diff options
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 85 |
1 files changed, 47 insertions, 38 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index dceb5999f3..59745ac19a 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2021.09.05 +% Molecular Coding Format manual by Akira Yamaji 2021.09.20 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage[pdftex]{graphicx} @@ -7,8 +7,8 @@ \usepackage{makeidx} \makeindex \hypersetup{colorlinks=true,linkcolor=blue} -\makeatletter \usepackage{mcf_setup} +\edef\MCFjobname{mcf_man_soc}% %---------------------------------------------------------------------------- %%%%\pdfpkresolution=1200 %---------------------------------------------------------------------------- @@ -38,7 +38,7 @@ \htmans=42mm% \fnum=1% %---------------------------------------------------------------------------- -\edef\MCFjobname{mcf_man_soc}% +\makeatletter %---------------------------------------------------------------------------- \font\@strufont=\MCFjobname\relax% %---------------------------------------------------------------------------- @@ -52,7 +52,7 @@ \fi% \global\advance\fnum\@ne\relax% }% -%--------------------------------------------------------------------------- +%---------------------------------------------------------------------------- \def\put@char{% \begin{picture}(75,100)% \put(0,95){\bf [\NO]\EN}% @@ -1542,27 +1542,27 @@ beginfont("EN:Cholesterol","MW:386.65", >information if check(mc)=0: MC(scantokens(mc)) fi > mc=mc1 - mc4 endfont > %------------------------------------------------------------------------------ -beginfont("f:mcf_data_base","t:EN","v:Adenine") > from mcf_data_base.mcf +beginfont("f:mcf_data_base.mcf","t:EN","v:Adenine") > from mcf_data_base.mcf if check(mc)=0: MC(scantokens(mc)) fi > select EN="Adenine" endfont > %------------------------------------------------------------------------------ -beginfont("f:mcf_data_base","t:EN","v:Guanine") > from mcf_data_base.mcf - if check(mc)=0: MC(scantokens(mc)) fi > select EN="Guanine" +beginfont("t:EN","v:Guanine") > select EN="Guanine" + if check(mc)=0: MC(scantokens(mc)) fi endfont %------------------------------------------------------------------------------ -beginfont("f:mcf_data_base","t:EN","v:Cytosine") > from mcf_data_base.mcf - if check(mc)=0: MC(scantokens(mc)) fi > select EN="Cytosine" +beginfont("t:EN","v:Cytosine") > select EN="Cytosine" + if check(mc)=0: MC(scantokens(mc)) fi > endfont > %------------------------------------------------------------------------------ -beginfont("f+:mcf_data_base","t:n","v:4") > from mcf_data_base.mcf - if check(mc)=0: MC(scantokens(mc)) fi > v:4 select No.4 -endfont > 'f+' keep file open +beginfont("t:n","v+:4") > v+:4 = select No.4 + if check(mc)=0: MC(scantokens(mc)) fi > keep file open +endfont > %------------------------------------------------------------------------------ forever: -%%%%%%%%%% beginfont("f+:mcf_data_base","v:*") > select all - beginfont("f+:mcf_data_base","t:EXA","v:1") > 'f+'=keep file open - if f_EOF=0: if check(mc)=0: MC(scantokens(mc)) fi fi > 'v:1' select EXA=1 - endfont > +%%%%%%%%%% beginfont("f:mcf_data_base","v+:*") > select all + beginfont("f:mcf_data_base","t:EXA","v+:1") > 'v+:1'= select EXA=1 + if f_EOF=0: if check(mc)=0: MC(scantokens(mc)) fi fi > keep file open + endfont > exitif (f_EOF=1)or(f_close=1); > exit if file end endfor %------------------------------------------------------------------------------ @@ -1639,25 +1639,25 @@ Cat:biological;EN:Linoleic acid;MW:280.45 %-------------------------------------------------------------- % query() % -% "i:filename" : input file name (default "mcf_data_base.mcf") +% "f:filename" : input file name (default "mcf_data_base.mcf") % "o:filename" : output file name (default "temp.mcf") % "s:sort-key" : sort by sort-key % -% = , <> , <= , >= , < , > +% operator : = , <> , <= , >= , < , > % -% filter 1 : Cat=biological -% filter 2 : MW>=285 -% filter 3 : MW<=295 +% filter 1 : Cat=biological +% filter 2 : MW>=285 +% filter 3 : MW<=295 %-------------------------------------------------------------- query("s:EN", -%%%%% "i:mcf_data_base.mcf","o:temp.mcf","s:EN", +%%%%% "f:mcf_data_base.mcf","o:temp.mcf","s:EN", "Cat=biological","MW>=285","MW<=295"); %-------------------------------------------------------------- forever: - beginfont("f+:temp","v:*") % use file temp.mcf / select all + beginfont("f:temp","v+:*") % use file temp.mcf / select all if f_EOF=0: if check(mc)=0: MC(scantokens(mc)) fi fi endfont - exitif (f_EOF=1)or(f_close=1); + exitif f_EOF=1; endfor %--------------------------------------------------------------- \end{verbatim} @@ -1713,6 +1713,7 @@ Cat:biological;EN:Piperine;MW:285.343;EXA:1 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; %% output jobname&'.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} @@ -1843,29 +1844,42 @@ endfont \index{Mcode}% \index{Temp}% \begin{verbatim} -sw_output:=Mcode; +sw_output:=Mcode; %% output 'jobname-nnn-EN-mc.aux' sw_output:=Mcode+Temp; %% output 'temp-mc.aux' +sw_output:=Info+Mcode; %% output 'jobname-data.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)} \begin{verbatim} - >mpost -s ahlength=8 FILENAME (sw_output=Mcode) + >mpost -s ahlength=8 FILENAME (sw_output=Info+Mcode) \end{verbatim} -\paragraph{(file name)} +\paragraph{(Output temporary file)} \begin{verbatim} 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 + +\end{verbatim} +\paragraph{(Output data-base file)} +\begin{verbatim} +sw_output=Mcode+Info ** file name = 'jobname-data.aux' + +(result) +Cat:biological;EN:Adenine;MW:135.13;EXA:1 ++ +<30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH ++-------------------------------------------------- + \end{verbatim} %------------------------------------------------------------------------ \paragraph{(Lualatex example)} %----------------------------------------------------------------------- \begin{verbatim} -beginfont("f:mcf_data_base","t:EN","v:Adenine") +beginfont("t:EN","v:Adenine") sw_output:=Mcode+Temp; endfont \end{verbatim} @@ -1873,7 +1887,7 @@ endfont \begin{verbatim} %----------------------------------------------------------------------- \begin{mplibcode} - beginfont("f:mcf_data_base","t:EN","v:Vancomycin") + beginfont("t:EN","v:Vancomycin") sw_output:=Mcode+Temp; %%%% output temp-mc.aux %%%% endfont; \end{mplibcode} @@ -1884,17 +1898,12 @@ endfont %----------------------------------------------------------------------- \begin{verbatim} (result) - 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 +<30,?6,@4,?6,@-4,\,!3,<-12,?5,@-3,<-12,?6,-3=?6,@-3,*\,!3, + ?6,@-4,?6,@6,\,!,/*Me^-40,*/OH^20,!,//O,!1,OH, + 3=wb,11=dl,15=dr,17=wf,19=wf,38=wb,{5,7,16,24,25,33,42}:O, + 32:*/H^60,10:/Me,{12,31}:*/_,27://_,37:/*_,28:/OH,{3,29}:/*OH \end{verbatim} %------------------------------------------------------------------------ \newpage |