diff options
Diffstat (limited to 'Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex')
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | 274 |
1 files changed, 201 insertions, 73 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex index 03b78cd584e..c2a73256dc8 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2016.11.15 +% Molecular Coding Format manual by Akira Yamaji 2017.01.03 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} %%%%\usepackage{graphicx} @@ -55,12 +55,6 @@ %---------------------------------------------------------------------------- \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} \title{\Huge\sf Molecular Coding Format manual} \author{Akira Yamaji} @@ -183,10 +177,13 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ dl : double left side dr : double right side tm : triple - <30,!~dm,!~dl,!~dr,!~tm \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + dm dl dr tm +\end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Wedge} \begin{verbatim} @@ -198,6 +195,10 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ <30,!~wf,!,!~wb,!,!~zf,!,!~zb \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + wf wb zf zb +\end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Vector} \begin{verbatim} @@ -207,25 +208,35 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ <30,!~vf,!,!~vb \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + vf vb +\end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Dotted,wave} \begin{verbatim} Bn=bond type : change bond type at Bn - dt : dotted - wv : wave + dt : dotted / wv : wave <30,!3,1=dt,3=wv \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + dt wv +\end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Broad} \begin{verbatim} - bd : broad - bz : broad dotted + bd : broad / bz : broad dotted <30,!3,1=bd,3=bz \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + bd bz +\end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Change multi bond type} \begin{verbatim} @@ -365,11 +376,15 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ (4,11)=?4[2] : fuse 2/4 ring to B11..B4 ** ?m[n] (4<=m<=6,n=m-2) - MCd(1,.7)( 0,0)(<30,?6,3=?6,(11,4)=?6[4]) - MCd(1,.6)(.54,1)(<30,?6,3=?6,(11,4)=?5[3]) - MCd(1,.6)( 1,0)(<30,?6,3=?6,(11,4)=?4[2]) +1:MCd(1,.7)( 0,0)(<30,?6,3=?6,(11,4)=?6[4]) +2:MCd(1,.6)(.54,1)(<30,?6,3=?6,(11,4)=?5[3]) +3:MCd(1,.6)( 1,0)(<30,?6,3=?6,(11,4)=?4[2]) \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + 1 2 3 +\end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Attached 3 bond} \begin{verbatim} @@ -377,10 +392,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ (16,4)=?5[2] : fuse 2/5 ring to B16..B4 ** ?m[n] (5<=m<=6,n=m-3) - MCd(1,.55)(0,0)(?6,$(3,10)?6,(16,4)=?6[3]) - MCd(1,.55)(1,0)(?6,$(3,10)?6,(16,4)=?5[2]) +1:MCd(1,.55)(0,0)(?6,$(3,10)?6,(16,4)=?6[3]) +2:MCd(1,.55)(1,0)(?6,$(3,10)?6,(16,4)=?5[2]) \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + 1 2 +\end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Attached 4 bond} \begin{verbatim} @@ -405,19 +424,19 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \subsection{Substituent} \subsubsection{Insert substituent} \begin{verbatim} + / : single <30,!,/Me,!,/Et,!3,/Pr,!,/iPr, !3,/tBu,!,/Ph^-30,! - ** Me:methyl Et:ethyl - Pr:propyl iPr:isopropyl - tBu:tertial buthyl Ph:phenyl + ** Me:methyl Et:ethyl(!) + Pr:propyl(!2) iPr:isopropyl + tBu:tertial buthyl(!3) Ph:phenyl \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Insert modified substituent} \begin{verbatim} - / : single - // : double + // : double (double middle) */ : wedge forward /* : wedge dotted forward ** : direct @@ -425,6 +444,10 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ <30,!,//O,!,/*H,!,*/H,!,/?3,!,**?3,! \end{verbatim} \MCFstructure +\vspace{-3mm}% +\begin{verbatim} + // /* */ ** +\end{verbatim} %----------------------------------------------------------------------------- \begin{verbatim} ~ : change type @@ -432,14 +455,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ ` : change length > : change enviroment - <30,``1,!,/Me~zf`2^30,!,/Me~zf`2^30, - !2,*/Pr>lr,!2,*/Pr>rl,!) + <30,``1,!,/Me~zf`2^30, + !2,*/!2>lr,!2,*/!2>rl,!) \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \subsubsection{Add substituent} \begin{verbatim} - <-30,!17,2:/Me,4:/Et,6:/Pr, + <-30,!17,2:/Me,4:/!,6:/!2, 10:/iPr,14:/tBu,16:/Ph^-60 \end{verbatim} \MCFstructure @@ -454,10 +477,11 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \MCFstructure %----------------------------------------------------------------------------- \begin{verbatim} + ^,`,> : change angle,length,environment <30,!7`1, - 3:/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl + 3:/*Me`2^30,5:*/!2>lr,7:*/!2>rl \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -585,43 +609,61 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \begin{verbatim} default: margin_top_bottom=0.4mm \end{verbatim} -\MCFstructure\\ -\figex{20mm}{0mm}{0.4mm}{5mm} +\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\\ -\figex{20mm}{0pt}{0.2pt}{0.5pt} +\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\\ -\figex{20mm}{0.0pt}{0.3pt}{1.0pt} +\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\\ -\figex{20mm}{0.0pt}{0.8pt}{2.0pt} +\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\\ -\figex{20mm}{0.0pt}{0.4pt}{1.0pt} +\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\\ -\figex{18mm}{6mm}{8mm}{20mm} +\MCFstructure +\vspace{-3mm}% +\begin{verbatim} + 6mm 8mm 20mm +\end{verbatim} %----------------------------------------------------------------------------- \subsection{Ratio parameter} %----------------------------------------------------------------------------- @@ -629,57 +671,81 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \begin{verbatim} default: ratio_thickness_bond=0.015 \end{verbatim} -\MCFstructure\\ -\figex{20mm}{0.005}{0.015}{0.030} +\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\\ -\figex{20mm}{1.0}{1.5}{2.0} +\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\\ -\figex{20mm}{0.10}{0.15}{0.20} +\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\\ -\figex{20mm}{0.25}{0.36}{0.46} +\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\\ -\figex{20mm}{0.10}{0.12}{0.20} +\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\\ -\figex{20mm}{0.0}{0.050}{0.12} +\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\\ -\figex{20mm}{0.4}{0.65}{1.0} +\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\\ -\figex{20mm}{0.06}{0.12}{0.20} +\MCFstructure +\vspace{-3mm}% +\begin{verbatim} + 0.06 0.12 0.20 +\end{verbatim} %----------------------------------------------------------------------------- \subsection{Drawing mode} %----------------------------------------------------------------------------- @@ -842,15 +908,16 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ %----------------------------------------------------------------------------- \subsection{Function MCf()} \begin{verbatim} - (Draw fit to font size) - + (Draw molecular fit to font size) MCf(...) : MCd(1,1)(0.5,0.5)(...) - beginfont() - MCf(<30,Ph,3:/F,4:/Cl) - endfont + beginfont() beginfont() + font_wd#:=25mm#; font_wd#:=13mm#; + font_ht#:=15mm#; font_ht#:=25mm#; + MCf(<30,Ph) MCf(<30,Ph) + endfont endfont \end{verbatim} -\MCFstructure +\MCFstructure\hspace{12mm}\MCFstructure %----------------------------------------------------------------------------- \newpage \subsection{Function EXT()} @@ -1034,9 +1101,9 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4 %----------------------------------------------------------------------------- \subsection{Colchicine} \begin{verbatim} - <30,Ph,@(1,2,6)/OMe, + <30,Ph,@(1,2,6)/O!, -4=?7,-5=?7, - $(-1,-4,-6)dl,-2://O,-3:/OH, + $(-1,-4,-6)dl,-2://O,-3:/O!, 9\,NH,!,//O,! \end{verbatim} \MCFstructure @@ -1048,7 +1115,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4 13=dl, 8:N,@(15,17)O, 9:/*H^180,10:*/H^60, - 13:*/OH,14:/*OH + 13:*/OH,14:/*OMe \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -1065,7 +1132,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4 %----------------------------------------------------------------------------- \subsection{Quinine} \begin{verbatim} - <30,Ph,3=Ph,7:N,6:/OMe, + <30,Ph,3=Ph,7:N,6:/O!, 10\,*/OH,/H~zf^-60,!, |,?6,2:N,1:*/H^60, 4*\,!~dr, @@ -1087,7 +1154,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4 <-60,?5,$(-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 + @(-2,-3)/O!,1*\,/Me,!~dl \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -1101,9 +1168,9 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4 %----------------------------------------------------------------------------- \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 + <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 %----------------------------------------------------------------------------- @@ -1298,8 +1365,69 @@ MW : molecular weight from literature data M END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \end{verbatim}% -\newpage %---------------------------------------------------------------------------- +\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,$(-3,-4)?6, + -5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf, + @(13,15,17,20)O,@(3,12,21)//O, + @(4~wf^60,8~zf^60,18^35,18^-35)/Me, + @(1^60,5^180,16^60)/*H, + 14\*,|,?5,$(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)/Me, + 4\,|,!18,$(1,3,5,7,9,11,13,15,17)dr, + @(3,7,12,16)/Me, + |,?6,6=dl,@(6,2^35,2^-35)/Me + ) + 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://Me,13:*/OH,8:/*OH, + 14:*/Me,@(1^60,4^60)*/H + ) +endfont; +\end{mplibcode}\\ +%-------------------------------------------------------------------- +\end{document} +%-------------------------------------------------------------------- +\end{verbatim}% +%############################################################################ +%------------------------------------------------------------------------ +\newpage \subsection{LaTeX file example} %############################################################################ \begin{verbatim} @@ -1333,14 +1461,14 @@ M END %-------------------------------------------------------------------- \begin{document} \unitlength=1mm% -\INFO{F:mcf_man_soc,C:114,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:115,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% +\INFO{F:mcf_man_soc,C:115,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% +\INFO{F:mcf_man_soc,C:116,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% \end{document} %-------------------------------------------------------------------- \end{verbatim}% %############################################################################ %------------------------------------------------------------------------ -\INFO{F:mcf_man_soc,C:114,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:115,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% +\INFO{F:mcf_man_soc,C:115,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% +\INFO{F:mcf_man_soc,C:116,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% %------------------------------------------------------------------------ \end{document} |