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authorKarl Berry <karl@freefriends.org>2018-06-03 21:16:34 +0000
committerKarl Berry <karl@freefriends.org>2018-06-03 21:16:34 +0000
commit318121054ebb87dd1e2d6759d77c51847b6e2ce1 (patch)
tree44e91e79f0159b7f5de1b60fdebdbef599c27ca3 /Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
parent5c227fc8809abf53bc5c149d0cf083f8025d08d9 (diff)
mcf2graph (3jun18)
git-svn-id: svn://tug.org/texlive/trunk@47911 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.tex62
1 files changed, 29 insertions, 33 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index d5e694c8ca4..f39d7cbf80c 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 2018.04.16
+% Molecular Coding Format manual by Akira Yamaji 2018.06.03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\documentclass[a4paper,twoside]{article}
@@ -85,7 +85,6 @@
\linethickness{0.08mm}%
%----------------------------------------------------------------------------
\newpage
-\setcounter{page}{1}
\section{Introduction}
Molecular Coding Format(MCF) is new linear notation
represent chemical structure diagrams.
@@ -93,7 +92,7 @@ This 'Coding' is named from coding(programing) technique
like adressing,grouping,macro,etc.
There are no Meta language commands in MCF.
mcf2graph convert MCF file to graphics file
-pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
+pk font,PNG,SVG,EPS or MDL MOL file.\\
%-----------------------------------------------------------------------------
\section{MCF syntax}
\subsection{Make bond}
@@ -227,28 +226,17 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
Bn=bond type : change bond type at Bn
dt : dotted / wv : wave
-
- <30,!3,1=dt,3=wv
-\end{verbatim}
-\MCFstructure
-\vspace{-3mm}%
-\begin{verbatim}
- dt wv
-\end{verbatim}
-%-----------------------------------------------------------------------------
-\subsubsection{Broad}
-\begin{verbatim}
bd : broad / bz : broad dotted
- <30,!3,1=bd,3=bz
+ <30,!7,1=dt,3=wv,5=bd,7=bz
\end{verbatim}
\MCFstructure
\vspace{-3mm}%
\begin{verbatim}
- bd bz
+ dt wv bd bz
\end{verbatim}
%-----------------------------------------------------------------------------
-\subsubsection{Change multi bond type}
+\subsubsection{Change multiple bond type}
\begin{verbatim}
{2,4,6}=dr : 2=dr,4=dr,6=dr
@@ -294,7 +282,6 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\newpage
\subsection{Change atom}
\subsubsection{Insert atom}
\begin{verbatim}
@@ -307,9 +294,9 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\subsubsection{Addressed atom}
\begin{verbatim}
2:O : change A2 C to O
- {3,5}:N : change A3,A5 C to N
+ {3,4}:N : change A3,A4 C to N
- <30,!6,2:O,{3,5}:N
+ <30,!4,2:O,{3,4}:N
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -346,6 +333,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
+\subsubsection{Charged atom}
+\begin{verbatim}
+ N[1]:N+ / O[-1]:O-
+
+ <-30,!2,N[1],!2,O[-1]
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
\subsection{Fuse ring}
\subsubsection{Attached 1 bond}
\begin{verbatim}
@@ -1053,6 +1048,8 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
p[m]: molecular origin position
w[m]: molecular width
h[m]: molecular height
+ ratio_thickness_char:
+ pen thickness / char width
%----------------------------------------
beginfont()
@@ -1064,17 +1061,13 @@ beginfont()
MCd(1,1)(0.1,0.5)
(<-210,60`1,60`1,60`1,{1,3}=dl,
1:/R1,4:/R2^-60)
- ext(
- defaultscale:=0.6;
- label.bot("Diene",p0+(0.5w,0));
- )
+ ext(defaultscale:=0.6;
+ label.bot("Diene",p0+(0.5w,0));)
%---------------------------------------
MCd(1,1)(0.4,0.5)
(<-30,-60`1,1=dl,1:/R3,2:/R4^60)
- ext(
- defaultscale:=0.6;
- label.bot("Dienophile",p0+(0.5w,0));
- )
+ ext(defaultscale:=0.6;
+ label.bot("Dienophile",p0+(0.5w,0));)
%---------------------------------------
MCd(1,1)(0.9,0.5)
(<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1)
@@ -1083,6 +1076,7 @@ beginfont()
drawarrow (0.52w,0.5h)..(0.6w,0.5h);
defaultscale:=0.7;
label("+",(0.25w,0.5h));
+ ratio_thickness_char:=0.125;
label.bot("Diels-Alder Reaction",
(0.5w,h));
)
@@ -1245,7 +1239,7 @@ drawarrow & drawdblarrow:
13=dl,6=wf,8=wb,
5:@,40~zf`1,O,60,//O^180,14~zb:&,
2:/COOH,7://_,13:*/OH,8:/*OH,
- 14:*/_,{1^60,4^60}:*/H
+ 14:*/_,{1,4}:*/H^60
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1494,15 +1488,17 @@ cFM : molecular formula calculated
\newpage
%------------------------------------------------------------------------
\noindent%
-\subsection{Molfile output}
+\subsection{MOL file output}
\paragraph{(Insert option parameter setting)}
\begin{verbatim}
- sw_MOLout:=1;
- ** default : sw_MOLout=0
+ sw_mol_out:=1; (V2000)
+ sw_mol_out:=2; (V3000)
+ ** default : sw_mol_out=0
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
- >mpost -s ahangle=3 FILENAME (molecular definition file)
+ >mpost -s ahangle=3 FILENAME (molecular definition file) V2000
+ >mpost -s ahangle=4 FILENAME (molecular definition file) V3000
\end{verbatim}
\paragraph{(Output)}
\begin{verbatim}