%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % 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}