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-rw-r--r--graphics/mcf2graph/mcf_manual.tex183
1 files changed, 120 insertions, 63 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex
index 6356d34094..f96a5357cf 100644
--- a/graphics/mcf2graph/mcf_manual.tex
+++ b/graphics/mcf2graph/mcf_manual.tex
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2021.04.04
+% Molecular Coding Format manual by Akira Yamaji 2021.04.18
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage[pdftex]{graphicx}
@@ -48,7 +48,7 @@
\edef\file@name{\MCFjobname-\z@num\fnum.\fext}%
\setbox\fbox=\hbox{\@strufont\char\fnum}%
\includegraphics[width=\wd\fbox,height=\ht\fbox]{\file@name}%
-%%%%%%%\includegraphics{\file@name}%
+%%%%%%\includegraphics{\file@name}%
\fi%
\global\advance\fnum\@ne\relax%
}%
@@ -1469,7 +1469,7 @@ endfont
\section{Example to use mcf2graph}
\subsection{Metafont/Metapost souce file}
\index{mcf2graph.mf}%
-\index{sw\_aux\_out}%
+\index{sw\_output}%
\index{sw\_file\_open}%
\index{tag}%
\index{var}%
@@ -1477,14 +1477,14 @@ endfont
%-------------------------------------------------------------------------
input mcf2graph.mf; > input main macro
%-------------------------------------------------------------------------
-sw_aux_out:=1; % aux(information) file output on > global setting
+sw_output:=Info1; % aux(information) file output on > global setting
+%%%% sw_output:=Report; > report output
+%%%% sw_output:=MOL2k; > MOL file output
fsize:=(60mm,40mm); % (font width,font height) >
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"; >
%-------------------------------------------------------------------------
@@ -1492,7 +1492,7 @@ 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
+endfont >
%------------------------------------------------------------------------
beginfont("EN:Cholesterol","MW:386.65", >information
%---------------------------------------- >
@@ -1502,7 +1502,7 @@ beginfont("EN:Cholesterol","MW:386.65", >information
": @-1,18,/*_,-60,!3,?! ") > mc4
%---------------------------------------- >
if check(mc)=0: MC(scantokens(mc)) fi > mc=mc1 - mc4
-endfont > end font
+endfont >
%------------------------------------------------------------------------------
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"
@@ -1516,16 +1516,14 @@ 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
+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 >
+endfont > 'f+' keep file open
%------------------------------------------------------------------------------
for i=5 upto 155: > from mcf_data_base.mcf
- beginfont("f:mcf_data_base","t:n","v:0") > v:0 no selection
+ beginfont("f+:mcf_data_base","v:*") > v:* no selection
if check(mc)=0: MC(scantokens(mc)) fi > No.5 - No.155
- endfont >
+ endfont > 'f+' keep file open
endfor >
%------------------------------------------------------------------------------
bye
@@ -1536,66 +1534,65 @@ bye
\subsection{Molecular data base file}
\begin{verbatim}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% molecular data base file mcf_data_base.mcf by Akira Yamaji 2021.04.04
+% molecular data base file mcf_data_base.mcf by Akira Yamaji 2021.04.18
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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
+% first character of line '+' begin MCF , end MCF
+%------------------------------------------------------------------------------
+Cat:biological;EN:Adenine;MW:135.13
++
+<30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH
++------------------------------------------------------------------------------
+Cat:biological;EN:Guanine;MW:151.13
++
+<30,?6,3=?5,{1,3,9}=dl,{2,9}:N,{6,7}:NH,5://O,1:/NH2
++------------------------------------------------------------------------------
+Cat:biological;EN:Cytosine;MW:111.10
+
<30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2
-----------------------------------------------------------------------------
-EN:Thymine;MW:126.11
++------------------------------------------------------------------------------
+Cat:biological;EN:Thymine;MW:126.11
+
<30,?6,3=dl,{2,6}:NH,{1,5}://O,4:/_
-----------------------------------------------------------------------------
-EN:Uracil;MW:112.09
++------------------------------------------------------------------------------
+Cat:biological;EN:Uracil;MW:112.09
+
<30,?6,6=dl,{3,5}://O,{2,4}:NH
-----------------------------------------------------------------------------
-EN:Geraniol;MW:154.25
++------------------------------------------------------------------------------
+Cat:biological;EN:Geraniol;MW:154.25
+
<30,!8,OH,{2,6}=dr,{2,6}:/_
-----------------------------------------------------------------------------
-EN:Limonene;MW:136.24
++------------------------------------------------------------------------------
+Cat:biological;EN:Limonene;MW:136.24
+
<30,?6,2=dl,2:/_,@5,*\,/_,!!
-----------------------------------------------------------------------------
-EN:l-Menthol;MW:156.27
++------------------------------------------------------------------------------
+Cat:biological;EN:l-Menthol;MW:156.27
+
<30,?6,2:/*?!,5:*/_,3:*/OH
-----------------------------------------------------------------------------
-EN:Vanillin;MW:152.15
++------------------------------------------------------------------------------
+Cat:biological;EN:Vanillin;MW:152.15
+
<30,Ph,2:/OH,3:/O!,5:/CHO
-+----------------------------------------------------------------------------
-EN:Allicin;MW:162.28
++------------------------------------------------------------------------------
+Cat:biological;EN:Allicin;MW:162.28
+
<-30,!!,!2,SO,!,S,!2,!!
-----------------------------------------------------------------------------
-EN:Stearic acid;MW:284.48;
++------------------------------------------------------------------------------
+Cat:biological;EN:Stearic acid;MW:284.48
+
<30,!17,COOH
-----------------------------------------------------------------------------
-EN:Linoleic acid;MW:280.45
++------------------------------------------------------------------------------
+Cat:biological;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}
+\subsection{Information aux file output}
\paragraph{(Insert option parameter setting)}
\index{J}%
\index{C}%
@@ -1612,14 +1609,13 @@ EN:Tocopherol;MW:430.717
\index{w}%
\index{h}%
\begin{verbatim}
- sw_aux_out=1 : tag1:var1;tag2:var2
- sw_aux_out=2 : tag1;tag2 var1;var2
- ** default : sw_aux_out=0
+ sw_output:=Info1; % tag1:var1;tag2:var2
+ sw_output:=Info2; % tag1;tag2 var1;var2
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
- >mpost -s ahlength=1 FILENAME (sw_aux_out=1)
- >mpost -s ahlength=2 FILENAME (sw_aux_out=2)
+ >mpost -s ahlength=1 FILENAME (sw_output=Info1)
+ >mpost -s ahlength=2 FILENAME (sw_output=Info2)
\end{verbatim}
\paragraph{(Sourse)}
\begin{verbatim}
@@ -1635,13 +1631,13 @@ tag1:="J"; tag2:="C"; tag3:="mw"; tag4:="fm"; tag5:="EN";
\paragraph{(Output)}
\index{aux\_delimiter}%
\begin{verbatim}
-(sw_aux_out=1)
+(sw_output=Info1)
F:mcf_man_soc;C:1;mw:349.40462;fm:C16H19N3O4S;EN:Ampicillin
F:mcf_man_soc;C:2;mw:386.6532;fm:C27H46O;EN:Cholesterol
F:mcf_exa_soc;C:3;mw:470.5113;fm:C26H30O8;EN:Limonin
F:mcf_exa_soc;C:4;mw:536.8722;fm:C40H56;EN:beta-Carotene
-(sw_aux_out=2)
+(sw_output=Info2)
F;C;mw;fm
mcf_man_soc;1;349.40462;C16H19N3O4S;Ampicillin
mcf_man_soc;2;386.6532;C27H46O;Cholesterol
@@ -1672,14 +1668,76 @@ w : font width
h : font height
\end{verbatim}
%------------------------------------------------------------------------
+\noindent%
+\newpage
+\subsection{Metafont aux file output}
+\paragraph{(Insert option parameter setting)}
+\begin{verbatim}
+ sw_output:=Mfont;
+\end{verbatim}
+\paragraph{(Command line)}
+\begin{verbatim}
+ >mpost -s ahlength=7 FILENAME (sw_output=Mfont)
+\end{verbatim}
+\paragraph{(Output)}
+\begin{verbatim}
+beginfont("Cat:biological","EN:Adenine","MW:135.13",
+": <30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Guanine","MW:151.13",
+": <30,?6,3=?5,{1,3,9}=dl,{2,9}:N,{6,7}:NH,5://O,1:/NH2")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Cytosine","MW:111.10",
+": <30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Thymine","MW:126.11",
+": <30,?6,3=dl,{2,6}:NH,{1,5}://O,4:/_")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Adenine","MW:135.13",
+": <30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Guanine","MW:151.13",
+": <30,?6,3=?5,{1,3,9}=dl,{2,9}:N,{6,7}:NH,5://O,1:/NH2")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Cytosine","MW:111.10",
+": <30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Thymine","MW:126.11",
+": <30,?6,3=dl,{2,6}:NH,{1,5}://O,4:/_")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Uracil","MW:112.09",
+": <30,?6,6=dl,{3,5}://O,{2,4}:NH")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Geraniol","MW:154.25",
+": <30,!8,OH,{2,6}=dr,{2,6}:/_")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:Limonene","MW:136.24",
+": <30,?6,2=dl,2:/_,@5,*\,/_,!!")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+beginfont("Cat:biological","EN:l-Menthol","MW:156.27",
+": <30,?6,2:/*?!,5:*/_,3:*/OH")
+if check(mc)=0: MC(scantokens(mc)) fi
+endfont
+\end{verbatim}
+%------------------------------------------------------------------------
\newpage
\noindent%
\subsection{Report output}
\paragraph{(Insert option parameter setting)}
-\index{sw\_rep\_out}%
+\index{sw\_output}%
\begin{verbatim}
- sw_rep_out:=1;
- ** default : sw_rep_out=0
+ sw_output:=Report;
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
@@ -1739,11 +1797,10 @@ h : font height
\noindent%
\subsection{MOL file output}
\paragraph{(Insert option parameter setting)}
-\index{sw\_mol\_out}%
+\index{sw\_output}%
\begin{verbatim}
- sw_mol_out:=1; % MOL(V2000)
- sw_mol_out:=2; % MOL(V3000)
- ** default : sw_mol_out=0
+ sw_output:=MOL2k; % MOL(V2000)
+ sw_output:=MOL3k; % MOL(V3000)
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
@@ -1802,7 +1859,7 @@ M END
\mplibnumbersystem{double}%
\everymplib{%
if unknown Ph1: input mcf2graph.mf; fi
- sw_calc:=1; sw_fframe:=4; max_blength:=4.5mm;
+ sw_output:=None; sw_fframe:=4; max_blength:=4.5mm;
defaultfont:="uhvr8r"; defaultsize:=8bp; defaultscale:=1;
}%
\begin{document}