mcf2graph (11jun16)

git-svn-id: svn://tug.org/texlive/trunk@41368 c570f23f-e606-0410-a88d-b1316a301751

1 files changed, 71 insertions, 66 deletions

diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index eee609e165e..bea273959d1 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
@@ -1,5 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%  Molecular Coding Format manual          by  Akira Yamaji 2016.05.05
+%  Molecular Coding Format manual          by  Akira Yamaji 2016.06.11
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \documentclass[a4paper]{article}
 \usepackage[dvipdfmx]{graphicx}
@@ -29,10 +29,11 @@
  \rlap{\makebox(72,4)[t]{\makebox(68,48){\@strufont\char\fontnum}}}%
  \advance\fontnum\@ne\relax}%
 \def\MCFstructure{%
- \makebox(72,4)[t]{\frame{\makebox(68,48){\@strufont\char\fontnum}}}%
+ \makebox(72,4)[t]{\frame{\
+ \makebox(68,48){\@strufont\char\fontnum}}}%
  \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax}%
 %--------------------------------------------------------------------
-\def\@F{F}\def\@C{C}\def\@EN{EN}\def\@NO{NO}\def\@MW{MW}\def\@cFM{cFM}%
+\def\@F{F}\def\@C{C}\def\@EN{EN}\def\@NO{NO}\def\@cMW{cMW}\def\@cFM{cFM}%
 \def\@fst#1:#2;{#1}\def\@sec#1:#2;{#2}%
 \def\mol@sel#1{%
 \if#1\empty\relax\else%
@@ -42,15 +43,15 @@
   \ifx\@tag\@C\edef\MOLchar{\@var}\fi%
   \ifx\@tag\@EN\edef\MOLnameE{\@var}\fi%
   \ifx\@tag\@NO\edef\MOLnum{\@var}\fi
-  \ifx\@tag\@MW\edef\MOLmw{\@var}\fi
+  \ifx\@tag\@cMW\edef\CALmw{\@var}\fi
   \ifx\@tag\@cFM\edef\CALfm{\@var}\fi
 \fi}%
 \def\put@char{%
-  \begin{picture}(120,40)%
-     \put(10,35){\bf [\MOLnum] \MOLnameE}%
-     \put(16,30){\tt MW:\MOLmw}%
-     \put(16,25){\tt FM:\CALfm}%
-     \put(0,0){\font\@strufont=\MOLfile\relax%
+  \begin{picture}(120,42)%
+     \put(0,35){\bf [\MOLnum] \MOLnameE}%
+     \put(6,30){\tt MW:\CALmw}%
+     \put(6,25){\tt FM:\CALfm}%
+     \put(40,0){\font\@strufont=\MOLfile\relax%
                \hbox{\@strufont\char\MOLchar}}%
   \end{picture}%
 }
@@ -88,55 +89,47 @@ font_wd#:=60mm#;      % font width                      >
 font_ht#:=40mm#;      % font height                     >
 var3:="cal_MW"; tag3:="cMW";                            > AUX file table
 var4:="cal_FM"; tag4:="cFM";                            >
-%%%% var5:="len_x";   tag5:="Lx";                       >
-%%%% var6:="len_y";   tag6:="Ly";                       >
-%%%% sw_auxfix:=1;    % fixed aux file                  > fixed AUX file
-%%%% auxtag_out;      % tag list output                 >
 outputformat:="png"; hppp:=vppp:=0.1;                   > PNG output
-%%%% outputformat:="svg";                               > SVG output
 outputtemplate:="%j-%3c.png";                           >
 %-------------------------------------------------------------------------
-beginfont("NO:1","EN:Chlorophyll a","MW:893.49")  % begin font(information)
-  sw_font_frame:=1;     % font frame on                 >
-  font_wd#:=120mm#;     % font width set                >  Local setting
-  font_ht#:=80mm#;      % font height set               >
-  %-----------------------------------------------------------------------
-  MCf(                                            % begin MCF
-    <54,{,``1,?5,$(2,5)d,4:N,3\,54~dl,            %
-    |,?5,$(2,4)d,5:N,                             %
-   -2\,54~dl,|,?5,2=d,5:N,-2\~dl,54,              %
-   |,?5,5=d,5:N,-2\~dl,&#5,                       %
-   -1*,24,/*COOMe^15,72,//O,&#1,},                %
-   4\`1.48,Mg,&17,-1*,&11~vb,-1*,&23~vb,          %
-   @(2,9,15,20~zf)/Me,8:/Et,14\,!~dr,             %
-   21*,-6~wf,!2,//O,!,O,!2,!~dl,                  %
-   |,!13,@(1,5,9,13)/Me,                          %
-  )                                               % end MCF
-endfont                                           % end font
+beginfont("NO:1","EN:Ampicillin")                 > begin font(information)
+  MCf(<45,?4,2:N,2=?5,-1:S,                             > begin MCF (1)
+     @(3^45,4^-45)/*H,1://O^15,5:/*COOH^-18,            >
+     @(6^35,6^-35)/Me,                                  >
+     4\^75,NH,!,//O,!,NH,!,Ph)                          > end MCF 
+endfont                                                 > end font
+%------------------------------------------------------------------------
+beginfont("NO:2","EN:Cholesterol")                > begin font(information)
+  MCf(<30,?6,$(-4,-2)?6,-4=?5,7=dl,                     > begin MCF (2)
+      1:*/OH,@(4,12)*/Me^60,9:*/H^60,                   >
+      10:/*H^180,@(11,-1)/*H^-60,                       >
+      -1\^17,/*Me,!4,/Me,!)                             > end MCF
+endfont                                                 > end font
 %------------------------------------------------------------------------
 bye
 \end{verbatim}
 %----------------------------------------------------------------------------
-{\bf (Molecular structure diagram output)}\\
- \makebox(120,30){\@strufont\char0}\\
-%----------------------------------------------------------------------------
 \noindent%
 {\bf (Molecular information output)}\\
 'filename'-info.aux : for use in \TeX, it takes over filename,
 char number, molecular information,etc.
 \begin{verbatim}
 (sw_auxfix=0)
-F:mcf_man_soc;C:0;cMW:893.48962;cFM:C55H72MgN4O5;NO:1;EN:Chlorophyll a;MW:893.49
+F:mcf_man_soc;C:85;cMW:335.37805;cFM:C15H17N3O4S;EN:Ampicillin
+F:mcf_man_soc;C:86;cMW:386.6532;cFM:C27H46O;EN:Cholesterol
+  .....................................................
 
 (sw_auxfix=1)
-F;C;cMW;cFM;NO;EN;MW
-mcf_man_soc;0;893.48962;C55H72MgN4O5;1;Chlorophyll a;893.49
-\end{verbatim}
-( tag : variable )\\
-F:filename C:char number,cMW:molecular weight calculated,
-cFM:molecular formula calculated\\
-NO:serial number, EN:english name,
-MW:molecular weight from literature data\vspace{5mm}\\
+F;C;cMW;cFM;EN
+mcf_man_soc;85;335.37805;C15H17N3O4S;Ampicillin
+mcf_man_soc;86;386.6532;C27H46O;Cholesterol
+  ......................................
+
+( tag : variable )
+F : filename   C : char number   NO : serial number   EN : english name
+cMW : molecular weight calculated   cFM : molecular formula calculated
+MW  : molecular weight from literature data
+\end{verbatim}
 %----------------------------------------------------------------------------
 {\bf (LaTeX file example)}
 %############################################################################
@@ -157,15 +150,15 @@ MW:molecular weight from literature data\vspace{5mm}\\
   \ifx\@tag\@C\edef\MOLchar{\@var}\fi%
   \ifx\@tag\@EN\edef\MOLnameE{\@var}\fi%
   \ifx\@tag\@NO\edef\MOLnum{\@var}\fi
-  \ifx\@tag\@MW\edef\MOLmw{\@var}\fi
+  \ifx\@tag\@MW\edef\CALmw{\@var}\fi
   \ifx\@tag\@FMc\edef\CALfm{\@var}\fi
 \fi}%
 \def\put@char{%
   \begin{picture}(120,45)%
      \put(10,35){\bf [\MOLnum] \MOLnameE}%
-     \put(16,30){\sf MW:\MOLmw}%
+     \put(16,30){\sf MW:\CALmw}%
      \put(16,25){\sf FM:\CALfm}%
-     \put(0,0){\font\@strufont=\MOLfile\relax%
+     \put(20,0){\font\@strufont=\MOLfile\relax%
                \hbox{\@strufont\char\MOLchar}}%
   \end{picture}}%
 \def\INFO#1{\@for\@temp:=#1\do{\mol@sel\@temp}\put@char}%
@@ -173,14 +166,15 @@ MW:molecular weight from literature data\vspace{5mm}\\
 %--------------------------------------------------------------------
 \begin{document}
 \unitlength=1mm%
-\INFO{F:mcf_man_soc ,C:0 ,cMW:893.48962 ,cFM:C55H72MgN4O5%
-      ,NO:1 ,EN:Chlorophyll a ,MW:893.49}%
+\INFO{F:mcf_man_soc,C:85,NO:1,cMW:335.37805,cFM:C15H17N3O4S,EN:Ampicillin}\\%
+\INFO{F:mcf_man_soc,C:86,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
 \end{document}
 %--------------------------------------------------------------------
-\end{verbatim}%
+\end{verbatim}\vspace{5mm}%
 %############################################################################
-\INFO{F:mcf_man_soc ,C:0 ,cMW:893.48962 ,cFM:C55H72MgN4O5%
-   ,NO:1 ,EN:Chlorophyll a ,MW:893.49}%
+{\bf (Molecular structure output)}\\
+\INFO{F:mcf_man_soc,C:85,NO:1,cMW:335.37805,cFM:C15H17N3O4S,EN:Ampicillin}\\%
+\INFO{F:mcf_man_soc,C:86,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
 \newpage
 %----------------------------------------------------------------------------
 \noindent
@@ -188,10 +182,10 @@ MW:molecular weight from literature data\vspace{5mm}\\
 \begin{minipage}[t][\htman]{90mm}
 \MCFtitle{Chain(1)}
 \begin{verbatim}
-plus (+): anticlockwize
-minus(-): clockwize
+real number plus (+): anticlockwize 
+real number minus(-): clockwize
 
-  <30,-60,60,-90,120,-90,60
+<30,-60,60,-90,120,-90,60
 
 \end{verbatim}
 \end{minipage}
@@ -231,9 +225,9 @@ minus(-): clockwize
 \begin{minipage}[t][\htman]{90mm}
 \MCFtitle{Connect atom}
 \begin{verbatim}
-&5 : Connect to A5
+&n : Connect to An
 
-  <30,!6,3\,!.&5
+  <30,!6,3\,!,&5
 
 \end{verbatim}
 \end{minipage}
@@ -273,7 +267,7 @@ a~type : ~~type,a
 dm:double middle,
 dl:double left side, dr:double right side,
 wf:wedge forward, wb:wedge backward,
-zf:wedge dotted, zb:wedge dotted backward
+zf:wedge dotted,  zb:wedge dotted backward
 
   <30,!~dm,!~dl,!~dr,!~wf,!~wb,!~zf,!~zb
 \end{verbatim}
@@ -343,7 +337,10 @@ $(2,4)dr : 2=dr,4=dr
 \begin{verbatim}
 ?n`length : change ring length
 
-  <30,?6,3\,?6`1.2,11=?6
+  ?6,4\,?6`1.2,5=?6,11=?6
+
+** fused ring size depend on 
+   attached bond length
 \end{verbatim}
 \end{minipage}
 \MCFstructure
@@ -354,7 +351,7 @@ $(2,4)dr : 2=dr,4=dr
 \begin{verbatim}
 Insert hetero atom
 
-  <30,!2,O,!2
+  <30,!2,O,!2,N,!2
 \end{verbatim}
 \end{minipage}
 \MCFstructure
@@ -511,7 +508,8 @@ MCf(<30,!8,2\,!,4*\,!,6\*,!,8\\,!)
 4\`1.5 : 4*,0`1.5
 6\^15  : 6*,0^15
 
-MCf(<-30,!6,2\~dr,!,4\`1.5,!,6\^15,-60)
+MCf(<-30,
+    !6,2\~dr,!,4\`1.5,!,6\^15,-60)
 
 \end{verbatim}
 \end{minipage}
@@ -524,7 +522,8 @@ MCf(<-30,!6,2\~dr,!,4\`1.5,!,6\^15,-60)
 MCf(<30,
 !,/Me,!,/Et,!3,/Pr,!,/iPr,!3,/tBu,!,/Ph^-30,!)
 
-** Me:methyl Et:ethyl Pr:propyl iPr:isopropyl
+** Me:methyl Et:ethyl
+   Pr:propyl iPr:isopropyl
    tBu:tertial buthyl Ph:phenyl
 \end{verbatim}
 \end{minipage}
@@ -549,8 +548,10 @@ MCf(<30,!,//O,!,/*H,!,*/H,!,/?3,!,**?3,!)
 \begin{minipage}[t][\htman]{90mm}
 \MCFtitle{Insert substituent(3)}
 \begin{verbatim}
-~,^,`,> : change type,angle,length,enviroment
-          of substituent
+~ : change type
+^ : change angle
+` : change length
+> : change enviroment
 
 MCf(<30,``1,
     !,/Me~zf`2^30,!,/Me~zf`2^30,
@@ -1040,10 +1041,14 @@ MCd(1,1)(0.9,0.5)(<30,Ph,2:/OH,5:/NH2)
 \begin{minipage}[t][\htman]{90mm}
 \MCFtitle{Switch font frame}
 \begin{verbatim}
-  sw_font_frame:=1;
-  MCf(<30,Ph,4:/Cl,3:/F)
+sw_font_frame=0 : no frame  **default
+sw_font_frame=1 : draw frame of font
+sw_font_frame=2 : draw frame inside margin
+sw_font_frame=3 : draw both
 
- ** default: sw_font_frame=0
+sw_font_frame:=3;
+margin_left_right:=5mm; margin_top_bottom:=2mm;
+MCf(<30,Ph,4:/Cl,3:/F)
 \end{verbatim}
 \end{minipage}
 \MCFstructure