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-rw-r--r--graphics/mcf2graph/mcf_manual.tex60
1 files changed, 23 insertions, 37 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex
index c83840b2a3..da90e22f98 100644
--- a/graphics/mcf2graph/mcf_manual.tex
+++ b/graphics/mcf2graph/mcf_manual.tex
@@ -1,24 +1,18 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2021.10.10
+% Molecular Coding Format manual by Akira Yamaji 2021.11.23
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage[pdftex]{graphicx}
\usepackage[pdftex]{hyperref}
+%%%\usepackage[dvipdfmx]{graphicx}
+%%%\usepackage[dvipdfmx]{hyperref}
\usepackage{makeidx}
\makeindex
\hypersetup{colorlinks=true,linkcolor=blue}
\usepackage{mcf_setup}
\edef\MCFjobname{mcf_man_soc}%
%----------------------------------------------------------------------------
-%%%%\pdfpkresolution=1200
-%----------------------------------------------------------------------------
-%%%%\edef\fext{pk}% **** for proof print (fast, not complete output)
-\edef\fext{mps}% **** for final print (it takes long time)
-%----------------------------------------------------------------------------
-%%%%\edef\fext{png}%
-%%%%\edef\fext{svg}%
-%%%%\edef\fext{eps}%
-%----------------------------------------------------------------------------
+\edef\fext{mps}%
\topmargin=-18mm
\textheight=254mm
\textwidth=168mm
@@ -40,16 +34,9 @@
%----------------------------------------------------------------------------
\makeatletter
%----------------------------------------------------------------------------
-\font\@strufont=\MCFjobname\relax%
-%----------------------------------------------------------------------------
\def\MCFgraph{%
-\ifx\fext\@pk{\@strufont\char\fnum}%
-\else%
\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}%
-\fi%
+\includegraphics{\file@name}%
\global\advance\fnum\@ne\relax%
}%
%----------------------------------------------------------------------------
@@ -207,7 +194,6 @@ $n (0<=n<360): absolute angle
\index{db}%
\index{tm}%
\begin{verbatim}
-
(Double,triple)
a~type : ~~type,a
dm : double middle
@@ -446,14 +432,14 @@ attached bond length
\begin{verbatim}
(Attached 2 bond)
-(4,11)=?6[4] : fuse 4/6 ring to B11..B4
-(4,11)=?5[3] : fuse 3/5 ring to B11..B4
-(4,11)=?4[2] : fuse 2/4 ring to B11..B4
+(4,11)=?6 : fuse 4/6 ring to B11..B4
+(4,11)=?5 : fuse 3/5 ring to B11..B4
+(4,11)=?4 : fuse 2/4 ring to B11..B4
** ?m[n] (4<=m<=6,n=m-2)
-1:<30,?6,3=?6,(11,4)=?6[4]
-2:<30,?6,3=?6,(11,4)=?5[3]
-3:<30,?6,3=?6,(11,4)=?4[2]
+1:<30,?6,3=?6,(11,4)=?6
+2:<30,?6,3=?6,(11,4)=?5
+3:<30,?6,3=?6,(11,4)=?4
\end{verbatim}
\MCFgraph
\vspace{-3mm}%
@@ -676,7 +662,7 @@ MC(<30,?6,{4,6}:/iBuOH)
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Serial number}
-\index{--}%
+\index{\-\-}%
\begin{verbatim}
6--10 : 6,7,8,9,10
<30,!14,{2,6--10,14}:/_~bd_r`0.5
@@ -1420,7 +1406,7 @@ endfont
\begin{verbatim}
beginfont("EN:Colchicine","MW:385.41",
%-------------------------------------
- ": <30,Ph,{1,2,6}:/O!,-4=?7,-5=?7, ",
+ ": <30,Ph,{1,2,6}:/O!,{-4,-5}=?7, ",
": {-1,-4,-6}=dl,-2://O,-3:/O!, ",
": @9,\,NH,!,//O,! ")
%-------------------------------------
@@ -1574,11 +1560,15 @@ bye
\subsection{Molecular data base file}
\begin{verbatim}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% molecular data base file mcf_data_base.mcf by Akira Yamaji 2021.04.18
+% molecular data base file mcf_data_base.mcf by Akira Yamaji 2021.11.14
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% tag1:var1;tag2:var2;tag3:var3 .....
+% first character of line "%" comment out
+% first character of line "+" begin MCF
+% first string of line "+-" end MCF
+% first string of line "%-" end header
+% Cat = Category
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% tag1:var1;tag2:var2;tag3:var3 ....
-% first character of line '%' comment out
-% first character of line '+' begin MCF , end MCF
%------------------------------------------------------------------------------
Cat:biological;EN:Adenine;MW:135.13
+
@@ -1624,10 +1614,6 @@ Cat:biological;EN:Stearic acid;MW:284.48
+
<30,!17,COOH
+------------------------------------------------------------------------------
-Cat:biological;EN:Linoleic acid;MW:280.45
-+
-<30,!5,-30,-30,!,-30,-30,!7,COOH,{6,9}=dr
-+------------------------------------------------------------------------------
\end{verbatim}
%------------------------------------------------------------------------------
\noindent%
@@ -1674,12 +1660,12 @@ Cat:biological;EN:Cianidanol;MW:290.27;EXA:1
+------------------------------------------------------------------------------
Cat:biological;EN:Lycorine;MW:287.315;EXA:1
+
-<30,Ph,-4=?6,-2=?6,6=?5,(9,12)=?5[3],13=dl,8:N,{15,17}:O,
+<30,Ph,{-4,-2}=?6,{6,(9,12)}=?5,13=dl,8:N,{15,17}:O,
9:/*H^180,10:*/H^60,13:*/OH,14:/*OH
+------------------------------------------------------------------------------
Cat:biological;EN:Morphine;MW:285.343;EXA:1
+
-<30,Ph,2=?6,-4=?6,(1,12)=?5[2],-1:O,-1=zb,
+<30,Ph,{2,-4}=?6,(1,12)=?5[2],-1:O,-1=zb,
@7,60~wf`0.75,70~si_`1.3,45,N!,&9~wb,15=dl,6:/OH,8^180:*/H,12:/*OH
+------------------------------------------------------------------------------
Cat:biological;EN:Piperine;MW:285.343;EXA:1