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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex274
1 files changed, 201 insertions, 73 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index 03b78cd584e..c2a73256dc8 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 2016.11.15
+% Molecular Coding Format manual by Akira Yamaji 2017.01.03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\usepackage{graphicx}
@@ -55,12 +55,6 @@
%----------------------------------------------------------------------------
\def\INFO#1{\@for\@temp:=#1\do{\mol@sel\@temp}\put@char}%
%----------------------------------------------------------------------------
-\def\figex#1#2#3#4{%
-\makebox[5mm]{}%%
-\makebox[#1]{\tt #2}%
-\makebox[#1]{\tt #3}%
-\makebox[#1]{\tt #4}}%
-%----------------------------------------------------------------------------
\begin{document}
\title{\Huge\sf Molecular Coding Format manual}
\author{Akira Yamaji}
@@ -183,10 +177,13 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
dl : double left side
dr : double right side
tm : triple
-
<30,!~dm,!~dl,!~dr,!~tm
\end{verbatim}
\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ dm dl dr tm
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Wedge}
\begin{verbatim}
@@ -198,6 +195,10 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
<30,!~wf,!,!~wb,!,!~zf,!,!~zb
\end{verbatim}
\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ wf wb zf zb
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Vector}
\begin{verbatim}
@@ -207,25 +208,35 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
<30,!~vf,!,!~vb
\end{verbatim}
\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ vf vb
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Dotted,wave}
\begin{verbatim}
Bn=bond type : change bond type at Bn
- dt : dotted
- wv : wave
+ 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
+ bd : broad / bz : broad dotted
<30,!3,1=bd,3=bz
\end{verbatim}
\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ bd bz
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Change multi bond type}
\begin{verbatim}
@@ -365,11 +376,15 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
(4,11)=?4[2] : fuse 2/4 ring to B11..B4
** ?m[n] (4<=m<=6,n=m-2)
- MCd(1,.7)( 0,0)(<30,?6,3=?6,(11,4)=?6[4])
- MCd(1,.6)(.54,1)(<30,?6,3=?6,(11,4)=?5[3])
- MCd(1,.6)( 1,0)(<30,?6,3=?6,(11,4)=?4[2])
+1:MCd(1,.7)( 0,0)(<30,?6,3=?6,(11,4)=?6[4])
+2:MCd(1,.6)(.54,1)(<30,?6,3=?6,(11,4)=?5[3])
+3:MCd(1,.6)( 1,0)(<30,?6,3=?6,(11,4)=?4[2])
\end{verbatim}
\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 1 2 3
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Attached 3 bond}
\begin{verbatim}
@@ -377,10 +392,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
(16,4)=?5[2] : fuse 2/5 ring to B16..B4
** ?m[n] (5<=m<=6,n=m-3)
- MCd(1,.55)(0,0)(?6,$(3,10)?6,(16,4)=?6[3])
- MCd(1,.55)(1,0)(?6,$(3,10)?6,(16,4)=?5[2])
+1:MCd(1,.55)(0,0)(?6,$(3,10)?6,(16,4)=?6[3])
+2:MCd(1,.55)(1,0)(?6,$(3,10)?6,(16,4)=?5[2])
\end{verbatim}
\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 1 2
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Attached 4 bond}
\begin{verbatim}
@@ -405,19 +424,19 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\subsection{Substituent}
\subsubsection{Insert substituent}
\begin{verbatim}
+ / : single
<30,!,/Me,!,/Et,!3,/Pr,!,/iPr,
!3,/tBu,!,/Ph^-30,!
- ** Me:methyl Et:ethyl
- Pr:propyl iPr:isopropyl
- tBu:tertial buthyl Ph:phenyl
+ ** Me:methyl Et:ethyl(!)
+ Pr:propyl(!2) iPr:isopropyl
+ tBu:tertial buthyl(!3) Ph:phenyl
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
\subsubsection{Insert modified substituent}
\begin{verbatim}
- / : single
- // : double
+ // : double (double middle)
*/ : wedge forward
/* : wedge dotted forward
** : direct
@@ -425,6 +444,10 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
<30,!,//O,!,/*H,!,*/H,!,/?3,!,**?3,!
\end{verbatim}
\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ // /* */ **
+\end{verbatim}
%-----------------------------------------------------------------------------
\begin{verbatim}
~ : change type
@@ -432,14 +455,14 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
` : change length
> : change enviroment
- <30,``1,!,/Me~zf`2^30,!,/Me~zf`2^30,
- !2,*/Pr>lr,!2,*/Pr>rl,!)
+ <30,``1,!,/Me~zf`2^30,
+ !2,*/!2>lr,!2,*/!2>rl,!)
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
\subsubsection{Add substituent}
\begin{verbatim}
- <-30,!17,2:/Me,4:/Et,6:/Pr,
+ <-30,!17,2:/Me,4:/!,6:/!2,
10:/iPr,14:/tBu,16:/Ph^-60
\end{verbatim}
\MCFstructure
@@ -454,10 +477,11 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\MCFstructure
%-----------------------------------------------------------------------------
\begin{verbatim}
+
^,`,> : change angle,length,environment
<30,!7`1,
- 3:/*Me`2^30,5:*/Pr>lr,7:*/Pr>rl
+ 3:/*Me`2^30,5:*/!2>lr,7:*/!2>rl
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -585,43 +609,61 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
default: margin_top_bottom=0.4mm
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0mm}{0.4mm}{5mm}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0mm 0.4mm 5mm
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Offset thickness of bond}
\begin{verbatim}
default: offset_thickness#=0.2pt#
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0pt}{0.2pt}{0.5pt}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0pt 0.2pt 0.5pt
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Offset of doublebond gap}
\begin{verbatim}
default: offset_bond_gap#=0.3pt#
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.0pt}{0.3pt}{1.0pt}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.0pt 0.3pt 1.0pt
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Offset of atom width}
\begin{verbatim}
default: offset_atom#=0.8pt#
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.0pt}{0.8pt}{2.0pt}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.0pt 0.8pt 2.0pt
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Offset of wedge width}
\begin{verbatim}
default: offset_wedge#=0.4pt#
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.0pt}{0.4pt}{1.0pt}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.0pt 0.4pt 1.0pt
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Max bond length}
\begin{verbatim}
default: max_bond_length#=10mm#
\end{verbatim}
-\MCFstructure\\
-\figex{18mm}{6mm}{8mm}{20mm}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 6mm 8mm 20mm
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsection{Ratio parameter}
%-----------------------------------------------------------------------------
@@ -629,57 +671,81 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\begin{verbatim}
default: ratio_thickness_bond=0.015
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.005}{0.015}{0.030}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.005 0.015 0.030
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Char/bond thickness}
\begin{verbatim}
default: ratio_char_bond=1.5
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{1.0}{1.5}{2.0}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 1.0 1.5 2.0
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Bondgap/bond length}
\begin{verbatim}
default: ratio_bondgap_bond= 0.15
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.10}{0.15}{0.20}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.10 0.15 0.20
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Atom/bond length}
\begin{verbatim}
default: ratio_atom_bond= 0.36
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.25}{0.36}{0.46}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.25 0.36 0.46
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Wedge/bond length}
\begin{verbatim}
default: ratio_wedge_bond=0.12
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.10}{0.12}{0.20}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.10 0.12 0.20
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Font atom gap/atom length}
\begin{verbatim}
default: ratio_atomgap_atom= 0.050
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.0}{0.050}{0.12}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.0 0.050 0.12
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Chain/ring length}
\begin{verbatim}
default: ratio_chain_ring= 0.66
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.4}{0.65}{1.0}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.4 0.65 1.0
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Zebra gap/bond length}
\begin{verbatim}
default: ratio_zebragap_bond=0.12
\end{verbatim}
-\MCFstructure\\
-\figex{20mm}{0.06}{0.12}{0.20}
+\MCFstructure
+\vspace{-3mm}%
+\begin{verbatim}
+ 0.06 0.12 0.20
+\end{verbatim}
%-----------------------------------------------------------------------------
\subsection{Drawing mode}
%-----------------------------------------------------------------------------
@@ -842,15 +908,16 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
%-----------------------------------------------------------------------------
\subsection{Function MCf()}
\begin{verbatim}
- (Draw fit to font size)
-
+ (Draw molecular fit to font size)
MCf(...) : MCd(1,1)(0.5,0.5)(...)
- beginfont()
- MCf(<30,Ph,3:/F,4:/Cl)
- endfont
+ beginfont() beginfont()
+ font_wd#:=25mm#; font_wd#:=13mm#;
+ font_ht#:=15mm#; font_ht#:=25mm#;
+ MCf(<30,Ph) MCf(<30,Ph)
+ endfont endfont
\end{verbatim}
-\MCFstructure
+\MCFstructure\hspace{12mm}\MCFstructure
%-----------------------------------------------------------------------------
\newpage
\subsection{Function EXT()}
@@ -1034,9 +1101,9 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
%-----------------------------------------------------------------------------
\subsection{Colchicine}
\begin{verbatim}
- <30,Ph,@(1,2,6)/OMe,
+ <30,Ph,@(1,2,6)/O!,
-4=?7,-5=?7,
- $(-1,-4,-6)dl,-2://O,-3:/OH,
+ $(-1,-4,-6)dl,-2://O,-3:/O!,
9\,NH,!,//O,!
\end{verbatim}
\MCFstructure
@@ -1048,7 +1115,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
13=dl,
8:N,@(15,17)O,
9:/*H^180,10:*/H^60,
- 13:*/OH,14:/*OH
+ 13:*/OH,14:/*OMe
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1065,7 +1132,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
%-----------------------------------------------------------------------------
\subsection{Quinine}
\begin{verbatim}
- <30,Ph,3=Ph,7:N,6:/OMe,
+ <30,Ph,3=Ph,7:N,6:/O!,
10\,*/OH,/H~zf^-60,!,
|,?6,2:N,1:*/H^60,
4*\,!~dr,
@@ -1087,7 +1154,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
<-60,?5,$(-3,-2,-3,-4)?6,
$(7,9,-2,-4)dl,$(3,17)dr,
@(2,13,16)O,10://O,@(11^-60,12^60)*/H,
- @(-2,-3)/OMe,1*\,/Me,!~dl
+ @(-2,-3)/O!,1*\,/Me,!~dl
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1101,9 +1168,9 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
%-----------------------------------------------------------------------------
\subsection{Validamycin}
\begin{verbatim}
- <30,?6,@(5,6)/OH,3\,-60,OH,
- #4\,O,-60,|,?6,2:O,@(3,4,5,6)/OH,
- #1\,NH,!,|,?6,2=d,@(4,5,6)/OH,-4\,!,OH
+ <30,?6,@(5,6)/OH,3:/!OH>rl,
+ #4\,O,-60,|,?6,2:O,@(3,4,5)/OH,6:/!OH,
+ #1\,NH,!,|,?6,2=dl,@(4,5,6)/OH,3:/!OH
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1298,8 +1365,69 @@ MW : molecular weight from literature data
M END
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\end{verbatim}%
-\newpage
%----------------------------------------------------------------------------
+\newpage
+\subsection{LuaTeX file example}
+%############################################################################
+\begin{verbatim}
+%--------------------------------------------------------------------
+\documentclass{article}
+\usepackage{luamplib}%
+\mplibcodeinherit{enable}%
+\mplibverbatim{enable}%
+\everymplib{if unknown Ph1:
+ input mcf2graph.mf;
+ mp_log_name:="temp-info.aux";
+ sw_auxout:=1;
+ fi}%
+%--------------------------------------------------------------------
+\begin{document}
+\noindent%
+%--------------------------------------------------------------------
+\begin{mplibcode}
+ font_wd:=50mm; font_ht:=50mm;
+ beginfont("NO:2","EN:Limonin","MW:470.51")
+ MCf(<30,
+ ?6,$(-3,-4)?6,
+ -5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf,
+ @(13,15,17,20)O,@(3,12,21)//O,
+ @(4~wf^60,8~zf^60,18^35,18^-35)/Me,
+ @(1^60,5^180,16^60)/*H,
+ 14\*,|,?5,$(1,4)dl,3:O
+ )
+ endfont
+\end{mplibcode}\\
+%--------------------------------------------------------------------
+\begin{mplibcode}
+ font_wd:=80mm; font_ht:=50mm;
+ beginfont("NO:3","EN:beta-carotene","MW:536.87")
+ MCf(<30,
+ ?6,3=dl,@(3,5^35,5^-35)/Me,
+ 4\,|,!18,$(1,3,5,7,9,11,13,15,17)dr,
+ @(3,7,12,16)/Me,
+ |,?6,6=dl,@(6,2^35,2^-35)/Me
+ )
+ endfont
+\end{mplibcode}\\
+%--------------------------------------------------------------------
+\begin{mplibcode}
+ font_wd:=50mm; font_ht:=50mm;
+ beginfont("NO:4","EN:Gibberellin A3","MW:346.37");
+ MCf(<18,?5,3=?7,5=?6[12],
+ 8*,160`1.3,&3,13=dl,6=wf,8=wb,
+ 5*,40~zf`1,O,60,//O^180,&14~zb,
+ 2:/COOH,7://Me,13:*/OH,8:/*OH,
+ 14:*/Me,@(1^60,4^60)*/H
+ )
+endfont;
+\end{mplibcode}\\
+%--------------------------------------------------------------------
+\end{document}
+%--------------------------------------------------------------------
+\end{verbatim}%
+%############################################################################
+%------------------------------------------------------------------------
+\newpage
\subsection{LaTeX file example}
%############################################################################
\begin{verbatim}
@@ -1333,14 +1461,14 @@ M END
%--------------------------------------------------------------------
\begin{document}
\unitlength=1mm%
-\INFO{F:mcf_man_soc,C:114,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:115,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:115,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:116,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
\end{document}
%--------------------------------------------------------------------
\end{verbatim}%
%############################################################################
%------------------------------------------------------------------------
-\INFO{F:mcf_man_soc,C:114,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:115,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:115,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:116,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
%------------------------------------------------------------------------
\end{document}