diff options
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 183 |
1 files changed, 120 insertions, 63 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index 6356d34094..f96a5357cf 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2021.04.04 +% Molecular Coding Format manual by Akira Yamaji 2021.04.18 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage[pdftex]{graphicx} @@ -48,7 +48,7 @@ \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}% +%%%%%%\includegraphics{\file@name}% \fi% \global\advance\fnum\@ne\relax% }% @@ -1469,7 +1469,7 @@ endfont \section{Example to use mcf2graph} \subsection{Metafont/Metapost souce file} \index{mcf2graph.mf}% -\index{sw\_aux\_out}% +\index{sw\_output}% \index{sw\_file\_open}% \index{tag}% \index{var}% @@ -1477,14 +1477,14 @@ endfont %------------------------------------------------------------------------- input mcf2graph.mf; > input main macro %------------------------------------------------------------------------- -sw_aux_out:=1; % aux(information) file output on > global setting +sw_output:=Info1; % 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) > tag1:="J"; > jobname tag2:="C"; > char No tag3:="mw"; % calculated molecular weight > tag4:="fm"; % calculated molecular formula > -%%%% sw_rep_out:=1; > report output -%%%% sw_mol_out:=1; > MOL file output outputformat:="png"; hppp:=vppp:=0.1; > PNG output outputtemplate:="%j-%3c.png"; > %------------------------------------------------------------------------- @@ -1492,7 +1492,7 @@ beginfont("EN:Ampicillin","MW:349.405") > information MC(<45,?4,-3=?5,2:N,7:S, > immediately compile 3^45:/*H,1://O^15,5:/*COOH^-18,6:??, > @4,*\^15,NH,!,//O,!,/*NH2,!,Ph) > -endfont > end font +endfont > %------------------------------------------------------------------------ beginfont("EN:Cholesterol","MW:386.65", >information %---------------------------------------- > @@ -1502,7 +1502,7 @@ beginfont("EN:Cholesterol","MW:386.65", >information ": @-1,18,/*_,-60,!3,?! ") > mc4 %---------------------------------------- > if check(mc)=0: MC(scantokens(mc)) fi > mc=mc1 - mc4 -endfont > end font +endfont > %------------------------------------------------------------------------------ beginfont("f:mcf_data_base","t:EN","v:Adenine") > from mcf_data_base.mcf if check(mc)=0: MC(scantokens(mc)) fi > select EN="Adenine" @@ -1516,16 +1516,14 @@ 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" endfont > %------------------------------------------------------------------------------ -sw_file_open:=1; > keep file open **default sw_file_open=0 -%------------------------------------------------------------------------------ -beginfont("f:mcf_data_base","t:n","v:4") > from mcf_data_base.mcf +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 > +endfont > 'f+' keep file open %------------------------------------------------------------------------------ for i=5 upto 155: > from mcf_data_base.mcf - beginfont("f:mcf_data_base","t:n","v:0") > v:0 no selection + beginfont("f+:mcf_data_base","v:*") > v:* no selection if check(mc)=0: MC(scantokens(mc)) fi > No.5 - No.155 - endfont > + endfont > 'f+' keep file open endfor > %------------------------------------------------------------------------------ bye @@ -1536,66 +1534,65 @@ bye \subsection{Molecular data base file} \begin{verbatim} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% molecular data base file mcf_data_base.mcf by Akira Yamaji 2021.04.04 +% molecular data base file mcf_data_base.mcf by Akira Yamaji 2021.04.18 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % tag1:var1;tag2:var2;tag3:var3 .... % first character of line '%' comment out -% first character of line '+' begin molecular definition -% first character of line '-' end molecular definition -%--------------------------------------------------------------------------- -EN:Cytosine;MW:111.10 +% first character of line '+' begin MCF , end MCF +%------------------------------------------------------------------------------ +Cat:biological;EN:Adenine;MW:135.13 ++ +<30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH ++------------------------------------------------------------------------------ +Cat:biological;EN:Guanine;MW:151.13 ++ +<30,?6,3=?5,{1,3,9}=dl,{2,9}:N,{6,7}:NH,5://O,1:/NH2 ++------------------------------------------------------------------------------ +Cat:biological;EN:Cytosine;MW:111.10 + <30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2 ----------------------------------------------------------------------------- -EN:Thymine;MW:126.11 ++------------------------------------------------------------------------------ +Cat:biological;EN:Thymine;MW:126.11 + <30,?6,3=dl,{2,6}:NH,{1,5}://O,4:/_ ----------------------------------------------------------------------------- -EN:Uracil;MW:112.09 ++------------------------------------------------------------------------------ +Cat:biological;EN:Uracil;MW:112.09 + <30,?6,6=dl,{3,5}://O,{2,4}:NH ----------------------------------------------------------------------------- -EN:Geraniol;MW:154.25 ++------------------------------------------------------------------------------ +Cat:biological;EN:Geraniol;MW:154.25 + <30,!8,OH,{2,6}=dr,{2,6}:/_ ----------------------------------------------------------------------------- -EN:Limonene;MW:136.24 ++------------------------------------------------------------------------------ +Cat:biological;EN:Limonene;MW:136.24 + <30,?6,2=dl,2:/_,@5,*\,/_,!! ----------------------------------------------------------------------------- -EN:l-Menthol;MW:156.27 ++------------------------------------------------------------------------------ +Cat:biological;EN:l-Menthol;MW:156.27 + <30,?6,2:/*?!,5:*/_,3:*/OH ----------------------------------------------------------------------------- -EN:Vanillin;MW:152.15 ++------------------------------------------------------------------------------ +Cat:biological;EN:Vanillin;MW:152.15 + <30,Ph,2:/OH,3:/O!,5:/CHO -+---------------------------------------------------------------------------- -EN:Allicin;MW:162.28 ++------------------------------------------------------------------------------ +Cat:biological;EN:Allicin;MW:162.28 + <-30,!!,!2,SO,!,S,!2,!! ----------------------------------------------------------------------------- -EN:Stearic acid;MW:284.48; ++------------------------------------------------------------------------------ +Cat:biological;EN:Stearic acid;MW:284.48 + <30,!17,COOH ----------------------------------------------------------------------------- -EN:Linoleic acid;MW:280.45 ++------------------------------------------------------------------------------ +Cat:biological;EN:Linoleic acid;MW:280.45 + <30,!5,-30,-30,!,-30,-30,!7,COOH,{6,9}=dr ----------------------------------------------------------------------------- -EN:Sphingosine;MW:299.50 -+ -<30,!18,OH,14=dr,-3:*/OH,-2:/*NH2 ----------------------------------------------------------------------------- -EN:Tocopherol;MW:430.717 -+ -<30,Ph,3=?6,7:O,{1,2,5}:/_,8:/*_^60,6:/OH,@8,\,|,!12,{4,8}:/*_,12:/_ ----------------------------------------------------------------------------- ++------------------------------------------------------------------------------ \end{verbatim} -%------------------------------------------------------------------------ +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \noindent% \newpage -\subsection{Information auxfile output} +\subsection{Information aux file output} \paragraph{(Insert option parameter setting)} \index{J}% \index{C}% @@ -1612,14 +1609,13 @@ EN:Tocopherol;MW:430.717 \index{w}% \index{h}% \begin{verbatim} - sw_aux_out=1 : tag1:var1;tag2:var2 - sw_aux_out=2 : tag1;tag2 var1;var2 - ** default : sw_aux_out=0 + sw_output:=Info1; % tag1:var1;tag2:var2 + sw_output:=Info2; % tag1;tag2 var1;var2 \end{verbatim} \paragraph{(Command line)} \begin{verbatim} - >mpost -s ahlength=1 FILENAME (sw_aux_out=1) - >mpost -s ahlength=2 FILENAME (sw_aux_out=2) + >mpost -s ahlength=1 FILENAME (sw_output=Info1) + >mpost -s ahlength=2 FILENAME (sw_output=Info2) \end{verbatim} \paragraph{(Sourse)} \begin{verbatim} @@ -1635,13 +1631,13 @@ tag1:="J"; tag2:="C"; tag3:="mw"; tag4:="fm"; tag5:="EN"; \paragraph{(Output)} \index{aux\_delimiter}% \begin{verbatim} -(sw_aux_out=1) +(sw_output=Info1) 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_aux_out=2) +(sw_output=Info2) F;C;mw;fm mcf_man_soc;1;349.40462;C16H19N3O4S;Ampicillin mcf_man_soc;2;386.6532;C27H46O;Cholesterol @@ -1672,14 +1668,76 @@ w : font width h : font height \end{verbatim} %------------------------------------------------------------------------ +\noindent% +\newpage +\subsection{Metafont aux file output} +\paragraph{(Insert option parameter setting)} +\begin{verbatim} + sw_output:=Mfont; +\end{verbatim} +\paragraph{(Command line)} +\begin{verbatim} + >mpost -s ahlength=7 FILENAME (sw_output=Mfont) +\end{verbatim} +\paragraph{(Output)} +\begin{verbatim} +beginfont("Cat:biological","EN:Adenine","MW:135.13", +": <30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Guanine","MW:151.13", +": <30,?6,3=?5,{1,3,9}=dl,{2,9}:N,{6,7}:NH,5://O,1:/NH2") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Cytosine","MW:111.10", +": <30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Thymine","MW:126.11", +": <30,?6,3=dl,{2,6}:NH,{1,5}://O,4:/_") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Adenine","MW:135.13", +": <30,?6,3=?5,{1,3,5,9}=dl,{2,6,9}:N,5:/NH2,7:NH") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Guanine","MW:151.13", +": <30,?6,3=?5,{1,3,9}=dl,{2,9}:N,{6,7}:NH,5://O,1:/NH2") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Cytosine","MW:111.10", +": <30,?6,{4,6}=dl,4:N,3://O,2:NH,5:/NH2") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Thymine","MW:126.11", +": <30,?6,3=dl,{2,6}:NH,{1,5}://O,4:/_") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Uracil","MW:112.09", +": <30,?6,6=dl,{3,5}://O,{2,4}:NH") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Geraniol","MW:154.25", +": <30,!8,OH,{2,6}=dr,{2,6}:/_") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:Limonene","MW:136.24", +": <30,?6,2=dl,2:/_,@5,*\,/_,!!") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +beginfont("Cat:biological","EN:l-Menthol","MW:156.27", +": <30,?6,2:/*?!,5:*/_,3:*/OH") +if check(mc)=0: MC(scantokens(mc)) fi +endfont +\end{verbatim} +%------------------------------------------------------------------------ \newpage \noindent% \subsection{Report output} \paragraph{(Insert option parameter setting)} -\index{sw\_rep\_out}% +\index{sw\_output}% \begin{verbatim} - sw_rep_out:=1; - ** default : sw_rep_out=0 + sw_output:=Report; \end{verbatim} \paragraph{(Command line)} \begin{verbatim} @@ -1739,11 +1797,10 @@ h : font height \noindent% \subsection{MOL file output} \paragraph{(Insert option parameter setting)} -\index{sw\_mol\_out}% +\index{sw\_output}% \begin{verbatim} - sw_mol_out:=1; % MOL(V2000) - sw_mol_out:=2; % MOL(V3000) - ** default : sw_mol_out=0 + sw_output:=MOL2k; % MOL(V2000) + sw_output:=MOL3k; % MOL(V3000) \end{verbatim} \paragraph{(Command line)} \begin{verbatim} @@ -1802,7 +1859,7 @@ M END \mplibnumbersystem{double}% \everymplib{% if unknown Ph1: input mcf2graph.mf; fi - sw_calc:=1; sw_fframe:=4; max_blength:=4.5mm; + sw_output:=None; sw_fframe:=4; max_blength:=4.5mm; defaultfont:="uhvr8r"; defaultsize:=8bp; defaultscale:=1; }% \begin{document} |