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authorNorbert Preining <norbert@preining.info>2023-01-10 03:01:21 +0000
committerNorbert Preining <norbert@preining.info>2023-01-10 03:01:21 +0000
commitdecba0e4470fd7bfe288f98ee709553fc13014b8 (patch)
tree781f266fc727864e1c9bb62f07c1069dc926fbec /graphics/mcf2graph/mcf_mplib_exa.tex
parent61f8490e549cb7af263b9d903bc20d61ea37a2d7 (diff)
CTAN sync 202301100301
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-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2022.11.12
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% ** mcf2graph.mp must be version 4.90
-% ** use mcf_library.mcf
-\documentclass{article}
-%------------------------------------------------------------------------------
-\usepackage{luamplib}%
-\usepackage[T1]{fontenc}%
-\usepackage{textcomp,verbatim}%
-\mplibcodeinherit{enable}%
-\mplibverbatim{enable}%
-\mplibnumbersystem{double}%
-\mpliblegacybehavior{disabled}%
-\everymplib{%
- if unknown Ph1: input mcf2graph; fi
- outputformat:="eps";
- sw_output:=Fig+Calc;
- tag1:="J"; tag2:="C"; tag3:="fm"; tag4:="mw"; tag5:="EN"; tag6:="MW";
- max_blength:=4.5mm;
- defaultsize:=8;
- defaultscale:=1;
-}%
-%------------------------------------------------------------------------------
-\pagestyle{empty}
-\topmargin=-20mm
-\oddsidemargin=0mm
-\textwidth=170mm
-\textheight=280mm
-\unitlength=1mm
-%------------------------------------------------------------------------------------
-\begin{document}
-\begin{center}
- {\Huge\sf MCF example for luamplib(Lua\LaTeX)}\vspace{5mm}\\
- Author : Akira Yamaji \quad Date : \today\\
- Located at : http://www.ctan.org/pkg/mcf2graph\vspace{2mm}\\
-\end{center}
-%------------------------------------------------------------------------------------
-\section{MCF example}
-\noindent%
-%------------------------------------------------------------------------------------
- use molecular library file 'mcf\_library.mcf' \\
-{{\tt FM(fm) :} molecular formula (calculated) \\
-{{\tt MW(mw) :} molecular weight (calculated)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Erythromycin}
-\noindent%
-%----------------------------------------------------------------------------
-( pass mcf to MC() )
-\begin{verbatim}
-beginfigm("EN:Erythromycin","MW:733.93")
- fsize:=(120mm,30mm);
- MC(<30,#1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,##,&1,
- 14:O,13:/*Et,{1,9}://O,{2',4,6^-35,8,10',12^35}:/*_,
- {6^35,11,12^-35}:*/OH,
- @$3,\*,O,30~zb,|,?6`.7,6:O,#.5,{5~wf,3^35}:/_,4:/*OH,3^-35:/*O!,##,
- @$5,\*^30`1.7,O,!~zb,|,?6`.7,6:O,#.5,5:/*_,2:*/OH,3:/*N?!)
- ext(defaultscale:=0.8; label.lrt("fm: "&cal_FM,(0,h-5mm));
- label.lrt("mw: "&cal_MW,(0,h-9mm)); label.lrt("MW: "&inf_MW,(0,h-13mm));)
-endfigm;
-\end{verbatim}
-%----------------------------------------------------------------------------
-\begin{mplibcode}
-beginfigm("EN:Erythromycin","MW:733.93")
- fsize:=(120mm,30mm);
- MC(<30,#1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,##,&1,
- 14:O,13:/*Et,{1,9}://O,{2',4,6^-35,8,10',12^35}:/*_,
- {6^35,11,12^-35}:*/OH,
- @$3,\*,O,30~zb,|,?6`.7,6:O,#.5,{5~wf,3^35}:/_,4:/*OH,3^-35:/*O!,##,
- @$5,\*^30`1.7,O,!~zb,|,?6`.7,6:O,#.5,5:/*_,2:*/OH,3:/*N?!)
- ext(defaultscale:=0.8; label.lrt("fm: "&cal_FM,(0,h-5mm));
- label.lrt("mw: "&cal_MW,(0,h-9mm)); label.lrt("MW: "&inf_MW,(0,h-13mm));)
-endfigm;
-\end{mplibcode}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Paclitaxel}
-\noindent%
-( pass mcf to beginfigm() )
-\begin{verbatim}
-beginfigm("EN:Paclitaxel","MW:853.918",
- %---------------------------------------------------------------------
- ": ?6,5=dl,@3,#1,36,45,45,45,45,##,&5,-4=?6,-4=?4,-1=wb,-3=wf,-1:O, ",
- ": 4:??,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:*/OCO!>rl,12:/*OCO!^-15>lr ")
- %---------------------------------------------------------------------
- fsize:=(140mm,30mm);
- if mc_check(mc)=0: MCat(0,0.5)(scantokens(mc))
- sw_numbering:=Atom; MCat(0.6,0.5)(scantokens(mc))
- sw_numbering:=Bond; MCat(1,0.5)(scantokens(mc))
- fi
-endfigm
-\end{verbatim}
-%----------------------------------------------------------------------------
-\begin{mplibcode}
-beginfigm("EN:Paclitaxel","MW:853.918",
- %---------------------------------------------------------------------
- ": ?6,5=dl,@3,#1,36,45,45,45,45,##,&5,-4=?6,-4=?4,-1=wb,-3=wf,-1:O, ",
- ": 4:??,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:*/OCO!>rl,12:/*OCO!^-15>lr ")
- %---------------------------------------------------------------------
- fsize:=(140mm,30mm);
- if mc_check(mc)=0: MCat(0,0.5)(scantokens(mc))
- sw_numbering:=Atom; MCat(0.6,0.5)(scantokens(mc))
- sw_numbering:=Bond; MCat(1,0.5)(scantokens(mc))
- fi
-endfigm
-\end{mplibcode}
-%----------------------------------------------------------------------------
-\newpage
-\subsection{Chlorophyll a}
-\noindent%
-( read library file )
-\begin{verbatim}
-beginfigm("f:mcf_library.mcf","t:EN","v:Chlorophyll a","NO:-",
- "= sw_output:=Fig+Calc+Mcode;",
- "= fsize:=(100mm,30mm);")
- if op_row>=1: scantokens(op) fi
- if mc_check(mc)=0:
- MC(scantokens(mc))
- VerbatimTeX("\gdef\EN{"&inf_EN&"}\gdef\MW{"&inf_MW&"}");
- VerbatimTeX("\gdef\mw{"&cal_MW&"}\gdef\fm{"&cal_FM&"}");
- fi
-endfigm
-\end{mplibcode}
-\verbatiminput{temp-mc.aux} %%%% input temp-mc.aux %%%%
-{\tt ** EN:\EN \quad mw:\MW \quad MW:\mw \quad fm:\fm}%
-\end{verbatim}
-%------------------------------------------------------------------------------------
-\begin{mplibcode}
-beginfigm("f:mcf_library.mcf","t:EN","v:Chlorophyll a","NO:-",
- "= sw_output:=Fig+Calc+Mcode;",
- "= fsize:=(100mm,30mm);")
- if op_row>=1: scantokens(op) fi
- if mc_check(mc)=0:
- MC(scantokens(mc))
- VerbatimTeX("\gdef\EN{"&inf_EN&"}\gdef\MW{"&inf_MW&"}");
- VerbatimTeX("\gdef\mw{"&cal_MW&"}\gdef\fm{"&cal_FM&"}");
- fi
-endfigm
-\end{mplibcode}
-\verbatiminput{temp-mc.aux} %%%% input temp-mc.aux %%%%
-{\tt ** EN:\EN \quad mw:\MW \quad MW:\mw \quad fm:\fm}%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Dinophysistoxin-1}
-\noindent%
-( read library file + pass mcf to beginfigm() )
-\begin{verbatim}
-beginfigm("t:EN","v:Okadaic acid","EN:Dinophysistoxin-1",
- "MW:819",":,38:*/_,65=red") %%%% add methyl group (color red) %%%%
- sw_output:=Fig+Calc+Mcode; %%%% output temp-mc.aux %%%%
- fsize:=(120mm,20mm);
- if mc_check(mc)=0: MC(scantokens(mc))
- VerbatimTeX("\gdef\EN{"&inf_EN&"}\gdef\MW{"&inf_MW&"}");
- VerbatimTeX("\gdef\mw{"&cal_MW&"}\gdef\fm{"&cal_FM&"}");
- fi
-endfigm;
-\end{mplibcode}
-\verbatiminput{temp-mc.aux} %%%% input temp-mc.aux %%%%
-{\tt ** EN:\EN \quad mw:\MW \quad MW:\mw \quad fm:\fm}%
-\end{verbatim}
-%----------------------------------------------------------------------------
-\begin{mplibcode}
-beginfigm("t:EN","v:Okadaic acid","EN:Dinophysistoxin-1",
- "MW:819",":,38:*/_,65=red") %%%% add methyl group (color red) %%%%
- sw_output:=Fig+Calc+Mcode; %%%% output temp-mc.aux %%%%
- fsize:=(120mm,20mm);
- if mc_check(mc)=0: MC(scantokens(mc))
- VerbatimTeX("\gdef\EN{"&inf_EN&"}\gdef\MW{"&inf_MW&"}");
- VerbatimTeX("\gdef\mw{"&cal_MW&"}\gdef\fm{"&cal_FM&"}");
- fi
-endfigm;
-\end{mplibcode}
-\verbatiminput{temp-mc.aux} %%%% input temp-mc.aux %%%%
-{\tt ** EN:\EN \quad mw:\MW \quad MW:\mw \quad fm:\fm}%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\newpage
-%----------------------------------------------------------------------------
-\subsection{Maitotoxin}
-\noindent%
-( read library file )
-%--------------------------------------------------------------------------------
-\begin{verbatim}
-%--------------------------------------------------------------------------------
-\begin{mplibcode}
- beginfigm("t:EN","v:Maitotoxin")
- sw_output:=Fig+Calc+Mcode; %%%% output temp-mc.aux %%%%
- fsize:=(120mm,60mm); fmargin:=(0,3mm); sw_frame:=Outside;
- if mc_check(mc)=0: MC(scantokens(mc))
- VerbatimTeX("\gdef\EN{"&inf_EN&"}\gdef\MW{"&inf_MW&"}");
- VerbatimTeX("\gdef\mw{"&cal_MW&"}\gdef\fm{"&cal_FM&"}");
- fi
- endfigm
-\end{mplibcode}
-\verbatiminput{temp-mc.aux} %%%% input temp-mc.aux %%%%
-{\tt ** EN:\EN \quad mw:\MW \quad MW:\mw \quad fm:\fm}%
-%--------------------------------------------------------------------------------
-\end{verbatim}
-%--------------------------------------------------------------------------------
-\begin{mplibcode}
- beginfigm("t:EN","v:Maitotoxin")
- sw_output:=Fig+Calc+Mcode;
- fsize:=(120mm,60mm); fmargin:=(0,3mm); sw_frame:=Outside; %% mc_length:=40;
- if mc_check(mc)=0: MC(scantokens(mc))
- VerbatimTeX("\gdef\EN{"&inf_EN&"}\gdef\MW{"&inf_MW&"}");
- VerbatimTeX("\gdef\mw{"&cal_MW&"}\gdef\fm{"&cal_FM&"}");
- fi
- endfigm
-\end{mplibcode}
-\verbatiminput{temp-mc.aux}
-{\tt ** EN:\EN \quad mw:\MW \quad MW:\mw \quad fm:\fm}%
-%--------------------------------------------------------------------------------
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\newpage
-\subsection{TCA cycle}
-\noindent%
-\begin{mplibcode}
-beginfigm("EN:TCA cycle")
-fsize:=(160mm,75mm);
-max_blength:=5mm;
-%--------------------------------------------------------------------------------
-COOH:='(//O,!,OH);
-HOCO:='(OH,!,//O,);
-MCat(0.33, 1)(<30,HOCO,!,//O,!2,COOH) % Oxaloacetate
-MCat(0.66, 1)(<30,HOCO,!4,COOH,@-4`1,\,COOH,4:/OH^-165) % Citrate
-MCat(1, 1)(<30,HOCO,!2,!~dr,!,COOH,@-4`1,\,COOH) % cis-Aconitate
-MCat(1, 0.58)(<30,HOCO,!4,COOH,@-4,\`1,COOH,5:/OH) % Isocitrate
-MCat(1, 0.05)(<30,HOCO,!3,//O,!,COOH,@-4,\`1,COOH) % Oxalosuccinate
-MCat(0.66,0.05)(<30,HOCO,!3,//O,!,COOH) % alfa-Ketoglutarate
-MCat(0.33,0.05)(<30,HOCO,!3,//O,!,"{S-CoA}") % Succinyl-CoA
-MCat(0, 0.05)(<30,HOCO,!3,COOH) % Succinate
-MCat(0, 0.55)(<30,HOCO,!,!~dr,!,COOH) % Fumarate
-MCat(0, 1)(<30,HOCO,!3,COOH,3:/OH) % L-Malate
-%--------------------------------------------------------------------------------
-ext(
-defaultfont:="uhvr8r";
-defaultscale:=0.75;
-ext_setup;
-def sel_dir(expr rot)=
- save tx; nA:=rot; if nA>=360: nA:=nA-360; fi
- if (nA<30)or(nA>330): def tx=top enddef; elseif (nA>=30)and(nA<=150): def tx=lft enddef;
- elseif (nA>150)and(nA<210): def tx=bot enddef; elseif (nA>=210)and(nA<=330): def tx=rt enddef; fi
-enddef;
-def reaction_arrow(expr a)(expr r)(expr p)(expr sa,la)(expr sb,lb)(expr sc,lc)(expr sd,ld)=
- drawarrow ((0,0)..(a,0)) rotated r shifted p;
- if sa<>"": draw ((0.5a,0){dir 180}..{dir 90}(0,.5a*la)) rotated r shifted p;
- sel_dir(r); label.tx(sa,p+((0,0.5a*la) rotated r)); fi
- if sb<>"": draw ((0.5a,0){dir 0}..{dir 90}(a,.5a*lb)) rotated r shifted p;
- sel_dir(r); label.tx(sb,p+((a,0.5a*lb) rotated r)); fi
- if sc<>"": draw ((0.5a,0){dir 180}..{dir -90}(0,-.5a*lc)) rotated r shifted p;
- sel_dir(r+180); label.tx(sc,p+((0,-0.5a*lc) rotated r)); fi
- if sd<>"": draw ((0.5a,0){dir 0}..{dir -90}(a,-.5a*ld)) rotated r shifted p;
- sel_dir(r+180); label.tx(sd,p+((a,-0.5a*ld) rotated r)); fi
-enddef;
-def r_arrow(expr a)(expr r)(expr p)(expr sc,lc)(expr sd,ld)=
- reaction_arrow(a)(r)(p)("",0)("",0)(sc,lc)(sd,ld)
-enddef;
-%------------------------------------------------------------------------
-save dx; pair dx; dx:=(12mm,0);
-label.bot("Oxaloacetate",p1+dx); label.bot("Citrate",p2+dx);
-label.bot("cis-Aconitate",p3+dx); label.bot("Isocitrate",p4+dx);
-label.bot("Oxalosuccinate",p5+dx); label.bot("alfa-Ketoglutarate",p6+dx);
-label.bot("Succinyl-CoA",p7+dx); label.bot("Succinate",p8+dx);
-label.bot("Fumarate",p9+dx); label.bot("L-Malate",p10+dx);
-sw_label_emu:=1;
-ext_setup;
-r_arrow(10mm)( 0)(p1+ ( 1.1w1, 0.3h1))("Acetyl-CoA",1.5)(" CoA-SH",1);
-r_arrow(10mm)( 0)(p2+ ( 1.1w2, 0.4h2))("",0)("H2O",1);
-r_arrow( 8mm)(270)(p3+ ( 0.5w3,-0.4h3))("H2O",1)("",0);
-r_arrow( 8mm)(270)(p4+ ( 0.5w4,-0.4h4))("NAD+",1)("NADH2+",1);
-r_arrow(10mm)(180)(p5+ (-0.1w5, 0.4h5))("",0)("CO2",1);
-r_arrow(10mm)(180)(p6+ (-0.1w6, 0.5h6))("NAD+,CoA-SH",1.7)("NADH2+,CO2",1);
-r_arrow(10mm)(180)(p7+ (-0.1w7, 0.5h7))("GDP,Pi",1.7)("GTP,CoA-SH",1);
-r_arrow( 8mm)( 90)(p8+ ( 0.4w8, 1.2h8))("FAD",1)("FADH2",1);
-r_arrow( 8mm)( 90)(p9+ ( 0.4w9, 1.2h9))("H2O",1)("",0);
-r_arrow(10mm)( 0)(p10+( 1.1w10,0.3h10))("NAD+",1)("NADH2+",1.5);
-defaultscale:=1.5;
-label("TCA-cycle",(0.5w,0.5h));
-)
-endfigm
-\end{mplibcode}
-%------------------------------------------------------------------------
-\begin{verbatim}
-beginfigmy"EN:TCA cycle")
-fsize:=(160mm,75mm);
-max_blength:=5mm;
-COOH:='(//O,!,OH);
-HOCO:='(OH,!,//O,);
-MCat(0.33, 1)(<30,HOCO,!,//O,!2,COOH) % Oxaloacetate
-MCat(0.66, 1)(<30,HOCO,!4,COOH,@-4`1,\,COOH,4:/OH^-165) % Citrate
-MCat(1, 1)(<30,HOCO,!2,!~dr,!,COOH,@-4`1,\,COOH) % cis-Aconitate
-MCat(1, 0.58)(<30,HOCO,!4,COOH,@-4,\`1,COOH,5:/OH) % Isocitrate
-MCat(1, 0.05)(<30,HOCO,!3,//O,!,COOH,@-4,\`1,COOH) % Oxalosuccinate
-MCat(0.66,0.05)(<30,HOCO,!3,//O,!,COOH) % alfa-Ketoglutarate
-MCat(0.33,0.05)(<30,HOCO,!3,//O,!,"{S-CoA}") % Succinyl-CoA
-MCat(0, 0.05)(<30,HOCO,!3,COOH) % Succinate
-MCat(0, 0.55)(<30,HOCO,!,!~dr,!,COOH) % Fumarate
-MCat(0, 1)(<30,HOCO,!3,COOH,3:/OH) % L-Malate
-ext(
-defaultfont:="uhvr8r";
-defaultscale:=0.75;
-ext_setup;
-save dx; pair dx; dx:=(12mm,0);
-label.bot("Oxaloacetate",p1+dx); label.bot("Citrate",p2+dx);
-label.bot("cis-Aconitate",p3+dx); label.bot("Isocitrate",p4+dx);
-label.bot("Oxalosuccinate",p5+dx); label.bot("alfa-Ketoglutarate",p6+dx);
-label.bot("Succinyl-CoA",p7+dx); label.bot("Succinate",p8+dx);
-label.bot("Fumarate",p9+dx); label.bot("L-Malate",p10+dx);
-sw_label_emu:=1;
-ext_setup;
-r_arrow(10mm)( 0)(p1+ ( 1.1w1, 0.3h1))("Acetyl-CoA",1.5)(" CoA-SH",1);
-r_arrow(10mm)( 0)(p2+ ( 1.1w2, 0.4h2))("",0)("H2O",1);
-r_arrow( 8mm)(270)(p3+ ( 0.5w3,-0.4h3))("H2O",1)("",0);
-r_arrow( 8mm)(270)(p4+ ( 0.5w4,-0.4h4))("NAD+",1)("NADH2+",1);
-r_arrow(10mm)(180)(p5+ (-0.1w5, 0.4h5))("",0)("CO_2_",1);
-r_arrow(10mm)(180)(p6+ (-0.1w6, 0.5h6))("NAD+,CoA-SH",1.7)("NADH2+,CO2",1);
-r_arrow(10mm)(180)(p7+ (-0.1w7, 0.5h7))("GDP,Pi",1.7)("GTP,CoA-SH",1);
-r_arrow( 8mm)( 90)(p8+ ( 0.4w8, 1.2h8))("FAD",1)("FADH2",1);
-r_arrow( 8mm)( 90)(p9+ ( 0.4w9, 1.2h9))("H2O",1)("",0);
-r_arrow(10mm)( 0)(p10+( 1.1w10,0.3h10))("NAD+",1)("NADH2+",1.5);
-defaultscale:=1.5;
-label("TCA-cycle",(0.5w,0.5h));
-)
-endfigm
-\end{verbatim}
-%----------------------------------------------------------------------------
-\end{document}