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authorKarl Berry <karl@freefriends.org>2015-07-30 21:59:50 +0000
committerKarl Berry <karl@freefriends.org>2015-07-30 21:59:50 +0000
commitb6f4cf0741ace7ba3bc432bead24db36b84985af (patch)
tree61116ed575f3bae2ab0891b5e9ebd69c33eb7be8 /Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
parent6dc0ccac671319a03fa217782f7cbd746556c426 (diff)
mcf2graph (30jul15)
git-svn-id: svn://tug.org/texlive/trunk@38004 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex')
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex130
1 files changed, 101 insertions, 29 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index 04aa16a1dc5..e1cd21a844e 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
@@ -1,9 +1,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2015.7
+% Molecular Coding Format manual by Akira Yamaji 2015.7.25
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage[dvipdfmx]{graphicx}
-%%%%%\usepackage[pdftex]{graphicx}
+%%%%\usepackage[pdftex]{graphicx}
+%%%%\usepackage{epstopdf}
\pagestyle{empty}
\topmargin=-17mm
\textheight=27.5cm
@@ -27,19 +28,11 @@
\advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
}%
%----------------------------------------------------------------------------
-%%%\def\MCFstructure{%
-%%% \makebox(75,0)[t]%
-%%% {\frame{\makebox(70,35){%
-%%% \ifnum\fontnum<10\includegraphics{mcf_man_soc-00\the\fontnum}%
-%%% \else\ifnum\fontnum<100\includegraphics{mcf_man_soc-0\the\fontnum}\fi\fi}}}%
-%%% \advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
-%%%}%
-%----------------------------------------------------------------------------
\begin{document}
\noindent%
\begin{picture}(180,0)
- \put(45,12){{\LARGE Molecular Coding Format manual}\hspace{10mm}
- by Akira Yamaji 2015.7}
+ \put(35,12){{\LARGE Molecular Coding Format manual}\hspace{10mm}
+ by Akira Yamaji 2015.7.25}
\end{picture}\vspace{-6mm}\\
%----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
@@ -113,9 +106,9 @@ six membered ring
\MCFtitle{Change bond (2)}
\begin{verbatim}
Bn=bond : change bond
- dm:double,dl:double(left),dr:double(right),
- wf:wedge forward,wb:wedge backward,
- zf:wedge dotted,zb:wedge dotted backward
+ vf:vector forward, vb:vector backward,
+ tm:triple, wv:waved, bd:broad single,
+ ov:over line
^^30,!9,1=vf,2=vb,3=tm,4=dt,5=wv,
@(7~bd^-45`2,9~ov^45`2)/Me
@@ -129,7 +122,7 @@ six membered ring
\begin{verbatim}
B`length : change bond length of B
- ^^30,!3,!`1.2,!2
+ ^^30,!2,!2`1.2,!
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -140,7 +133,18 @@ B`length : change bond length of B
\begin{verbatim}
``length : change all bond length after
- ^^30,!3,``1.2,!3
+ ^^30,!2,``1.2,!2,!
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{6mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{100mm}
+\MCFtitle{Change chain length (3)}
+\begin{verbatim}
+?n`length : change ring length
+
+ ^^30,?6,3\,?6`1.2,4=??6
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -217,6 +221,18 @@ Insert hetero atom
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Fused ring (1)}
\begin{verbatim}
+?6,3=?6 : fuse ?6 at B3
+
+ ?6,3=?6
+
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{6mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{100mm}
+\MCFtitle{Fused ring (2)}
+\begin{verbatim}
?6,$(3,3,3)??6 NG
?6,$(3,9,14)??6 OK
@@ -229,7 +245,7 @@ Insert hetero atom
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
-\MCFtitle{Fused ring (2)}
+\MCFtitle{Fused ring (3)}
\begin{verbatim}
?6,$(3,3,3)?6 OK
@@ -243,7 +259,7 @@ Insert hetero atom
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
-\MCFtitle{Fused ring (3)}
+\MCFtitle{Fused ring (4)}
\begin{verbatim}
(4,11)=??6[4] : fuse 4/6 ring to B4 ..B11
(16,17)=??6[3] : fuse 3/6 ring to B16..B17
@@ -258,7 +274,7 @@ Insert hetero atom
\vspace{6mm}\\
%-----------------------------------------------------------------------------
\begin{minipage}[t][38mm]{100mm}
-\MCFtitle{Fused ring (4)}
+\MCFtitle{Fused ring (5)}
\begin{verbatim}
(20,5)=??5[3] : fuse 3/5 ring to B20..B5
(16,17)=??5[2] : fuse 2/5 ring to B16..B17
@@ -436,7 +452,7 @@ $(3)red : change color of B3 red
\end{minipage}
%%%%\MCFstructure % for Metafont
\makebox(75,0)[t]{\frame{\makebox(70,35)%
-{\includegraphics{mcf_man_soc-030.eps}}}}% for dvipdfmx
+{\includegraphics{mcf_man_soc-032.eps}}}}% for dvipdfmx
%%%%{\includegraphics[width=30mm]{mcf_man_soc-030.png}}}}% for pdfLaTeX
\advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
\vspace{6mm}\\
@@ -553,10 +569,12 @@ Insert user defined substructure
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(1) Ampicillin}
\begin{verbatim}
- ^^45,?4,2:N,2=??5,-1:S,
- @(3^45,4^-45)/*H,1://O^15,
- 5:/*COOH^-18,@(6^35,6^-35)/Me,
- 4\^75,NH,!,//O,!,NH,!,Ph
+
+ ^^45,
+ ?4,2:N,2=??5,-1:S,
+ @(3^45,4^-45)/*H,1://O^15,
+ 5:/*COOH^-18,@(6^35,6^-35)/Me,
+ 4\^75,NH,!,//O,!,NH,!,Ph
\end{verbatim}
\end{minipage}
\MCFstructure
@@ -565,10 +583,64 @@ Insert user defined substructure
\begin{minipage}[t][38mm]{100mm}
\MCFtitle{Example(2) Cholesterol}
\begin{verbatim}
- ^^30,?6,$(-4,-2)??6,-4=??5,7=dl,
- 1:*/OH,@(4,12)*/Me^60,9:*/H^60,
- 10:/*H^180,@(11,-1)/*H^-60,
- -1\^17,/*Me,!4,/Me,!,
+
+ ^^30,
+ ?6,$(-4,-2)??6,-4=??5,7=dl,
+ 1:*/OH,@(4,12)*/Me^60,9:*/H^60,
+ 10:/*H^180,@(11,-1)/*H^-60,
+ -1\^17,/*Me,!4,/Me,!,
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{6mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{100mm}
+\MCFtitle{Example(3) alfa-Tocopherol}
+\begin{verbatim}
+
+ ^^30,
+ Ph,3=??6,
+ 7:O,@(1,2,5)/Me,8:/*Me^60,6:/OH,
+ 8\,!12,@(4,8)/*Me,12:/Me
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{6mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{100mm}
+\MCFtitle{Example(4) Caffeine}
+\begin{verbatim}
+
+ ^^30,
+ ?6,-4=??5,$(3,8)dl,@(2,6,7,9)N,
+ @(2,6,9)/Me,@(1,5)//O
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{6mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{100mm}
+\MCFtitle{Example(5) Lycorine}
+\begin{verbatim}
+
+ ^^30,
+ Ph,-4=??6,-2=??6,6=??5,(9,12)=??5[3],
+ 13=dl,8:N,@(15,17)O,
+ 9:/*H^180,10:*/H^60,13:*/OH,14:/*OH
+\end{verbatim}
+\end{minipage}
+\MCFstructure
+\vspace{6mm}\\
+%-----------------------------------------------------------------------------
+\begin{minipage}[t][38mm]{100mm}
+\MCFtitle{Example(6) Gibberellin}
+\begin{verbatim}
+
+ ^^12,
+ ?6`1.3,3=??5,9=??7,12\^160`1.6,&8,
+ 4\^155~zf`-1.2,O,55,//O^180`1,&2~zb,
+ 3=dr,11=wf,13=wb,7:/COOH,11://Me,1:*/OH,
+ 12:/*OH,2:*/Me,@(3^-60,9^60)*/H
\end{verbatim}
\end{minipage}
\MCFstructure