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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex170
1 files changed, 89 insertions, 81 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index c1c525a118f..005dbfe129e 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 2021.05.23
+% Molecular Coding Format manual by Akira Yamaji 2021.06.06
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage[pdftex]{graphicx}
@@ -12,7 +12,7 @@
%----------------------------------------------------------------------------
%%%%\pdfpkresolution=1200
%----------------------------------------------------------------------------
-%%%%\edef\fext{pk}% **** for proof print (fast)
+%%%%\edef\fext{pk}% **** for proof print (fast, not complete output)
\edef\fext{mps}% **** for final print (it takes long time)
%----------------------------------------------------------------------------
%%%%\edef\fext{png}%
@@ -609,11 +609,8 @@ MC(<-30,?6,{3,10,15}=?6,(21,4)=?6[2])
\index{SO}%
\index{SOO}%
\begin{verbatim}
-NH : N,/H~nl
-N! : N,/_
-N!2 : N,/!
-SO : S,//O
-SOO : S,//O^35,//^-35
+NH : N,/H~nl N! : N,/_ N!2 : N,/!
+SO : S,//O SOO : S,//O^35,//^-35
<-30,!2,NH,!2,N!,!2,N!2,SO,!2,SOO,!
\end{verbatim}
@@ -623,14 +620,11 @@ SOO : S,//O^35,//^-35
\index{??"!}%
\index{N?"!}%
\begin{verbatim}
-?! : /_,!
-?? : /_^35,/_-35
-/?! : isopropyl
-/??! : tert-butyl
+?! : /_,! ?? : /_^35,/_-35
+/?! : isopropyl /??! : tert-butyl
/N?! : dimethylamino
-<30,!9`1,?!,!,??,!,
-2:??,4:/??,6:/??!,8:/N?!
+<30,!9`1,?!,!,??,!,2:??,4:/??,6:/??!,8:/N?!
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -645,8 +639,6 @@ MC(<30,?6,{4,6}:/iBuOH)
%-----------------------------------------------------------------------------
\subsubsection{Parts inline definition}
\begin{verbatim}
-<30,!, /'(!,/_,!,OH),!
-
<30,!8,{2,6}:/'(!,/_,!,OH)
\end{verbatim}
\MCFgraph
@@ -661,6 +653,15 @@ MC(<30,?6,{4,6}:/iBuOH)
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
+\subsubsection{Serial number}
+\index{--}%
+\begin{verbatim}
+6--10 : 6,7,8,9,10
+<30,!14,{2,6--10,14}:/_~bd`0.5
+\end{verbatim}
+\MCFgraph
+\newpage
+%-----------------------------------------------------------------------------
\subsubsection{Change color}
\index{red}%
\index{blue}%
@@ -884,35 +885,40 @@ default: ratio_hashgap_bond=0.12
\subsection{Drawing mode}
%-----------------------------------------------------------------------------
\subsubsection{Numbering atom}
-\index{numberA}%
-\index{numberA\_start}%
-\index{numberA\_end}%
+\index{sw\_numbering}%
+\index{Atom}%
+\index{Brock}%
+\index{Inverse}%
+\index{numbering\_start}%
+\index{numbering\_end}%
\begin{verbatim}
-numberA_start:=3; numberA_end:=8;
-default: sw_numberA=0 :
- numberA_start=1 numberA_end=4095
+sw_numbering=Atom
+numbering_start:=3; numbering_end:=8;
+default: sw_numbering=0 :
\end{verbatim}
\MCFgraph
\begin{picture}(5,20)
-\put(0,14){\makebox[5mm]{\tt 1}}
-\put(0, 8){\makebox[5mm]{\tt 2}}
-\put(0, 2){\makebox[5mm]{\tt 3}}
+\put(0,14){\makebox[9mm]{\tt Atom}}
+\put(0, 8){\makebox[12mm]{\tt +Brock}}
+\put(0, 2){\makebox[16mm]{\tt +Inverse}}
\end{picture}
%-----------------------------------------------------------------------------
\subsubsection{Numbering bond}
-\index{numberB}%
-\index{numberB\_start}%
-\index{numberB\_end}%
+\index{numbering\_start}%
+\index{numbering\_end}%
+\index{Bond}%
+\index{Brock}%
+\index{Inverse}%
\begin{verbatim}
-numberB_start:=3; numberB_end:=8;
-default: sw_numberB=0 :
- numberB_start=1 numberB_end=4095
+sw_numbering=Bond
+numbering_start:=3; numbering_end:=8;
+default: sw_numbering=0 :
\end{verbatim}
\MCFgraph
\begin{picture}(5,20)
-\put(0,14){\makebox[5mm]{\tt 1}}
-\put(0, 8){\makebox[5mm]{\tt 2}}
-\put(0, 2){\makebox[5mm]{\tt 3}}
+\put(0,14){\makebox[9mm]{\tt Bond}}
+\put(0, 8){\makebox[12mm]{\tt +Brock}}
+\put(0, 2){\makebox[16mm]{\tt +Inverse}}
\end{picture}
%-----------------------------------------------------------------------------
\subsubsection{Trimming mode}
@@ -941,55 +947,60 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{Group off mode}
-\index{sw\_group\_off}%
+\subsubsection{Abbreviate group}
+\index{Group}%
+\index{sw\_abbreviate}%
\begin{verbatim}
-** default: sw_group_off=0
+** default: sw_abbreviate=Group
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
-\subsubsection{Single bond mode}
-\index{sw\_single}%
+\subsubsection{Abbreviate bond type}
+\index{Bond}%
+\index{sw\_abbreviate}%
\begin{verbatim}
-** default: sw_single=0
+** default: sw_abbreviate=Bond
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsection{Frame}
%-----------------------------------------------------------------------------
\subsubsection{Font frame}
-\index{sw\_fframe}%
+\index{sw\_frame}%
+\index{Bothside}%
+\index{Inside}%
+\index{Outside}%
\begin{verbatim}
-** default:sw_fframe=0
+** default:sw_frame=0
(Draw font frame)
fmargin:=(5mm,2mm);
-sw_fframe=1
+sw_frame=Outside
\end{verbatim}
\MCFgraph
\begin{verbatim}
(Frame inside margin)
-sw_fframe=2
+sw_frame=Inside
\end{verbatim}
\MCFgraph
\begin{verbatim}
(Draw both frame)
-sw_fframe=3
+sw_frame=Bothside=Inside+Outside
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Molecular frame}
-\index{sw\_mframe}%
+\index{Mol}%
\begin{verbatim}
-sw_mframe=1
-** default:sw_mframe=0
+sw_frame=Mol
+** default:sw_frame=0
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Atom frame}
-\index{sw\_aframe}%
+\index{Atom}%
\begin{verbatim}
-sw_aframe=1
-** default: sw_aframe=0
+sw_frame=Atom
+** default: sw_frame=0
MC(<30,COOH,!,COOH)
\end{verbatim}
@@ -1067,7 +1078,7 @@ d: y axis position
defaultsize:=5bp;
fsize:=(60mm,40mm); fmargin:=(3mm,3mm);
-blength:=0.07; sw_fframe:=1;
+blength:=0.07; sw_frame:=Outside;
mangle:=0;
for i=1 step -0.5 until 0:
for j=0 step 0.33 until 1:
@@ -1189,7 +1200,7 @@ a /* b : point b of a
beginfont("EN:add() 1")
fsize:=(70mm,40mm);
- sw_aframe:=sw_mframe:=1;
+ sw_frame:=Bothside;
max_blength:=10mm;
msize:=(.91,.9);
MCat(.5,.85)(<30,?6,{2,5}:O)
@@ -1476,7 +1487,7 @@ endfont
%-------------------------------------------------------------------------
input mcf2graph.mf; > input main macro
%-------------------------------------------------------------------------
-sw_output:=Info1; % aux(information) file output on > global setting
+sw_output:=Info; % 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) >
@@ -1607,20 +1618,20 @@ Cat:biological;EN:Linoleic acid;MW:280.45
\index{mi}%
\index{w}%
\index{h}%
-\index{Info1}%
-\index{Info2}%
-\index{Info\_t}%
+\index{Info}%
+\index{Table}%
+\index{Temp}%
\begin{verbatim}
- sw_output:=Info1; %% tag1:var1;tag2:var2
- sw_output:=Info2; %% tag1;tag2 var1;var2
- sw_output:=Info_t; %% tag1:var1;tag2:var2 / output 'temp-info.aux'
- sw_output:=Info_Mcode_t; %% output 'temp-info.aux','temp-mc.aux'
- sw_output:=None_Info_t; %% output font,'temp-mc.aux'
+ sw_output:=Info; %% tag1:var1;tag2:var2
+ sw_output:=Info+Table; %% tag1;tag2 var1;var2
+ sw_output:=Info+Temp; %% tag1:var1;tag2:var2 / output 'temp-info.aux'
+ sw_output:=Info+Mcode+Temp; %% output 'temp-info.aux','temp-mc.aux'
+ sw_output:=Font+Info+Temp; %% output font,'temp-info.aux','temp-mc.aux'
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
- >mpost -s ahlength=1 FILENAME (sw_output=Info1)
- >mpost -s ahlength=2 FILENAME (sw_output=Info2)
+ >mpost -s ahlength=1 FILENAME (sw_output=Info)
+ >mpost -s ahlength=2 FILENAME (sw_output=Info+Table)
\end{verbatim}
\paragraph{(Sourse)}
\begin{verbatim}
@@ -1636,13 +1647,13 @@ tag1:="J"; tag2:="C"; tag3:="mw"; tag4:="fm"; tag5:="EN";
\paragraph{(Output)}
\index{aux\_delimiter}%
\begin{verbatim}
-(sw_output=Info1)
+(sw_output=Info)
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_output=Info2)
+(sw_output=Info+Table)
F;C;mw;fm
mcf_man_soc;1;349.40462;C16H19N3O4S;Ampicillin
mcf_man_soc;2;386.6532;C27H46O;Cholesterol
@@ -1742,26 +1753,22 @@ endfont
\subsection{MCF aux file output}
\paragraph{(Insert option parameter setting)}
\index{Mcode}%
+\index{Temp}%
\begin{verbatim}
sw_output:=Mcode;
-sw_output:=Mcode_t; %% output 'temp-mc.aux'
-sw_output:=Info_Mcode_t; %% output 'temp-info.aux','temp-mc.aux'
-sw_output:=None_Mcode_t; %% output font,'temp-mc.aux'
-sw_output:=None_Info_Mcode_t; %% output font,'temp-info.aux','temp-mc.aux'
+sw_output:=Mcode+Temp; %% output 'temp-mc.aux'
+sw_output:=Info+Mcode+Temp; %% output 'temp-info.aux','temp-mc.aux'
+sw_output:=Font+Mcode+Temp; %% output font,'temp-mc.aux'
+sw_output:=Font+Info+Mcode+Temp; %% output font,'temp-info.aux','temp-mc.aux'
\end{verbatim}
\paragraph{(Command line)}
-\index{Mcode\_t}%
\begin{verbatim}
>mpost -s ahlength=8 FILENAME (sw_output=Mcode)
\end{verbatim}
\paragraph{(file name)}
\begin{verbatim}
-sw_output=Mcode
-file name = 'mcf_exa_soc-001-Adenine-mc.aux'
- 'jobname -nnn-EN -mc.auc'
-
-sw_output=Mcode_t
-file name = 'temp-mc.aux'
+sw_output=Mcode ** file name = 'jobname-nnn-EN-mc.aux'
+sw_output=Mcode+Temp ** file name = 'temp-mc.aux'
(result)
<30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH
@@ -1771,7 +1778,7 @@ file name = 'temp-mc.aux'
%-----------------------------------------------------------------------
\begin{verbatim}
beginfont("f:mcf_data_base","t:EN","v:Adenine")
- sw_output:=Mcode_t;
+ sw_output:=Mcode+Temp;
endfont
\end{verbatim}
%-----------------------------------------------------------------------
@@ -1779,7 +1786,7 @@ endfont
%-----------------------------------------------------------------------
\begin{mplibcode}
beginfont("f:mcf_data_base","t:EN","v:Vancomycin")
- sw_output:=Mcode_t; %%%% output temp-mc.aux %%%%
+ sw_output:=Mcode+Temp; %%%% output temp-mc.aux %%%%
endfont;
\end{mplibcode}
%-----------------------------------------------------------------------
@@ -1809,7 +1816,8 @@ file name = 'temp-mc.aux'
\index{sw\_output}%
\index{Report}%
\begin{verbatim}
- sw_output:=Report;
+ sw_output:=Report; ** file name = 'jobname-report.aux'
+ sw_output:=Report+Temp; ** file name = 'temp-report.aux'
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
@@ -1922,7 +1930,7 @@ M END
%----------------------------------------------------------------------------
\newpage
\subsection{LuaTeX file example}
-\index{None}%
+\index{Font}%
%############################################################################
\begin{verbatim}
\documentclass{article}
@@ -1934,7 +1942,7 @@ M END
\mplibnumbersystem{double}%
\everymplib{%
if unknown Ph1: input mcf2graph.mf; fi
- sw_output:=None; sw_fframe:=4; max_blength:=4.5mm;
+ sw_output:=Font; max_blength:=4.5mm;
defaultfont:="uhvr8r"; defaultsize:=8bp; defaultscale:=1;
}%
\begin{document}
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-01 01:15:22 +0000