diff options
Diffstat (limited to 'Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex')
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | 210 |
1 files changed, 168 insertions, 42 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex index 265c66c9d8a..cb9ea163a93 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 2016.10.10 +% Molecular Coding Format manual by Akira Yamaji 2016.10.13 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} %%%%\usepackage{graphicx} @@ -45,9 +45,9 @@ \ifx\@tag\@cFM\edef\CALfm{\@var}\fi \fi}% \def\put@char{% - \begin{picture}(84,30)% - \put(0,25){\bf [\MOLnum]\MOLnameE}% - \put(5,20){\small\tt FM:\CALfm{ }MW:\CALmw}% + \begin{picture}(84,28)% + \put(0,23){\bf [\MOLnum]\MOLnameE}% + \put(5,18){\small\tt FM:\CALfm{ }MW:\CALmw}% \put(5,0){\font\@strufont=\MOLfile\relax% \hbox{\@strufont\char\MOLchar}}% \end{picture}% @@ -146,7 +146,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ <-30,!6, 2\~dr,!, - 4\`1.5,!, + 4\`1.5,-90, 6\^15,-60 \end{verbatim} \MCFstructure @@ -208,15 +208,22 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- -\subsubsection{Dotted,wave,broad} +\subsubsection{Dotted,wave} \begin{verbatim} Bn=bond type : change bond type at Bn dt : dotted wv : wave + + <30,!3,1=dt,3=wv +\end{verbatim} +\MCFstructure +%----------------------------------------------------------------------------- +\subsubsection{Broad} +\begin{verbatim} bd : broad bz : broad dotted - <30,!7,1=dt,3=wv,5=bd,7=bz + <30,!3,1=bd,3=bz \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -225,8 +232,6 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ $(2,4,6)dr : 2=dr,4=dr,6=dr <30,!7,$(2,4,6)dr - - ** <30,!7,2=dr,4=dr,6=dr \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -264,10 +269,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \begin{verbatim} ?n`length : change ring length - ?6,4\,?6`1.2,5=?6,11=?6 - - ** fused ring size depend on - attached bond length + ?6,4\,?6`1.2 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -334,6 +336,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \MCFstructure %----------------------------------------------------------------------------- \begin{verbatim} + ** fused ring size depend on + attached bond length + + ?6,4\,?6`1.2,5=?6,11=?6 +\end{verbatim} +\MCFstructure +%----------------------------------------------------------------------------- +\begin{verbatim} ?6,3=?6[13] : fuse ?6[13] at B3 ?6[13]: 6 membered ring scaled 13/10 ** ?m[n] (5<=m<=8,11<=n<=15) @@ -430,7 +440,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \subsubsection{Add substituent} \begin{verbatim} <-30,!17,2:/Me,4:/Et,6:/Pr, - 10:/iPr,14:/tBu,16:/Ph^-30 + 10:/iPr,14:/tBu,16:/Ph^-60 \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -438,14 +448,16 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \begin{verbatim} ~,^,` : change type,angle,length - <-30,!6,@(2~wf,4~zf,6^-30)/H + <-30,!6, + @(2~wf,4~zf,6^-30)/H \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- \begin{verbatim} ^,`,> : change angle,length,environment - <30,!7`1,@(3)/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl + <30,!7`1, + 3:/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -497,10 +509,9 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \begin{verbatim} @(5)green : change color of A5 green $(3)red : change color of B3 red + ** METAFONT ignore color command <30,Ph,@(2,5)N,2:red,5:blue,3=green - - ** METAFONT ignore color command \end{verbatim} %%%%\MCFstructure % for Metafont \includegraphics{mcf_man_soc-060.eps}% for dvipdfmx @@ -520,9 +531,11 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ if chain start multi charactor string, use !0 instead of ! - MCd( 1,1)(0 ,0.9)(<30,COOH,!0,!3,COOH) - - MCd(.8,1)(0.3,0.1)(<30,COOH,!4,COOH) + MCf(<30,COOH,!0,!3,COOH) +\end{verbatim} +\MCFstructure +\begin{verbatim} + MCf(<30,COOH,!4,COOH) \end{verbatim} \MCFstructure %----------------------------------------------------------------------------- @@ -779,7 +792,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\ \subsubsection{Atom frame} \begin{verbatim} sw_atom_frame:=1; - MCf(<30,Ph,4:/COOH,3:/OH) + MCf(<30,Ph,1:/Cl,4:/COOH,3:/OH) ** default: sw_atom_frame=0 \end{verbatim} \MCFstructure @@ -1016,7 +1029,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4 %----------------------------------------------------------------------------- \onecolumn% \section{Example to use mcf2graph} -\subsection{Molecular definition file example} +\subsection{Molecular definition file} \begin{verbatim} %------------------------------------------------------------------------- input mcf2graph.mf; % input macro @@ -1026,14 +1039,6 @@ font_wd#:=60mm#; % font width > font_ht#:=40mm#; % font height > var3:="cal_MW"; tag3:="cMW"; > AUX file table var4:="cal_FM"; tag4:="cFM"; > -%%%% var5:="cal_MW"; tag5:="cMW"; > -%%%% var6:="cal_FM"; tag6:="cFM"; > -%%%% var7:="inf_USE"; tag7:="USE"; > -%%%% var8:="inf_EXA"; tag8:="EXA"; > -%%%% var9:="inf_EXB"; tag9:="EXB"; > -%%%% auxtag_out; > -%%%% sw_checklist:=1; > -%%%% sw_MOLout:=1; > outputformat:="png"; hppp:=vppp:=0.1; > PNG output outputtemplate:="%j-%3c.png"; > %------------------------------------------------------------------------- @@ -1054,15 +1059,18 @@ endfont > end font bye \end{verbatim} %------------------------------------------------------------------------ -\subsection{Molecular structure output example} -\INFO{F:mcf_man_soc,C:100,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:101,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% -\newpage -%------------------------------------------------------------------------ \noindent% -\subsection{Molecular information output example} -'filename'-info.aux : for use in \TeX, it takes over filename, -char number, molecular information,etc. +\subsection{Information auxfile output} +\paragraph{(Insert option parameter setting)} +\begin{verbatim} + sw_auxout:=1; + ** default : sw_auxout=0 +\end{verbatim} +\paragraph{(Command line)} +\begin{verbatim} + >mpost -s ahangle=0 FILENAME (molecular difinition file) +\end{verbatim} +\paragraph{(Output)} \begin{verbatim} (sw_auxfix=0) F:mcf_man_soc;C:109;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin @@ -1082,8 +1090,122 @@ F : filename C : char number NO : serial number EN : english name cMW : molecular weight calculated cFM : molecular formula calculated MW : molecular weight from literature data \end{verbatim} +%------------------------------------------------------------------------ +\newpage +\noindent% +\subsection{Checklist output} +\paragraph{(Insert option parameter setting)} +\begin{verbatim} + sw_checklist:=1; + ** default : sw_checklist=0 +\end{verbatim} +\paragraph{(Command line)} +\begin{verbatim} + >mpost -s ahangle=0 -s ahlength=2 FILENAME (molecular difinition file) +\end{verbatim} +\paragraph{(Output)} +\begin{verbatim} +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% Molecular name = Caffeine +% There were 0 warnings / Expanded command count= 75 +% width * height = 39.54677 * 36.84769 +% Shift width * height = -9.33592 * -12.77518 +% Bond length = 9.23628 Atom size = 4.12209 +% Atom count= 14 Bond count= 15 Ring count= 2 Hide H = 10 +%-----------------------------------< atom >< bond >------- +% 1 ( 0 ) ( 0 ) C 4 +% 2 ( 0.86603 ) ( -0.5 ) N 3 +% 3 ( 1.73206 ) ( 0 ) C 4 +% 4 ( 1.73206 ) ( 1 ) C 4 +% 5 ( 0.86603 ) ( 1.5 ) C 4 +% 6 ( 0 ) ( 1 ) N 3 +% 7 ( 2.6831 ) ( -0.30902 ) N 3 +% 8 ( 3.27089 ) ( 0.5 ) C 3 +% 9 ( 2.6831 ) ( 1.30902 ) N 3 +% 10 ( 0.86603 ) ( -1.38315 ) C 1 +% 11 ( -0.78764 ) ( 1.45474 ) C 1 +% 12 ( 2.95923 ) ( 2.15886 ) C 1 +% 13 ( -0.78764 ) ( -0.45474 ) O 2 +% 14 ( 0.86603 ) ( 2.38315 ) O 2 +%Bond list--------------------------------------------------------- +% 1 1 -> 2 ( 1) +% 2 2 -> 3 ( 1) +% 3 3 -> 4 ( 2) +% 4 4 -> 5 ( 1) +% 5 5 -> 6 ( 1) +% 6 6 -> 1 ( 1) +% 7 3 -> 7 ( 1) +% 8 7 -> 8 ( 2) +% 9 8 -> 9 ( 1) +% 10 9 -> 4 ( 1) +% 11 2 -> 10 ( 1) +% 12 6 -> 11 ( 1) +% 13 9 -> 12 ( 1) +% 14 1 -> 13 ( 2) +% 15 5 -> 14 ( 2) +%Fomula / Molecular weight --------------------------------------- +% C ( 12.0107) * 8 = 96.08557 +% H ( 1.00793) * 10 = 10.07935 +% N ( 14.0067) * 4 = 56.0268 +% O ( 15.9994) * 2 = 31.99881 +% Weight Calc: 194.19052 / Input: 194.19 / weight gap= 0.00052 +% Fomula Calc: C8H10N4O2 / Input: C8H10N4O2 / MACTCH +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\end{verbatim}% +\newpage +%------------------------------------------------------------------------ +\noindent% +\subsection{Molfile output} +\paragraph{(Insert option parameter setting)} +\begin{verbatim} + sw_MOLout:=1; + ** default : sw_MOLout=0 +\end{verbatim} +\paragraph{(Command line)} +\begin{verbatim} + >mpost -s ahangle=3 FILENAME (molecular difinition file) +\end{verbatim} +\paragraph{(Output)} +\begin{verbatim} +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + -MCFtoMOL- EN:Caffeine + + 14 15 0 0 0 0 0 0 0 0999 V2000 + 0 0 0 C 0 0 0 0 + 0.86603 -0.5 0 N 0 0 0 0 + 1.73206 0 0 C 0 0 0 0 + 1.73206 1 0 C 0 0 0 0 + 0.86603 1.5 0 C 0 0 0 0 + 0 1 0 N 0 0 0 0 + 2.6831 -0.30902 0 N 0 0 0 0 + 3.27089 0.5 0 C 0 0 0 0 + 2.6831 1.30902 0 N 0 0 0 0 + 0.86603 -1.36383 0 C 0 0 0 0 + -0.76894 1.44394 0 C 0 0 0 0 + -0.76894 -0.44394 0 O 0 0 0 0 + 0.86603 2.36383 0 O 0 0 0 0 + 2.95299 2.1396 0 C 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 5 6 1 0 0 0 + 6 1 1 0 0 0 + 3 7 1 0 0 0 + 7 8 2 0 0 0 + 8 9 1 0 0 0 + 9 4 1 0 0 0 + 2 10 1 0 0 0 + 6 11 1 0 0 0 + 1 12 2 0 0 0 + 5 13 2 0 0 0 + 9 14 1 0 0 0 +M END +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\end{verbatim}% +\newpage %---------------------------------------------------------------------------- -\subsection{LaTeX file example} +\subsection{\LaTeX file example} %############################################################################ \begin{verbatim} %-------------------------------------------------------------------- @@ -1116,10 +1238,14 @@ MW : molecular weight from literature data %-------------------------------------------------------------------- \begin{document} \unitlength=1mm% -\INFO{F:mcf_man_soc,C:100,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% -\INFO{F:mcf_man_soc,C:101,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% +\INFO{F:mcf_man_soc,C:103,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% +\INFO{F:mcf_man_soc,C:104,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% \end{document} %-------------------------------------------------------------------- \end{verbatim}% %############################################################################ +%------------------------------------------------------------------------ +\INFO{F:mcf_man_soc,C:103,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}% +\INFO{F:mcf_man_soc,C:104,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}% +%------------------------------------------------------------------------ \end{document} |