ( 8.42) B8 7 -> 8 ( 1) 336 ( -24) 1 ( 12.76) B9 8 -> 9 ( 1) 48 ( 48) 1 ( 12.76) B10 9 -> 10 ( 1) 120 ( 120) 1 ( 12.76) B11 10 -> 11 ( 1) 192 ( -168) 1 ( 12.76) B12 11 -> 7 ( 1) 264 ( -96) 1 ( 12.76) B13 8 -> 12 ( 1) 282 ( -78) 0.66 ( 8.42) ------------------------------------------------------------------ ( atom wt )[ mi wt ] < cnt > < sum wt >[ sum mi wt ] C ( 12.0107)[ 12] * 10 = 120.10696[ 120] H ( 1.00793)[ 1.00783] * 14 = 14.11108[ 14.10959] N ( 14.0067)[ 14.00307] * 2 = 28.0134[ 28.00613] Molecular Weight [Mono Isotopic] = 162.2314[ 162.11572] ------------------------------------------------------------------ Weight Calc: 162.2314 / Input: 162.23 / weight gap= 0.00145 Fomula Calc: C10H14N2 / Input: ================================================================== \end{verbatim}% \newpage %------------------------------------------------------------------------ \noindent% \subsection{Molfile output} \paragraph{(Insert option parameter setting)} \begin{verbatim} sw_MOLout:=1; ** default : sw_MOLout=0 \end{verbatim} \paragraph{(Command line)} \begin{verbatim} >mpost -s ahangle=3 FILENAME (molecular definition file) \end{verbatim} \paragraph{(Output)} \begin{verbatim} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -MCFtoMOL- EN:Caffeine 14 15 0 0 0 0 0 0 0 0999 V2000 0 0 0 C 0 0 0 0 0.86603 -0.5 0 N 0 0 0 0 1.73206 0 0 C 0 0 0 0 1.73206 1 0 C 0 0 0 0 0.86603 1.5 0 C 0 0 0 0 0 1 0 N 0 0 0 0 2.6831 -0.30902 0 N 0 0 0 0 3.27089 0.5 0 C 0 0 0 0 2.6831 1.30902 0 N 0 0 0 0 0.86603 -1.36383 0 C 0 0 0 0 -0.76894 1.44394 0 C 0 0 0 0 -0.76894 -0.44394 0 O 0 0 0 0 0.86603 2.36383 0 O 0 0 0 0 2.95299 2.1396 0 C 0 0 0 0 1 2 1 0 0 0 2 3 1 0 0 0 3 4 2 0 0 0 4 5 1 0 0 0 5 6 1 0 0 0 6 1 1 0 0 0 3 7 1 0 0 0 7 8 2 0 0 0 8 9 1 0 0 0 9 4 1 0 0 0 2 10 1 0 0 0 6 11 1 0 0 0 1 12 2 0 0 0 5 13 2 0 0 0 9 14 1 0 0 0 M END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \end{verbatim}% %---------------------------------------------------------------------------- \newpage \subsection{LuaTeX file example} %############################################################################ \begin{verbatim} %-------------------------------------------------------------------- \documentclass{article} \usepackage{luamplib}% \mplibcodeinherit{enable}% \mplibverbatim{enable}% \everymplib{if unknown Ph1: input mcf2graph.mf; mp_log_name:="temp-info.aux"; sw_auxout:=1; fi}% %-------------------------------------------------------------------- \begin{document} \noindent% %-------------------------------------------------------------------- \begin{mplibcode} font_wd:=50mm; font_ht:=50mm; beginfont("NO:2","EN:Limonin","MW:470.51") MCf(<30, ?6,{-3,-4}=?6, -5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf, {13,15,17,20}:O,{3,12,21}://O, {4~wf^60,8~zf^60,18^35,18^-35}:/_, {1^60,5^180,16^60}:/*H, 14:\*,|,?5,{1,4}=dl,3:O ) endfont \end{mplibcode}\\ %-------------------------------------------------------------------- \begin{mplibcode} font_wd:=80mm; font_ht:=50mm; beginfont("NO:3","EN:beta-carotene","MW:536.87") MCf(<30, ?6,3=dl,{3,5^35,5^-35}:/_, 4:\,|,!18,{1,3,5,7,9,11,13,15,17}=dr, {3,7,12,16}:/_, |,?6,6=dl,{6,2^35,2^-35}:/_ ) endfont \end{mplibcode}\\ %-------------------------------------------------------------------- \begin{mplibcode} font_wd:=50mm; font_ht:=50mm; beginfont("NO:4","EN:Gibberellin A3","MW:346.37"); MCf(<18,?5,3=?7,5=?6[12], 8:@,160`1.3,3:&,13=dl,6=wf,8=wb, 5:@,40~zf`1,O,60,//O^180,14~zb:&, 2:/COOH,7://_,13:*/OH,8:/*OH, 14:*/_,{1^60,4^60}:*/H ) endfont; \end{mplibcode}\\ %-------------------------------------------------------------------- \end{document} %-------------------------------------------------------------------- \end{verbatim}% %############################################################################ %------------------------------------------------------------------------ \newpage \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:134,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% \INFO{F:mcf_man_soc,C:135,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% \end{document} %-------------------------------------------------------------------- \end{verbatim}% %############################################################################ %------------------------------------------------------------------------ \INFO{F:mcf_man_soc,C:134,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% \INFO{F:mcf_man_soc,C:135,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% %------------------------------------------------------------------------ \end{document}