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authorKarl Berry <karl@freefriends.org>2020-11-03 22:17:49 +0000
committerKarl Berry <karl@freefriends.org>2020-11-03 22:17:49 +0000
commitf843c3726969f1ad1dfd8851fa7784d1b43cdcda (patch)
treeb37c8a00f19546fa70299ffda2a30f3f48566c3e /Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
parent7ca2811db642b89ee352d71791418c7113877b78 (diff)
mcf2graph (3nov20)
git-svn-id: svn://tug.org/texlive/trunk@56846 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.tex146
1 files changed, 130 insertions, 16 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index 4664a2eea00..165b0c721f5 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 2020.08.30
+% Molecular Coding Format manual by Akira Yamaji 2020.11.03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\documentclass[a4paper,twoside]{article}
@@ -8,6 +8,8 @@
%%%%\usepackage{epstopdf}
%%%%\usepackage[dvipdfmx]{graphicx}
\usepackage[pdftex]{hyperref}
+\usepackage{makeidx}
+\makeindex
%%%%\usepackage[dvipdfmx]{hyperref}
%---------------------
\usepackage{mcf_setup}
@@ -112,9 +114,10 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Chain use !,!n}
+\index{"!}%
\begin{verbatim}
- ! : take value 60 or -60 depend on
- current angle and enviroment
+ ! : take value 60 or -60 depend on
+ current angle and environment
!6 : !,!,!,!,!,!
<-30,!,!,!,!,!,!
@@ -123,6 +126,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Jump to atom}
+\index{"@}%
\begin{verbatim}
n:@ : Jump to An
** An: atom number(-999<=n<=4095)
@@ -132,6 +136,7 @@ exact mass, molecular formula.
\MCFgraph
%------------------------------------
\subsubsection{Branch bond}
+\index{\textbackslash}%
\begin{verbatim}
3:\ : 3:@,0
@@ -140,6 +145,10 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Branch modified bond}
+\index{*\textbackslash}%
+\index{\textbackslash*}%
+\index{\textbackslash\textbackslash}%
+\index{*\textbackslash*}%
\begin{verbatim}
2:\ : 2:@,0
4:*\ : 4:@,0~wf
@@ -152,6 +161,9 @@ exact mass, molecular formula.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
+\index{\textasciicircum}% ^
+\index{\textasciitilde}% ~
+\index{`}%
\begin{verbatim}
<30,!6,
2:\~dr,!, : 2:@,0~dr,!
@@ -161,6 +173,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Connect atom}
+\index{\#}%
\begin{verbatim}
n:# : Connect to An
n1@#n2 : n1:@,n2:#
@@ -170,6 +183,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Ring}
+\index{?}%
\begin{verbatim}
?n : n membered ring(3<=n<=20)
?6 : <-120,60,60,60,60,60,1:#
@@ -178,6 +192,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Rotate current angle}
+\index{\textgreater}%
\begin{verbatim}
<angle : rotate current angle
@@ -187,6 +202,14 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsection{Change bond type}
\subsubsection{Double,triple}
+\index{\textasciitilde}%
+\index{\textasciitilde\textasciitilde}%
+\index{"!"!}%
+\index{"!"!"!}%
+\index{dm}%
+\index{dl}%
+\index{db}%
+\index{tm}%
\begin{verbatim}
a~type : ~~type,a
dm : double middle
@@ -206,6 +229,10 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Wedge}
+\index{wf}%
+\index{wb}%
+\index{zf}%
+\index{zb}%
\begin{verbatim}
wf : wedge forward / wb : wedge backward
zf : wedge dotted
@@ -220,6 +247,8 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Vector}
+\index{vf}%
+\index{vb}%
\begin{verbatim}
vf:vector forward / vb:vector backward
@@ -232,6 +261,10 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Dotted,wave}
+\index{dt}%
+\index{wv}%
+\index{bd}%
+\index{bz}%
\begin{verbatim}
Bn=bond type : change bond type at Bn
dt : dotted / wv : wave
@@ -246,6 +279,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Change multiple bond type}
+\index{vf}%
\begin{verbatim}
{2,4,6}=dr : 2=dr,4=dr,6=dr
@@ -254,6 +288,10 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Over line}
+\index{si\_}%
+\index{wf\_}%
+\index{wb\_}%
+\index{bd\_}%
\begin{verbatim}
si_ : single over line
wf_ : wedge forward over line
@@ -267,6 +305,7 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsection{Change bond length}
\subsubsection{Chain length}
+\index{`}%
\begin{verbatim}
(!,!n)`length : change length of !,!n
@@ -276,6 +315,7 @@ exact mass, molecular formula.
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
+\index{``}%
\begin{verbatim}
``length : change all bond length after
@@ -301,6 +341,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Addressed atom}
+\index{:}%
\begin{verbatim}
2:O : change A2 C to O
{3,4}:N : change A3,A4 C to N
@@ -310,6 +351,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Brock address}
+\index{\textbar}% |
\begin{verbatim}
| : divide brock
@@ -318,6 +360,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Reset brock address}
+\index{\textbar\textbar}% ||
\begin{verbatim}
|| : reset brock adress
@@ -326,6 +369,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Absolute address}
+\index{\$}% $
\begin{verbatim}
$2:N : change A$2 C to N
** $n : (1<=n<=3095)
@@ -451,6 +495,11 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Insert modified group}
+\index{//}%
+\index{*/}%
+\index{/*}%
+\index{*/*}%
+\index{**}%
\begin{verbatim}
// : double (double middle)
*/ : wedge forward
@@ -466,11 +515,15 @@ exact mass, molecular formula.
// /* */ */* **
\end{verbatim}
%-----------------------------------------------------------------------------
+\index{\textasciicircum}% ^
+\index{\textasciitilde}% ~
+\index{`}%
+\index{\textless}%
\begin{verbatim}
~ : change type
^ : change angle
` : change length
- > : change enviroment
+ > : change environment
<-30,``1,!,
/_`2^30,!2,/!2>lr,!2,/!2>rl,!)
@@ -504,9 +557,11 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsection{Chain environment}
\subsubsection{Horizontal,vertical}
+\index{hz}%
+\index{vt}%
\begin{verbatim}
- >hz : horizontal enviroment (default)
- >vt : vertical enviroment
+ >hz : horizontal environment (default)
+ >vt : vertical environment
?4,
{3^-90,3^-30,3^90}:/'(!3,"{hz}")>hz,
@@ -515,9 +570,11 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Left-right,right-left}
+\index{lr}%
+\index{rl}%
\begin{verbatim}
- >lr : left-right enviroment
- >rl : right-left enviroment
+ >lr : left-right environment
+ >rl : right-left environment
<-30,!6,
{3^-30,3,3^30}:/'(!3,"{lr}")>lr,
@@ -526,6 +583,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Fixed rotate angle}
+\index{\textgreater}%
\begin{verbatim}
>45 : rotate 45
@@ -544,10 +602,10 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsection{Miscellaneous}
%-----------------------------------------------------------------------------
-\subsubsection{Change atom and add group}
+\subsubsection{}
\begin{verbatim}
NH,SO,SOO :
- inset hetero atom and group
+ insert hetero atom and group
simultaneously
<-30,!2,NH,!,SO,!,SOO,!
@@ -556,6 +614,8 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Make block}
+\index{\textbar\textless \textgreater\textbar}% |<
+\index{\textbar= =\textbar}% |=
\begin{verbatim}
|< : start brock
>| : end brock
@@ -591,6 +651,7 @@ exact mass, molecular formula.
\section{Option parameter}
%------------------------------------------------------------------------------
\subsection{Angle parameter}
+\index{mangle}%
\begin{verbatim}
mangle=0 ** default
@@ -603,6 +664,7 @@ exact mass, molecular formula.
\subsection{Size/Ratio parameter}
%-----------------------------------------------------------------------------
\subsubsection{Bond length}
+\index{blength}%
\begin{verbatim}
(fit to font size)
blength=0 ** default
@@ -624,6 +686,7 @@ exact mass, molecular formula.
\MCFgraph
%------------------------------------------------------------------------------
\subsubsection{Molecular size}
+\index{msize}%
\begin{verbatim}
msize=(1,1) ** default
\end{verbatim}
@@ -641,6 +704,7 @@ exact mass, molecular formula.
\MCFgraph
%------------------------------------------------------------------------------
\subsubsection{Molecular position}
+\index{mposition}%
\begin{verbatim}
mposition=(0.5,0.5) ** default
\end{verbatim}
@@ -659,6 +723,7 @@ exact mass, molecular formula.
\subsection{Size parameter}
%-----------------------------------------------------------------------------
\subsubsection{Font size}
+\index{fsize}%
\begin{verbatim}
fsize=(font width,font height)
** default: (30mm,20mm)
@@ -668,6 +733,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Font margin}
+\index{fmargin}%
\begin{verbatim}
fmargin=(margin left rigth,top bottom)
** default: (0.4mm,0.4mm)
@@ -677,6 +743,7 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Offset thickness of bond}
+\index{offset\_thickness}%
\begin{verbatim}
default: offset_thickness=0.2pt
\end{verbatim}
@@ -686,7 +753,8 @@ exact mass, molecular formula.
0pt 0.2pt 0.5pt
\end{verbatim}
%-----------------------------------------------------------------------------
-\subsubsection{Offset of doublebond gap}
+\subsubsection{Offset of double bond gap}
+\index{offset\_bond\_gap}%
\begin{verbatim}
default: offset_bond_gap=0.3pt
\end{verbatim}
@@ -697,6 +765,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Offset of atom width}
+\index{offset\_atom}%
\begin{verbatim}
default: offset_atom=0.8pt
\end{verbatim}
@@ -707,6 +776,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Offset of wedge width}
+\index{offset\_wedge}%
\begin{verbatim}
default: offset_wedge=0.4pt
\end{verbatim}
@@ -717,6 +787,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Max bond length}
+\index{max\_blength}%
\begin{verbatim}
default: max_blength=10mm
\end{verbatim}
@@ -729,6 +800,7 @@ exact mass, molecular formula.
\subsection{Ratio parameter}
%-----------------------------------------------------------------------------
\subsubsection{Thickness/bond length}
+\index{ratio\_thickness\_bond}%
\begin{verbatim}
default: ratio_thickness_bond=0.015
\end{verbatim}
@@ -739,6 +811,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Char/bond thickness}
+\index{ratio\_char\_bond}%
\begin{verbatim}
default: ratio_char_bond=1.5
\end{verbatim}
@@ -748,7 +821,8 @@ exact mass, molecular formula.
1.0 1.5 2.0
\end{verbatim}
%-----------------------------------------------------------------------------
-\subsubsection{Bondgap/bond length}
+\subsubsection{Bond gap/bond length}
+\index{ratio\_bondgap\_bond}%
\begin{verbatim}
default: ratio_bondgap_bond= 0.15
\end{verbatim}
@@ -759,6 +833,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Atom/bond length}
+\index{ratio\_atom\_bond}%
\begin{verbatim}
default: ratio_atom_bond= 0.36
\end{verbatim}
@@ -769,6 +844,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Wedge/bond length}
+\index{ratio\_wedge\_bond}%
\begin{verbatim}
default: ratio_wedge_bond=0.12
\end{verbatim}
@@ -779,6 +855,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Font atom gap/atom length}
+\index{ratio\_atomgap\_atom}%
\begin{verbatim}
default: ratio_atomgap_atom= 0.050
\end{verbatim}
@@ -789,6 +866,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Chain/ring length}
+\index{ratio\_chain\_ring}%
\begin{verbatim}
default: ratio_chain_ring= 0.66
\end{verbatim}
@@ -799,6 +877,7 @@ exact mass, molecular formula.
\end{verbatim}
%-----------------------------------------------------------------------------
\subsubsection{Zebra gap/bond length}
+\index{ratio\_zebragap\_bond}%
\begin{verbatim}
default: ratio_zebragap_bond=0.12
\end{verbatim}
@@ -813,6 +892,9 @@ exact mass, molecular formula.
\subsection{Drawing mode}
%-----------------------------------------------------------------------------
\subsubsection{Numbering atom}
+\index{numberA}%
+\index{numberA\_start}%
+\index{numberA\_end}%
\begin{verbatim}
numberA_start:=3; numberA_end:=8;
default: sw_numberA=0 :
@@ -826,6 +908,9 @@ exact mass, molecular formula.
\end{picture}
%-----------------------------------------------------------------------------
\subsubsection{Numbering bond}
+\index{numberB}%
+\index{numberB\_start}%
+\index{numberB\_end}%
\begin{verbatim}
numberB_start:=3; numberB_end:=8;
default: sw_numberB=0 :
@@ -839,6 +924,7 @@ exact mass, molecular formula.
\end{picture}
%-----------------------------------------------------------------------------
\subsubsection{Trimming mode}
+\index{sw\_trimming}%
\begin{verbatim}
sw_trimming:=0; ** default
msize:=(1,0.7);
@@ -854,21 +940,24 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Expand mode}
+\index{sw\_expand}%
\begin{verbatim}
MCat(0, .5)(<30,Ph,4:/COOH,3:/NH2)
sw_expand:=1;
MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
** default: sw_expand=0
\end{verbatim}
-\MCFgraph\\
+\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Group off mode}
+\index{sw\_group\_off}%
\begin{verbatim}
** default: sw_group_off=0
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Single bond mode}
+\index{sw\_single}%
\begin{verbatim}
** default: sw_single=0
\end{verbatim}
@@ -877,6 +966,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\subsection{Frame}
%-----------------------------------------------------------------------------
\subsubsection{Font frame}
+\index{sw\_fframe}%
\begin{verbatim}
(Draw font frame)
fmargin:=(5mm,2mm);
@@ -900,12 +990,14 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Molecular frame}
+\index{sw\_mframe}%
\begin{verbatim}
sw_mframe=1 ** default:sw_mframe=0
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Atom frame}
+\index{sw\_aframe}%
\begin{verbatim}
sw_aframe=1 ** default: sw_aframe=0
MC(<30,COOH,!,COOH)
@@ -951,6 +1043,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\section{Function}
%-----------------------------------------------------------------------------
\subsection{Function MC()}
+\index{MC()}%
\begin{verbatim}
(Draw molecule)
@@ -969,6 +1062,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\MCFgraph
%-----------------------------------------------------------------------------
\subsection{Function MCat()}
+\index{MCat()}%
\begin{verbatim}
(Draw molecule at mposition)
@@ -1007,6 +1101,17 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
%===============================================================================
\newpage
\subsection{Function add()}
+\index{add()}%
+\index{plus}%
+\index{minus}%
+\index{lonepair}%
+\index{lonepairdiam}%
+\index{lonepairdiam}%
+\index{circlediam}%
+\index{circlepen}%
+\index{/*}%
+\index{**}%
+\index{\textgreater\textgreater}%
\begin{verbatim}
(Add graphic to molecule)
@@ -1114,6 +1219,7 @@ endfont
%-----------------------------------------------------------------------------
\newpage
\subsection{Function ext()}
+\index{ext()}%
\begin{verbatim}
(Extra graphic to font)
@@ -1191,6 +1297,7 @@ endfont
\end{verbatim}
\MCFgraph\MCFgraph\MCFgraph\MCFgraph
\subsubsection{Global ext() setting}
+\index{ext\_clear}%
\begin{verbatim}
ext_clear: reset global ext()
@@ -1240,10 +1347,10 @@ endfont
beginfont("EN:Colchicine","MW:385.41")
fsize:=(60mm,25mm);
MC(
- <30,Ph,{1,2,6}:/O!,|,-4=?7,
- |,-5=?7,{-1,-4,-6}=dl,
+ <30,Ph,{1,2,6}:/O!,-4=?7,
+ -5=?7,{-1,-4,-6}=dl,
-2://O,-3:/O!,
- $9:\,NH,!,//O,!
+ 9:\,NH,!,//O,!
)
endfont
\end{verbatim}
@@ -1312,6 +1419,7 @@ endfont
\onecolumn
\section{Example to use mcf2graph}
\subsection{Molecular definition file}
+\index{sw\_aux\_out}%
\begin{verbatim}
%-------------------------------------------------------------------------
input mcf2graph.mf; % input macro
@@ -1386,6 +1494,7 @@ beginfont("EN:beta-Carotene") .... endfont
tag1:="F"; tag2:="C"; tag3:="mw"; tag4:="fm"; tag5:="EN";
\end{verbatim}
\paragraph{(Output)}
+\index{aux\_delimiter}%
\begin{verbatim}
(sw_aux_out=1)
F:mcf_man_soc;C:1;mw:349.40462;fm:C16H19N3O4S;EN:Ampicillin
@@ -1427,6 +1536,7 @@ h : font height
\noindent%
\subsection{Report output}
\paragraph{(Insert option parameter setting)}
+\index{sw\_rep\_out}%
\begin{verbatim}
sw_rep_out:=1;
** default : sw_rep_out=0
@@ -1489,6 +1599,7 @@ h : font height
\noindent%
\subsection{MOL file output}
\paragraph{(Insert option parameter setting)}
+\index{sw\_mol\_out}%
\begin{verbatim}
sw_mol_out:=1; % MOL(V2000)
sw_mol_out:=2; % MOL(V3000)
@@ -1602,6 +1713,7 @@ endfont;
\newpage
\subsection{LaTeX file example}
%############################################################################
+\index{mcf\_setup.sty}%
\begin{verbatim}
%--------------------------------------------------------------------
\documentclass[a4paper]{article}
@@ -1634,4 +1746,6 @@ endfont;
\INFO{F:mcf_man_soc,C:139,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}%
\INFO{F:mcf_man_soc,C:140,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}%
%------------------------------------------------------------------------
+\printindex
+%------------------------------------------------------------------------
\end{document}