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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex167
1 files changed, 119 insertions, 48 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index 2573d33c6d3..f8678eb7167 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
@@ -1,18 +1,14 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2021.01.03
+% Molecular Coding Format manual by Akira Yamaji 2021.01.31
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
-%%%%\documentclass[a4paper,twoside]{article}
-%%%%\usepackage{graphicx}
\usepackage[pdftex]{graphicx}
-%%%%\usepackage{epstopdf}
-%%%%\usepackage[dvipdfmx]{graphicx}
\usepackage[pdftex]{hyperref}
\usepackage{makeidx}
\makeindex
-%%%%\usepackage[dvipdfmx]{hyperref}
%---------------------
\usepackage{mcf_setup}
+%%%%\pdfpkresolution=1200
%---------------------
\hypersetup{colorlinks=true,linkcolor=blue}
\topmargin=-18mm
@@ -56,9 +52,9 @@
}%
%---------------------------------------------------------------------------
\def\put@char{%
- \begin{picture}(75,28)%
- \put(0,23){\bf [\NO]\EN}%
- \put(5,18){\small\tt FM:\fm{ }MW:\mw}%
+ \begin{picture}(75,110)%
+ \put(0,100){\bf [\NO]\EN}%
+ \put(5,95){\small\tt FM:\fm{ }MW:\mw}%
\put(5,0){\font\@strufont=\File\relax%
\hbox{\@strufont\char\Char}}%
\end{picture}%
@@ -174,6 +170,7 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsubsection{Connect atom}
\index{\#}%
+\index{"@\#}%
\begin{verbatim}
n:# : Connect to An
n1@#n2 : n1:@,n2:#
@@ -208,6 +205,7 @@ exact mass, molecular formula.
\index{"!"!"!}%
\index{dm}%
\index{dl}%
+\index{dr}%
\index{db}%
\index{tm}%
\begin{verbatim}
@@ -291,15 +289,26 @@ exact mass, molecular formula.
\index{si\_}%
\index{wf\_}%
\index{wb\_}%
+\index{zf\_}%
+\index{zb\_}%
\index{bd\_}%
+\index{dl\_}%
+\index{dr\_}%
+\index{dm\_}%
\begin{verbatim}
si_ : single over line
wf_ : wedge forward over line
wb_ : wedge backward over line
+ zf_ : wedge dotted forward over line
+ zb_ : wedge dotted backward over line
bd_ : broad over line
+ dl_ : duble left over line
+ dr_ : duble right over line
+ dm_ : duble over line
- <30,!8,!,60,90`8,
- {2~si_,4~wf_,6~wb_,8~bd_}:/_`2
+ <30,!8,!,60,90`18,
+ {2~si_,4~wf_,6~wb_,8~zf_,10~zb_,
+ 12~bd_,14~dl_,16~dr_,18~dm_}:/_`2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -311,7 +320,7 @@ exact mass, molecular formula.
<-30,!2,!2`1.2,!2
- ** !2`1.2 : '`1.2,!2
+ ** !2`1.2 : !`1.2,!`1.2
\end{verbatim}
\MCFgraph
%-----------------------------------------------------------------------------
@@ -483,6 +492,8 @@ exact mass, molecular formula.
%-----------------------------------------------------------------------------
\subsection{Group}
\subsubsection{Insert group}
+\index{/}%
+\index{Ph}%
\begin{verbatim}
/ : single
<-30,!,/_,!,/!,!3,/!2,!,/?!,
@@ -559,6 +570,7 @@ exact mass, molecular formula.
\subsubsection{Horizontal,vertical}
\index{hz}%
\index{vt}%
+\index{"'}%
\begin{verbatim}
>hz : horizontal environment (default)
>vt : vertical environment
@@ -605,7 +617,11 @@ exact mass, molecular formula.
\subsection{Miscellaneous}
%-----------------------------------------------------------------------------
\subsubsection{Abbreviated parts}
-\index{N!}%
+\index{NH}%
+\index{N"!}%
+\index{N"!2}%
+\index{SO}%
+\index{SOO}%
\begin{verbatim}
NH : N,/H~nl
N! : N,/_
@@ -616,8 +632,10 @@ exact mass, molecular formula.
<-30,!2,NH,!2,N!,!2,N!2,SO,!2,SOO,!
\end{verbatim}
\MCFgraph
-\index{?!}%
+\index{?"!}%
\index{??}%
+\index{??"!}%
+\index{N?"!}%
\begin{verbatim}
?! : /_,!
?? : /_^35,/_-35
@@ -631,7 +649,8 @@ exact mass, molecular formula.
\MCFgraph
%-----------------------------------------------------------------------------
\subsubsection{Make block}
-\index{\textbar= =\textbar}% |=
+\index{\textbar=}% |=
+\index{=\textbar}% =|
\begin{verbatim}
|= : start brock / bond length=n
=| : end brock
@@ -1018,6 +1037,8 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
%-----------------------------------------------------------------------------
\subsection{Parameter setting}
\subsubsection{Local parameter setting}
+\index{beginfont()}%
+\index{endfont}%
\begin{verbatim}
beginfont()
MC(Ph)
@@ -1117,12 +1138,37 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2)
\index{minus}%
\index{lonepair}%
\index{lonepairdiam}%
-\index{lonepairdiam}%
+\index{lonepairspace}%
\index{circlediam}%
\index{circlepen}%
+\index{w}%
+\index{h}%
+\index{aw}%
+\index{em}%
+\index{p0}%
+\index{l}%
\index{/*}%
\index{**}%
\index{\textgreater\textgreater}%
+\index{An}%
+\index{A[]}%
+\index{A[]ang}%
+\index{A[]up}%
+\index{A[]left}%
+\index{A[]right}%
+\index{A[]down}%
+\index{Bn}%
+\index{B[]}%
+\index{B[]s}%
+\index{B[]m}%
+\index{B[]e}%
+\index{B[]ang}%
+\index{B[]up}%
+\index{B[]left}%
+\index{B[]right}%
+\index{B[]down}%
+\index{defaultscale}%
+\index{labeloffset}%
\begin{verbatim}
(Add graphic to molecule)
@@ -1231,6 +1277,13 @@ endfont
\newpage
\subsection{Function ext()}
\index{ext()}%
+\index{w0}%
+\index{h0}%
+\index{aw}%
+\index{em}%
+\index{n}%
+\index{ratio\_thickness\_char}%
+\index{defaultscale}%
\begin{verbatim}
(Extra graphic to font)
@@ -1429,7 +1482,10 @@ endfont
\onecolumn
\section{Example to use mcf2graph}
\subsection{Molecular definition file}
+\index{mcf2graph.mf}%
\index{sw\_aux\_out}%
+\index{tag}%
+\index{var}%
\begin{verbatim}
%-------------------------------------------------------------------------
input mcf2graph.mf; % input macro
@@ -1481,6 +1537,20 @@ bye
\newpage
\subsection{Information auxfile output}
\paragraph{(Insert option parameter setting)}
+\index{F}%
+\index{C}%
+\index{NO}%
+\index{MW}%
+\index{MI}%
+\index{EN}%
+\index{JN}%
+\index{FM}%
+\index{USE}%
+\index{mw}%
+\index{fm}%
+\index{mi}%
+\index{w}%
+\index{h}%
\begin{verbatim}
sw_aux_out=1 : tag1:var1;tag2:var2
sw_aux_out=2 : tag1;tag2 var1;var2
@@ -1533,6 +1603,7 @@ EN : english name
JN : japanese name
FM : formula from literature data
MW : molecular weight from literature data
+MI : monoisotopic mass from literature data
USE : the use
mw : molecular weight calculated
mi : monoisotopic mass calculated
@@ -1558,46 +1629,46 @@ h : font height
\begin{verbatim}
------------------------------------------------------------------
Molecular name = Nicotine
- Warnings = 0 / Command count= 40
+ Warnings = 0 / Command count= 44
Width * Height = 49.57332 * 41.37605
Shift width * height = 0 * -9.07253
Bond length = 12.75589 Atom size = 5.38914
Atom count= 12 Bond count= 13 Ring count= 2 Hide H count= 14
------------------------------------------------------------------
-< NO. >( x axis , y axis )< atom >< bond >< hide_H >
- A1 ( 0 , 0 ) C 3 1
- A2 ( 0.866 , -0.5 ) N 3
- A3 ( 1.732 , 0 ) C 3 1
- A4 ( 1.732 , 1 ) C 4
- A5 ( 0.866 , 1.5 ) C 3 1
- A6 ( 0 , 1 ) C 3 1
- A7 ( 2.304 , 1.33 ) C 3 1
- A8 ( 3.217 , 0.923 ) N 3
- A9 ( 3.886 , 1.666 ) C 2 2
- A10 ( 3.386 , 2.532 ) C 2 2
- A11 ( 2.408 , 2.325 ) C 2 2
- A12 ( 3.399 , 0.067 ) C 1 3
+< NO. ><atom(s) >( x axis , y axis )<bond><hideH><chg>
+ A1 C ( 0 , 0 ) 3 1
+ A2 N ( 0.866 , -0.5 ) 3
+ A3 C ( 1.732 , 0 ) 3 1
+ A4 C ( 1.732 , 1 ) 4
+ A5 C ( 0.866 , 1.5 ) 3 1
+ A6 C ( 0 , 1 ) 3 1
+ A7 C ( 2.304 , 1.33 ) 3 1
+ A8 N ( 3.217 , 0.923 ) 3
+ A9 C ( 3.886 , 1.666 ) 2 2
+ A10 C ( 3.386 , 2.532 ) 2 2
+ A11 C ( 2.408 , 2.325 ) 2 2
+ A12 C ( 3.399 , 0.067 ) 1 3
------------------------------------------------------------------
-< NO. >< bond (sdt)><angle + ( +- )><length ( pt )>
- B1 1 -> 2 ( 2) 330 ( -30) 1 ( 12.76)
- B2 2 -> 3 ( 1) 30 ( 30) 1 ( 12.76)
- B3 3 -> 4 ( 2) 90 ( 90) 1 ( 12.76)
- B4 4 -> 5 ( 1) 150 ( 150) 1 ( 12.76)
- B5 5 -> 6 ( 2) 210 ( -150) 1 ( 12.76)
- B6 6 -> 1 ( 1) 270 ( -90) 1 ( 12.76)
- B7 4 -> 7 ( 1) 30 ( 30) 0.66 ( 8.42)
- B8 7 -> 8 ( 1) 336 ( -24) 1 ( 12.76)
- B9 8 -> 9 ( 1) 48 ( 48) 1 ( 12.76)
- B10 9 -> 10 ( 1) 120 ( 120) 1 ( 12.76)
- B11 10 -> 11 ( 1) 192 ( -168) 1 ( 12.76)
- B12 11 -> 7 ( 1) 264 ( -96) 1 ( 12.76)
- B13 8 -> 12 ( 1) 282 ( -78) 0.66 ( 8.42)
+< NO. >< bond (sdt)><angle +( +- )><length ( pt )>
+ B1 1 -> 2 ( 2) 330 ( -30) 1 ( 12.76)
+ B2 2 -> 3 ( 1) 30 ( 30) 1 ( 12.76)
+ B3 3 -> 4 ( 2) 90 ( 90) 1 ( 12.76)
+ B4 4 -> 5 ( 1) 150 ( 150) 1 ( 12.76)
+ B5 5 -> 6 ( 2) 210 ( -150) 1 ( 12.76)
+ B6 6 -> 1 ( 1) 270 ( -90) 1 ( 12.76)
+ B7 4 -> 7 ( 1) 30 ( 30) 0.66 ( 8.42)
+ B8 7 -> 8 ( 1) 336 ( -24) 1 ( 12.76)
+ B9 8 -> 9 ( 1) 48 ( 48) 1 ( 12.76)
+ B10 9 -> 10 ( 1) 120 ( 120) 1 ( 12.76)
+ B11 10 -> 11 ( 1) 192 ( -168) 1 ( 12.76)
+ B12 11 -> 7 ( 1) 264 ( -96) 1 ( 12.76)
+ B13 8 -> 12 ( 1) 282 ( -78) 0.66 ( 8.42)
------------------------------------------------------------------
<atom>( atom wt )[ mi wt ] < cnt > < sum wt >[ sum mi wt ]
- C ( 12.0107)[ 12] * 10 = 120.10696[ 120]
- H ( 1.00793)[ 1.00783] * 14 = 14.11108[ 14.10959]
- N ( 14.0067)[ 14.00307] * 2 = 28.0134[ 28.00613]
- Molecular Weight [Mono Isotopic] = 162.2314[ 162.11572]
+ C ( 12.0107)[ 12] * 10 120.10696[ 120]
+ H ( 1.00793)[ 1.00783] * 14 14.11108[ 14.10959]
+ N ( 14.0067)[ 14.00307] * 2 28.0134[ 28.00613]
+ Molecular Weight [Mono Isotopic] = 162.2314[ 162.11572]
------------------------------------------------------------------
Weight Calc: 162.2314 / Input: 162.23 / weight gap= 0.00145
Fomula Calc: C10H14N2 / Input: