summaryrefslogtreecommitdiff
path: root/graphics/mcf2graph/mcf_manual.tex
diff options
context:
space:
mode:
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r--graphics/mcf2graph/mcf_manual.tex85
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