diff options
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 168 |
1 files changed, 114 insertions, 54 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index e41355ff48..6356d34094 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2021.03.21 +% Molecular Coding Format manual by Akira Yamaji 2021.04.04 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage[pdftex]{graphicx} @@ -12,8 +12,8 @@ %---------------------------------------------------------------------------- %%%%\pdfpkresolution=1200 %---------------------------------------------------------------------------- -%%%%\edef\fext{pk}% **** for proof print (fast) -\edef\fext{mps}% **** for final print (it takes long time) +\edef\fext{pk}% **** for proof print (fast) +%%%%\edef\fext{mps}% **** for final print (it takes long time) %---------------------------------------------------------------------------- %%%%\edef\fext{png}% %%%%\edef\fext{svg}% @@ -1374,12 +1374,10 @@ endfont \subsection{Luciferin} \index{check()}% \begin{verbatim} -beginfont("EN:Luciferin","MW:280.33", - %------------------------------------- - ": <30,Ph,3=?5,@8,\,?5,{9,16}=dl, ", - ": {9,14}:N,{7,11}:S,1:/OH,-2:*/COOH ") - %------------------------------------- - fsize:=(50mm,20mm); +(use data base file 'mcf_data_base') +beginfont("f:mcf_data_base", + "t:EN","v:Luciferin") + fsize:=(50mm,15mm); if check(mc)=0: MC(scantokens(mc)) fi endfont \end{verbatim} @@ -1469,33 +1467,31 @@ endfont %------------------------------------------------------------------------ \onecolumn \section{Example to use mcf2graph} -\subsection{Molecular definition file} +\subsection{Metafont/Metapost souce file} \index{mcf2graph.mf}% \index{sw\_aux\_out}% +\index{sw\_file\_open}% \index{tag}% \index{var}% \begin{verbatim} %------------------------------------------------------------------------- -input mcf2graph.mf; % input macro +input mcf2graph.mf; > input main macro %------------------------------------------------------------------------- -sw_aux_out:=1; % aux(information) file output on > Global setting +sw_aux_out:=1; % aux(information) file output on > global setting fsize:=(60mm,40mm); % (font width,font height) > -tag1:="F"; > AUX file table -tag2:="C"; > -tag3:="mw"; > -tag4:="fm"; > -%%%% sw_rep_out:=1; > Report output +tag1:="J"; > jobname +tag2:="C"; > char No +tag3:="mw"; % calculated molecular weight > +tag4:="fm"; % calculated molecular formula > +%%%% sw_rep_out:=1; > report output %%%% sw_mol_out:=1; > MOL file output outputformat:="png"; hppp:=vppp:=0.1; > PNG output outputtemplate:="%j-%3c.png"; > %------------------------------------------------------------------------- -beginfont("EN:Ampicillin","MW:349.405", > information - %---------------------------------------- > - ": <45,?4,-3=?5,2:N,7:S, ", > mc1 - ": 3^45:/*H,1://O^15,5:/*COOH^-18,6:??, ", > mc2 - ": @4,*\^15,NH,!,//O,!,/*NH2,!,Ph ") > mc3 - %---------------------------------------- > - if check(mc)=0: MC(scantokens(mc)) fi > mc=mc1&mc2&mc3 +beginfont("EN:Ampicillin","MW:349.405") > information + MC(<45,?4,-3=?5,2:N,7:S, > immediately compile + 3^45:/*H,1://O^15,5:/*COOH^-18,6:??, > + @4,*\^15,NH,!,//O,!,/*NH2,!,Ph) > endfont > end font %------------------------------------------------------------------------ beginfont("EN:Cholesterol","MW:386.65", >information @@ -1507,37 +1503,101 @@ beginfont("EN:Cholesterol","MW:386.65", >information %---------------------------------------- > if check(mc)=0: MC(scantokens(mc)) fi > mc=mc1 - mc4 endfont > end font -%------------------------------------------------------------------------ -beginfont("EN:Limonin", > information - %----------------------------------------- > - ": <30,?6,{-3,-4}=?6, ", > mc1 - ": -5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf, ", > mc2 - ": {13,15,17,20}:O,{3,12,21}://O, ", > mc3 - ": {4~wf^60,8~zf^60,18^35,18^-35}:/_, ", > mc4 - ": {1^60,5^180,16^60}:/*H, ", > mc5 - ": @14,\*,|,?5,{1,4}=dl,3:O) ") > mc6 - %----------------------------------------- > - if check(mc)=0: MC(scantokens(mc)) fi > mc=mc1 - mc6 -endfont > end font -%------------------------------------------------------------------------ -beginfont("EN:beta-carotene", > information - %------------------------------------------ > - ": <30,?6,3=dl,{3,5^35,5^-35}:/_, ", > mc1 - ": @4,\,|,!18,{1,3,5,7,9,11,13,15,17}=dr, ", > mc2 - ": {3,7,12,16}:/_, ", > mc3 - ": |,?6,6=dl,2:??,6:/_) ") > mc4 - %------------------------------------------ > - if check(mc)=0: MC(scantokens(mc)) fi > mc=mc1 - mc4 -endfont > end font -%------------------------------------------------------------------------ +%------------------------------------------------------------------------------ +beginfont("f:mcf_data_base","t:EN","v:Adenine") > from mcf_data_base.mcf + if check(mc)=0: MC(scantokens(mc)) fi > select EN="Adenine" +endfont > +%------------------------------------------------------------------------------ +beginfont("f:mcf_data_base","t:EN","v:Guanine") > from mcf_data_base.mcf + if check(mc)=0: MC(scantokens(mc)) fi > select EN="Guanine" +endfont +%------------------------------------------------------------------------------ +beginfont("f:mcf_data_base","t:EN","v:Cytosine") > from mcf_data_base.mcf + if check(mc)=0: MC(scantokens(mc)) fi > select EN="Cytosine" +endfont > +%------------------------------------------------------------------------------ +sw_file_open:=1; > keep file open **default sw_file_open=0 +%------------------------------------------------------------------------------ +beginfont("f:mcf_data_base","t:n","v:4") > from mcf_data_base.mcf + if check(mc)=0: MC(scantokens(mc)) fi > v:4 select No.4 +endfont > +%------------------------------------------------------------------------------ +for i=5 upto 155: > from mcf_data_base.mcf + beginfont("f:mcf_data_base","t:n","v:0") > v:0 no selection + if check(mc)=0: MC(scantokens(mc)) fi > No.5 - No.155 + endfont > +endfor > +%------------------------------------------------------------------------------ bye \end{verbatim} %------------------------------------------------------------------------ \noindent% \newpage +\subsection{Molecular data base file} +\begin{verbatim} +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% molecular data base file mcf_data_base.mcf by Akira Yamaji 2021.04.04 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% tag1:var1;tag2:var2;tag3:var3 .... +% first character of line '%' comment out +% first character of line '+' begin molecular definition +% first character of line '-' end molecular definition +%--------------------------------------------------------------------------- +EN:Cytosine;MW:111.10 ++ +<30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2 +---------------------------------------------------------------------------- +EN:Thymine;MW:126.11 ++ +<30,?6,3=dl,{2,6}:NH,{1,5}://O,4:/_ +---------------------------------------------------------------------------- +EN:Uracil;MW:112.09 ++ +<30,?6,6=dl,{3,5}://O,{2,4}:NH +---------------------------------------------------------------------------- +EN:Geraniol;MW:154.25 ++ +<30,!8,OH,{2,6}=dr,{2,6}:/_ +---------------------------------------------------------------------------- +EN:Limonene;MW:136.24 ++ +<30,?6,2=dl,2:/_,@5,*\,/_,!! +---------------------------------------------------------------------------- +EN:l-Menthol;MW:156.27 ++ +<30,?6,2:/*?!,5:*/_,3:*/OH +---------------------------------------------------------------------------- +EN:Vanillin;MW:152.15 ++ +<30,Ph,2:/OH,3:/O!,5:/CHO ++---------------------------------------------------------------------------- +EN:Allicin;MW:162.28 ++ +<-30,!!,!2,SO,!,S,!2,!! +---------------------------------------------------------------------------- +EN:Stearic acid;MW:284.48; ++ +<30,!17,COOH +---------------------------------------------------------------------------- +EN:Linoleic acid;MW:280.45 ++ +<30,!5,-30,-30,!,-30,-30,!7,COOH,{6,9}=dr +---------------------------------------------------------------------------- +EN:Sphingosine;MW:299.50 ++ +<30,!18,OH,14=dr,-3:*/OH,-2:/*NH2 +---------------------------------------------------------------------------- +EN:Tocopherol;MW:430.717 ++ +<30,Ph,3=?6,7:O,{1,2,5}:/_,8:/*_^60,6:/OH,@8,\,|,!12,{4,8}:/*_,12:/_ +---------------------------------------------------------------------------- +\end{verbatim} +%------------------------------------------------------------------------ +\noindent% +\newpage \subsection{Information auxfile output} \paragraph{(Insert option parameter setting)} -\index{F}% +\index{J}% \index{C}% \index{NO}% \index{MW}% @@ -1570,7 +1630,7 @@ beginfont("EN:beta-Carotene") .... endfont \end{verbatim} \paragraph{(Setting)} \begin{verbatim} -tag1:="F"; tag2:="C"; tag3:="mw"; tag4:="fm"; tag5:="EN"; +tag1:="J"; tag2:="C"; tag3:="mw"; tag4:="fm"; tag5:="EN"; \end{verbatim} \paragraph{(Output)} \index{aux\_delimiter}% @@ -1596,7 +1656,7 @@ F:mcf_exa_soc/C:4/mw:536.8722/fm:C40H56/EN:beta-Carotene \end{verbatim} \paragraph{(Tag)} \begin{verbatim} -F : filename +J : jobname C : char number NO : serial number EN : english name @@ -1820,15 +1880,15 @@ endfont; %-------------------------------------------------------------------- \begin{document} \unitlength=1mm% -\INFO{F:mcf_man_soc,C:141,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:142,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}% +\INFO{J:mcf_man_soc,C:141,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}% +\INFO{J:mcf_man_soc,C:142,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}% \end{document} %-------------------------------------------------------------------- \end{verbatim}% %############################################################################ %------------------------------------------------------------------------ -\INFO{F:mcf_man_soc,C:141,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:142,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}% +\INFO{J:mcf_man_soc,C:141,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}% +\INFO{J:mcf_man_soc,C:142,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}% %------------------------------------------------------------------------ \texttt{\printindex} %------------------------------------------------------------------------ |