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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex210
1 files changed, 168 insertions, 42 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index 265c66c9d8a..cb9ea163a93 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 2016.10.10
+% Molecular Coding Format manual by Akira Yamaji 2016.10.13
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\usepackage{graphicx}
@@ -45,9 +45,9 @@
\ifx\@tag\@cFM\edef\CALfm{\@var}\fi
\fi}%
\def\put@char{%
- \begin{picture}(84,30)%
- \put(0,25){\bf [\MOLnum]\MOLnameE}%
- \put(5,20){\small\tt FM:\CALfm{ }MW:\CALmw}%
+ \begin{picture}(84,28)%
+ \put(0,23){\bf [\MOLnum]\MOLnameE}%
+ \put(5,18){\small\tt FM:\CALfm{ }MW:\CALmw}%
\put(5,0){\font\@strufont=\MOLfile\relax%
\hbox{\@strufont\char\MOLchar}}%
\end{picture}%
@@ -146,7 +146,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
<-30,!6,
2\~dr,!,
- 4\`1.5,!,
+ 4\`1.5,-90,
6\^15,-60
\end{verbatim}
\MCFstructure
@@ -208,15 +208,22 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsubsection{Dotted,wave,broad}
+\subsubsection{Dotted,wave}
\begin{verbatim}
Bn=bond type : change bond type at Bn
dt : dotted
wv : wave
+
+ <30,!3,1=dt,3=wv
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\subsubsection{Broad}
+\begin{verbatim}
bd : broad
bz : broad dotted
- <30,!7,1=dt,3=wv,5=bd,7=bz
+ <30,!3,1=bd,3=bz
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -225,8 +232,6 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
$(2,4,6)dr : 2=dr,4=dr,6=dr
<30,!7,$(2,4,6)dr
-
- ** <30,!7,2=dr,4=dr,6=dr
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -264,10 +269,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
?n`length : change ring length
- ?6,4\,?6`1.2,5=?6,11=?6
-
- ** fused ring size depend on
- attached bond length
+ ?6,4\,?6`1.2
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -334,6 +336,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\MCFstructure
%-----------------------------------------------------------------------------
\begin{verbatim}
+ ** fused ring size depend on
+ attached bond length
+
+ ?6,4\,?6`1.2,5=?6,11=?6
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\begin{verbatim}
?6,3=?6[13] : fuse ?6[13] at B3
?6[13]: 6 membered ring scaled 13/10
** ?m[n] (5<=m<=8,11<=n<=15)
@@ -430,7 +440,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\subsubsection{Add substituent}
\begin{verbatim}
<-30,!17,2:/Me,4:/Et,6:/Pr,
- 10:/iPr,14:/tBu,16:/Ph^-30
+ 10:/iPr,14:/tBu,16:/Ph^-60
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -438,14 +448,16 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
~,^,` : change type,angle,length
- <-30,!6,@(2~wf,4~zf,6^-30)/H
+ <-30,!6,
+ @(2~wf,4~zf,6^-30)/H
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
\begin{verbatim}
^,`,> : change angle,length,environment
- <30,!7`1,@(3)/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl
+ <30,!7`1,
+ 3:/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -497,10 +509,9 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
@(5)green : change color of A5 green
$(3)red : change color of B3 red
+ ** METAFONT ignore color command
<30,Ph,@(2,5)N,2:red,5:blue,3=green
-
- ** METAFONT ignore color command
\end{verbatim}
%%%%\MCFstructure % for Metafont
\includegraphics{mcf_man_soc-060.eps}% for dvipdfmx
@@ -520,9 +531,11 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
if chain start multi charactor string,
use !0 instead of !
- MCd( 1,1)(0 ,0.9)(<30,COOH,!0,!3,COOH)
-
- MCd(.8,1)(0.3,0.1)(<30,COOH,!4,COOH)
+ MCf(<30,COOH,!0,!3,COOH)
+\end{verbatim}
+\MCFstructure
+\begin{verbatim}
+ MCf(<30,COOH,!4,COOH)
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -779,7 +792,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\subsubsection{Atom frame}
\begin{verbatim}
sw_atom_frame:=1;
- MCf(<30,Ph,4:/COOH,3:/OH)
+ MCf(<30,Ph,1:/Cl,4:/COOH,3:/OH)
** default: sw_atom_frame=0
\end{verbatim}
\MCFstructure
@@ -1016,7 +1029,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
%-----------------------------------------------------------------------------
\onecolumn%
\section{Example to use mcf2graph}
-\subsection{Molecular definition file example}
+\subsection{Molecular definition file}
\begin{verbatim}
%-------------------------------------------------------------------------
input mcf2graph.mf; % input macro
@@ -1026,14 +1039,6 @@ font_wd#:=60mm#; % font width >
font_ht#:=40mm#; % font height >
var3:="cal_MW"; tag3:="cMW"; > AUX file table
var4:="cal_FM"; tag4:="cFM"; >
-%%%% var5:="cal_MW"; tag5:="cMW"; >
-%%%% var6:="cal_FM"; tag6:="cFM"; >
-%%%% var7:="inf_USE"; tag7:="USE"; >
-%%%% var8:="inf_EXA"; tag8:="EXA"; >
-%%%% var9:="inf_EXB"; tag9:="EXB"; >
-%%%% auxtag_out; >
-%%%% sw_checklist:=1; >
-%%%% sw_MOLout:=1; >
outputformat:="png"; hppp:=vppp:=0.1; > PNG output
outputtemplate:="%j-%3c.png"; >
%-------------------------------------------------------------------------
@@ -1054,15 +1059,18 @@ endfont > end font
bye
\end{verbatim}
%------------------------------------------------------------------------
-\subsection{Molecular structure output example}
-\INFO{F:mcf_man_soc,C:100,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:101,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
-\newpage
-%------------------------------------------------------------------------
\noindent%
-\subsection{Molecular information output example}
-'filename'-info.aux : for use in \TeX, it takes over filename,
-char number, molecular information,etc.
+\subsection{Information auxfile output}
+\paragraph{(Insert option parameter setting)}
+\begin{verbatim}
+ sw_auxout:=1;
+ ** default : sw_auxout=0
+\end{verbatim}
+\paragraph{(Command line)}
+\begin{verbatim}
+ >mpost -s ahangle=0 FILENAME (molecular difinition file)
+\end{verbatim}
+\paragraph{(Output)}
\begin{verbatim}
(sw_auxfix=0)
F:mcf_man_soc;C:109;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin
@@ -1082,8 +1090,122 @@ 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}
+%------------------------------------------------------------------------
+\newpage
+\noindent%
+\subsection{Checklist output}
+\paragraph{(Insert option parameter setting)}
+\begin{verbatim}
+ sw_checklist:=1;
+ ** default : sw_checklist=0
+\end{verbatim}
+\paragraph{(Command line)}
+\begin{verbatim}
+ >mpost -s ahangle=0 -s ahlength=2 FILENAME (molecular difinition file)
+\end{verbatim}
+\paragraph{(Output)}
+\begin{verbatim}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Molecular name = Caffeine
+% There were 0 warnings / Expanded command count= 75
+% width * height = 39.54677 * 36.84769
+% Shift width * height = -9.33592 * -12.77518
+% Bond length = 9.23628 Atom size = 4.12209
+% Atom count= 14 Bond count= 15 Ring count= 2 Hide H = 10
+%-----------------------------------< atom >< bond >-------
+% 1 ( 0 ) ( 0 ) C 4
+% 2 ( 0.86603 ) ( -0.5 ) N 3
+% 3 ( 1.73206 ) ( 0 ) C 4
+% 4 ( 1.73206 ) ( 1 ) C 4
+% 5 ( 0.86603 ) ( 1.5 ) C 4
+% 6 ( 0 ) ( 1 ) N 3
+% 7 ( 2.6831 ) ( -0.30902 ) N 3
+% 8 ( 3.27089 ) ( 0.5 ) C 3
+% 9 ( 2.6831 ) ( 1.30902 ) N 3
+% 10 ( 0.86603 ) ( -1.38315 ) C 1
+% 11 ( -0.78764 ) ( 1.45474 ) C 1
+% 12 ( 2.95923 ) ( 2.15886 ) C 1
+% 13 ( -0.78764 ) ( -0.45474 ) O 2
+% 14 ( 0.86603 ) ( 2.38315 ) O 2
+%Bond list---------------------------------------------------------
+% 1 1 -> 2 ( 1)
+% 2 2 -> 3 ( 1)
+% 3 3 -> 4 ( 2)
+% 4 4 -> 5 ( 1)
+% 5 5 -> 6 ( 1)
+% 6 6 -> 1 ( 1)
+% 7 3 -> 7 ( 1)
+% 8 7 -> 8 ( 2)
+% 9 8 -> 9 ( 1)
+% 10 9 -> 4 ( 1)
+% 11 2 -> 10 ( 1)
+% 12 6 -> 11 ( 1)
+% 13 9 -> 12 ( 1)
+% 14 1 -> 13 ( 2)
+% 15 5 -> 14 ( 2)
+%Fomula / Molecular weight ---------------------------------------
+% C ( 12.0107) * 8 = 96.08557
+% H ( 1.00793) * 10 = 10.07935
+% N ( 14.0067) * 4 = 56.0268
+% O ( 15.9994) * 2 = 31.99881
+% Weight Calc: 194.19052 / Input: 194.19 / weight gap= 0.00052
+% Fomula Calc: C8H10N4O2 / Input: C8H10N4O2 / MACTCH
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\end{verbatim}%
+\newpage
+%------------------------------------------------------------------------
+\noindent%
+\subsection{Molfile output}
+\paragraph{(Insert option parameter setting)}
+\begin{verbatim}
+ sw_MOLout:=1;
+ ** default : sw_MOLout=0
+\end{verbatim}
+\paragraph{(Command line)}
+\begin{verbatim}
+ >mpost -s ahangle=3 FILENAME (molecular difinition file)
+\end{verbatim}
+\paragraph{(Output)}
+\begin{verbatim}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ -MCFtoMOL- EN:Caffeine
+
+ 14 15 0 0 0 0 0 0 0 0999 V2000
+ 0 0 0 C 0 0 0 0
+ 0.86603 -0.5 0 N 0 0 0 0
+ 1.73206 0 0 C 0 0 0 0
+ 1.73206 1 0 C 0 0 0 0
+ 0.86603 1.5 0 C 0 0 0 0
+ 0 1 0 N 0 0 0 0
+ 2.6831 -0.30902 0 N 0 0 0 0
+ 3.27089 0.5 0 C 0 0 0 0
+ 2.6831 1.30902 0 N 0 0 0 0
+ 0.86603 -1.36383 0 C 0 0 0 0
+ -0.76894 1.44394 0 C 0 0 0 0
+ -0.76894 -0.44394 0 O 0 0 0 0
+ 0.86603 2.36383 0 O 0 0 0 0
+ 2.95299 2.1396 0 C 0 0 0 0
+ 1 2 1 0 0 0
+ 2 3 1 0 0 0
+ 3 4 2 0 0 0
+ 4 5 1 0 0 0
+ 5 6 1 0 0 0
+ 6 1 1 0 0 0
+ 3 7 1 0 0 0
+ 7 8 2 0 0 0
+ 8 9 1 0 0 0
+ 9 4 1 0 0 0
+ 2 10 1 0 0 0
+ 6 11 1 0 0 0
+ 1 12 2 0 0 0
+ 5 13 2 0 0 0
+ 9 14 1 0 0 0
+M END
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\end{verbatim}%
+\newpage
%----------------------------------------------------------------------------
-\subsection{LaTeX file example}
+\subsection{\LaTeX file example}
%############################################################################
\begin{verbatim}
%--------------------------------------------------------------------
@@ -1116,10 +1238,14 @@ MW : molecular weight from literature data
%--------------------------------------------------------------------
\begin{document}
\unitlength=1mm%
-\INFO{F:mcf_man_soc,C:100,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:101,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:103,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:104,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
\end{document}
%--------------------------------------------------------------------
\end{verbatim}%
%############################################################################
+%------------------------------------------------------------------------
+\INFO{F:mcf_man_soc,C:103,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:104,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+%------------------------------------------------------------------------
\end{document}