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-rw-r--r--graphics/mcf2graph/mcf_manual.tex168
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}
%------------------------------------------------------------------------