diff options
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 79 |
1 files changed, 72 insertions, 7 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index f96a5357cf..e5842f9eac 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2021.04.18 +% Molecular Coding Format manual by Akira Yamaji 2021.05.05 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage[pdftex]{graphicx} @@ -12,8 +12,8 @@ %---------------------------------------------------------------------------- %%%%\pdfpkresolution=1200 %---------------------------------------------------------------------------- -\edef\fext{pk}% **** for proof print (fast) -%%%%\edef\fext{mps}% **** for final print (it takes long time) +%%%%\edef\fext{pk}% **** for proof print (fast) +\edef\fext{mps}% **** for final print (it takes long time) %---------------------------------------------------------------------------- %%%%\edef\fext{png}% %%%%\edef\fext{svg}% @@ -54,9 +54,9 @@ }% %--------------------------------------------------------------------------- \def\put@char{% - \begin{picture}(75,130)% - \put(0,120){\bf [\NO]\EN}% - \put(5,115){\small\tt FM:\fm{ }MW:\mw}% + \begin{picture}(75,100)% + \put(0,95){\bf [\NO]\EN}% + \put(5,90){\small\tt FM:\fm{ }MW:\mw}% \put(5,0){\MCFgraph}% \end{picture}% }% @@ -1470,7 +1470,6 @@ endfont \subsection{Metafont/Metapost souce file} \index{mcf2graph.mf}% \index{sw\_output}% -\index{sw\_file\_open}% \index{tag}% \index{var}% \begin{verbatim} @@ -1608,9 +1607,13 @@ Cat:biological;EN:Linoleic acid;MW:280.45 \index{mi}% \index{w}% \index{h}% +\index{Info1}% +\index{Info2}% +\index{Info\_t}% \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' \end{verbatim} \paragraph{(Command line)} \begin{verbatim} @@ -1671,6 +1674,7 @@ h : font height \noindent% \newpage \subsection{Metafont aux file output} +\index{Mfont}% \paragraph{(Insert option parameter setting)} \begin{verbatim} sw_output:=Mfont; @@ -1731,11 +1735,69 @@ if check(mc)=0: MC(scantokens(mc)) fi endfont \end{verbatim} %------------------------------------------------------------------------ +\noindent% +\newpage +\subsection{MCF aux file output(1)} +\paragraph{(Insert option parameter setting)} +\index{Mcode}% +\begin{verbatim} +sw_output:=Mcode; +\end{verbatim} +\paragraph{(Command line)} +\index{Mcode\_t}% +\begin{verbatim} + >mpost -s ahlength=8 FILENAME (sw_output=Mcode) +\end{verbatim} +\paragraph{(Output)} +\begin{verbatim} +file name = 'mcf_exa_soc-001-Adenine-mc.aux' + +<30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH +\end{verbatim} +%------------------------------------------------------------------------ +\subsection{MCF aux file output(2)} +\paragraph{(Insert option parameter setting)} +\begin{verbatim} +beginfont("f:mcf_data_base","t:EN","v:Adenine") + sw_output:=Mcode_t; +endfont +\end{verbatim} +%----------------------------------------------------------------------- +\paragraph{(Lualatex example)} +%----------------------------------------------------------------------- +\begin{verbatim} +%----------------------------------------------------------------------- +\begin{mplibcode} + beginfont("f:mcf_data_base","t:EN","v:Vancomycin") + sw_output:=Mcode_t; %%%% output temp-mc.aux %%%% + endfont; +\end{mplibcode} +%----------------------------------------------------------------------- +\verbatiminput{temp-mc.aux} +%----------------------------------------------------------------------- +\end{verbatim} +%----------------------------------------------------------------------- +\paragraph{(Output)} +%----------------------------------------------------------------------- +\begin{verbatim} +file name = 'temp-mc.aux' + +<-30,#1,!12,{1,3,12}=zf,7=wf,/H^-60,60,*/OH,60, + Ph,-4:/Cl,@-3,\,O,!,Ph,@-4,\,O,!,Ph,-1^15:/Cl,@-3,\,/*OH,*/H^-60,&1, + @7,&26,@$1,60,//O,60,NH,60,/*H,*/COOH^180,-60, + Ph,{-2,-4}:/OH,@-1,\,Ph,-5:/OH,@-2,&4,##, + {3^40,6,9,12}://O,{2,5,8,11}:NH,{1,4^180}:*/H,{7^-60,10^60,14^60}:/*H, + @10,*\^-60,60,//O,!,NH2,@13,*\,NH,!,//O,!,/??!,*/H^60,!~zf,NH,!, + @23,\,O,!,|,?6`.7,2:O,3^10:/!OH,{4,5}:/OH, + @-1,\,O,!,|,?6`.7,6:O,{3^35,5}:/_,3^-35:/NH2,4:/OH +\end{verbatim} +%------------------------------------------------------------------------ \newpage \noindent% \subsection{Report output} \paragraph{(Insert option parameter setting)} \index{sw\_output}% +\index{Report}% \begin{verbatim} sw_output:=Report; \end{verbatim} @@ -1798,6 +1860,8 @@ endfont \subsection{MOL file output} \paragraph{(Insert option parameter setting)} \index{sw\_output}% +\index{MOL2k}% +\index{MOL3k}% \begin{verbatim} sw_output:=MOL2k; % MOL(V2000) sw_output:=MOL3k; % MOL(V3000) @@ -1848,6 +1912,7 @@ M END %---------------------------------------------------------------------------- \newpage \subsection{LuaTeX file example} +\index{None}% %############################################################################ \begin{verbatim} \documentclass{article} |