diff options
author | Karl Berry <karl@freefriends.org> | 2020-11-03 22:17:49 +0000 |
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committer | Karl Berry <karl@freefriends.org> | 2020-11-03 22:17:49 +0000 |
commit | f843c3726969f1ad1dfd8851fa7784d1b43cdcda (patch) | |
tree | b37c8a00f19546fa70299ffda2a30f3f48566c3e /Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | |
parent | 7ca2811db642b89ee352d71791418c7113877b78 (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.tex | 146 |
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} |