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author | Norbert Preining <norbert@preining.info> | 2021-02-01 03:00:47 +0000 |
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committer | Norbert Preining <norbert@preining.info> | 2021-02-01 03:00:47 +0000 |
commit | 87c74b3292e1c3efc4427ae0536a1d30a0dc8e4b (patch) | |
tree | 219447f0cb875a4889a8cac2bea6deb012b7ca7b /graphics/mcf2graph/mcf_manual.tex | |
parent | 8eab566745f1c61319c17e6a1aeea0f18bcfc34c (diff) |
CTAN sync 202102010300
Diffstat (limited to 'graphics/mcf2graph/mcf_manual.tex')
-rw-r--r-- | graphics/mcf2graph/mcf_manual.tex | 167 |
1 files changed, 119 insertions, 48 deletions
diff --git a/graphics/mcf2graph/mcf_manual.tex b/graphics/mcf2graph/mcf_manual.tex index 2573d33c6d..f8678eb716 100644 --- a/graphics/mcf2graph/mcf_manual.tex +++ b/graphics/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: |