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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG7
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/README2
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf3
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdfbin246546 -> 246561 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf118
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdfbin425268 -> 433700 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex197
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdfbin122137 -> 122138 bytes
-rw-r--r--Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf258
9 files changed, 380 insertions, 205 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
index 446920fa3c9..b4cbb0de331 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
@@ -1,6 +1,11 @@
*******************************************************************************
- Changelog of mcf2graph software package by Akira Yamaji 2016-10-23
+ Changelog of mcf2graph software package by Akira Yamaji 2016-10-30
*******************************************************************************
+[ver. 4.02 / 2016-10-30]
+ -add finction EXT(),ext()
+ -delete option parameter sw_start_vector
+ -update MCF syntax manual
+
[ver. 4.01 / 2016-10-23]
-many fixes for robustness
-update MCF syntax manual
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README
index 7c064a1881c..b144de7a905 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/README
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/README
@@ -1,7 +1,7 @@
********************************************************************************
mcf2graph : Convert Molecular Coding Format to graphics with METAFONT/METAPOST
Author : Akira Yamaji
- version : 4.01 2016-10-23
+ version : 4.02 2016-10-30
E-mail : mcf2graph@gmail.com
Located at : http://www.ctan.org/pkg/mcf2graph
********************************************************************************
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
index a226e61c5d9..bbf4929b2e4 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2016.10.19
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %%% it must be version 4.00 or later
+input mcf2graph.mf; %%% it must be version 4.02 or later
%-------------------------------------------------------------------------
font_wd#:=33mm#;
font_ht#:=24mm#;
@@ -9,7 +9,6 @@ font_ht#:=24mm#;
sw_auxout:=1;
sw_font_frame:=0;
sw_atom_frame:=0;
-sw_start_vector:=0;
%%%% sw_expand:=1;
var3:="cal_FM"; tag3:="cFM";
var4:="cal_MW"; tag4:="cMW";
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf
index e1842b93b60..6dcbe03b339 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf
Binary files differ
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
index 70380700644..8e32a79bc39 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
@@ -1,12 +1,11 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2016.10.19
+% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2016.10.30
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %% it must be version 4.00 or later
+input mcf2graph.mf; %% it must be version 4.02 or later
%------------------------------------------------------------------------
sw_auxout:=0;
sw_mol_frame:=0;
sw_expand:=0;
-sw_start_vector:=0;
sw_solid:=2;
%%%%%sw_checklist:=1;
%***********************************************************************
@@ -690,17 +689,25 @@ beginfont("EN:Switwch numberingB")
sw_numberB:=3; MCd(1,1)(.5,.1)(<30,!9)
endfont
%***********************************************************************
-beginfont("EN:Switwch Solid ratio")
- font_wd#:=70mm#;
- font_ht#:=20mm#;
+beginfont("EN:Switwch Solid ratio=0")
+ font_ht#:=18mm#;
+ bond_len#:=8mm#;
+ MCf(<30,Ph)
+endfont
+%-----------------------------------------------------------------------
+beginfont("EN:Switwch Solid ratio=1")
+ font_ht#:=18mm#;
bond_len#:=8mm#;
- MCd(1,1)(0,.5)(Ph)
sw_solid:=1;
ratio_bond_width:=0.1;
- MCd(1,1)(.55,.5)(Ph)
+ MCf(<30,Ph)
+endfont
+%-----------------------------------------------------------------------
+beginfont("EN:Switwch Solid ratio=2")
+ font_ht#:=18mm#;
+ bond_len#:=10mm#;
sw_solid:=2;
- bond_len#:=6mm#;
- MCd(1,1)(1,.5)(Ph)
+ MCf(<30,Ph)
endfont
%***********************************************************************
beginfont("EN:Switwch Expand")
@@ -724,14 +731,28 @@ beginfont("EN:Switwch bondtype off")
MCd(1,1)(.85, .5)(<30,Ph,4:/Cl,3:/F)
endfont
%***********************************************************************
-beginfont("EN:Switwch start vector")
+beginfont("EN:Switwch font frame 0")
+ font_ht#:=15mm#;
+ margin_left_right:=5mm;
+ margin_top_bottom:=2mm;
+ sw_font_frame:=0;
+ MCf(<30,Ph,4:/Cl,3:/F)
+endfont
+beginfont("EN:Switwch font frame 1")
font_ht#:=15mm#;
- MCd(1,1)(.1, .5)(<30,Ph,4:/Cl,3:/F)
- sw_start_vector:=1;
- MCd(1,1)(.9, .5)(<30,Ph,4:/Cl,3:/F)
+ margin_left_right:=5mm;
+ margin_top_bottom:=2mm;
+ sw_font_frame:=1;
+ MCf(<30,Ph,4:/Cl,3:/F)
endfont
-%***********************************************************************
-beginfont("EN:Switwch font frame")
+beginfont("EN:Switwch font frame 2")
+ font_ht#:=15mm#;
+ margin_left_right:=5mm;
+ margin_top_bottom:=2mm;
+ sw_font_frame:=2;
+ MCf(<30,Ph,4:/Cl,3:/F)
+endfont
+beginfont("EN:Switwch font frame 3")
font_ht#:=15mm#;
margin_left_right:=5mm;
margin_top_bottom:=2mm;
@@ -756,6 +777,7 @@ beginfont("EN:Switwch clipping")
sw_mol_frame:=1;
MCf(<30,Ph,4:/Cl,3:/F)
endfont
+%-----------------------------------------------------------------------
beginfont("EN:Switwch clipping")
font_ht#:=15mm#;
sw_mol_frame:=1;
@@ -779,22 +801,62 @@ beginfont("EN:MCf()")
MCf(<30,Ph,4:/Cl,3:/F)
endfont
%***********************************************************************
-beginfont("EN:Local setting")
- font_ht#:=15mm#;
- MCd(1,1)(0.0,0.5)(Ph)
- ratio_thickness_bond:=0.05;
- MCd(1,1)(0.5,0.5)(Ph)
- ratio_thickness_bond:=0.015;
- MCd(1,1)(1.0,0.5)(Ph)
+beginfont("EN:EXT()")
+ sw_solid:=1;
+ font_ht#:=26mm#;
+ bond_len#:=8mm#;
+ sw_mol_frame:=1;
+ MCd(1,1)(0,0.5)(<30,Ph,2:/OH,5:/OH)
+ MCd(1,1)(1,0.5)(<30,?6,$(3,6)dl,@(2,5)//O)
+ EXT(draw ((0,0)--(26mm,0)--(22mm,2mm)) shifted (0.3w,0.5h);
+ drawdot p1 withpen pencircle scaled 2mm;
+ drawdot p2 withpen pensquare scaled 2mm;)
endfont
%***********************************************************************
-beginfont("EN:Global setting")
- font_ht#:=15mm#;
+beginfont("EN:ext()")
+ font_wd#:=60mm#;
+ font_ht#:=20mm#;
+ bond_len#:=10mm#;
+ MCf(<30,Ph,4:/Cl,3:/F)
+ ext(draw p0--(p0+(wd,0))--(p0+(wd,ht));
+ draw_vector(p6,a6-180,8mm);)
+endfont
+%***********************************************************************
+beginfont("EN:Local setting 1")
+ font_wd#:=15mm#;
+ font_ht#:=12mm#;
+ MCf(Ph)
+endfont
+beginfont("EN:Local setting 2")
+ font_wd#:=15mm#;
+ font_ht#:=12mm#;
ratio_thickness_bond:=0.05;
- MCd(1,1)(0.0,0.5)(Ph)
- MCd(1,1)(0.5,0.5)(Ph)
- MCd(1,1)(1.0,0.5)(Ph)
+ MCf(Ph)
+endfont
+beginfont("EN:Local setting 3")
+ font_wd#:=15mm#;
+ font_ht#:=12mm#;
+ MCf(Ph)
+endfont
+%***********************************************************************
+save_ratio:=ratio_thickness_bond;
+ratio_thickness_bond:=0.05;
+beginfont("EN:Local setting 1")
+ font_wd#:=15mm#;
+ font_ht#:=12mm#;
+ MCf(Ph)
+endfont
+beginfont("EN:Local setting 2")
+ font_wd#:=15mm#;
+ font_ht#:=12mm#;
+ MCf(Ph)
+endfont
+beginfont("EN:Local setting 3")
+ font_wd#:=15mm#;
+ font_ht#:=12mm#;
+ MCf(Ph)
endfont
+ratio_thickness_bond:=save_ratio;
%***********************************************************************
sw_clip:=1;
%% Output molecular infomation
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf
index 7f52968e2da..2275403c8c1 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf
Binary files differ
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
index f3fc19b2fee..ee720dc7eca 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 2016.10.23
+% Molecular Coding Format manual by Akira Yamaji 2016.10.30
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\usepackage{graphicx}
@@ -711,21 +711,26 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
%-----------------------------------------------------------------------------
\subsubsection{Solid mode}
\begin{verbatim}
- sw_solid=1 :
+ (sw_solid=0 : fit to font size)
+ ** default
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------
+\begin{verbatim}
+ (sw_solid=1 : solid ratio bond/font width)
ratio_bond_width=0.1
- font_width=70mm
- (bond_len#=70mm*0.1=7mm)
+ font_width=60mm
+ (bond_len#=60mm#*0.1=6mm#)
** ignore bond_len#
-
- sw_solid=2 :
- bond_len#=6mm#
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------
+\begin{verbatim}
+ (sw_solid=2 : solid bond length)
+ bond_len#=10mm#
** ignore ratio_bond_width
\end{verbatim}
-\MCFstructure\\
-\makebox[5mm]{}%
-\makebox[25mm]{\tt 0 :default}%
-\makebox[25mm]{\tt 1}%
-\makebox[20mm]{\tt 2}%
+\MCFstructure
%-----------------------------------------------------------------------------
\subsubsection{Expand mode}
\begin{verbatim}
@@ -754,27 +759,33 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\makebox[30mm]{\tt 0 :default}%
\makebox[30mm]{\tt 1}%
%-----------------------------------------------------------------------------
-\subsection{Frame,vector}
-%-----------------------------------------------------------------------------
-\subsubsection{Start vector}
-\begin{verbatim}
- default: sw_start_vector=0
-\end{verbatim}
-\MCFstructure\\
-\makebox[5mm]{}%
-\makebox[30mm]{\tt 0 :default}%
-\makebox[30mm]{\tt 1}%
+\newpage
+\subsection{Frame}
%-----------------------------------------------------------------------------
\subsubsection{Font frame}
\begin{verbatim}
- sw_font_frame=0 : no frame **default
- sw_font_frame=1 : draw frame of font
- sw_font_frame=2 : draw frame inside margin
- sw_font_frame=3 : draw both
-
- sw_font_frame:=3;
+ (No font frame)
margin_left_right:=5mm;
margin_top_bottom:=2mm;
+ sw_font_frame:=0; ** default
+ MCf(<30,Ph,4:/Cl,3:/F)
+\end{verbatim}
+\MCFstructure
+\begin{verbatim}
+ (Draw font frame)
+ sw_font_frame:=1;
+ MCf(<30,Ph,4:/Cl,3:/F)
+\end{verbatim}
+\MCFstructure
+\begin{verbatim}
+ (Draw frame inside margin)
+ sw_font_frame:=2;
+ MCf(<30,Ph,4:/Cl,3:/F)
+\end{verbatim}
+\MCFstructure
+\begin{verbatim}
+ (Draw both frame)
+ sw_font_frame:=3;
MCf(<30,Ph,4:/Cl,3:/F)
\end{verbatim}
\MCFstructure
@@ -798,44 +809,105 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\subsection{Clipping font}
\begin{verbatim}
beginfont()
- sw_clip:=0;
- MCf(<30,Ph,4:/Cl,3:/F) endfont
+ sw_clip:=0;
+ MCf(<30,Ph,4:/Cl,3:/F)
+ endfont
** default: sw_clip=0
\end{verbatim}
\MCFstructure
\begin{verbatim}
beginfont()
- sw_clip:=1;
- MCf(<30,Ph,4:/Cl,3:/F) endfont
+ sw_clip:=1;
+ MCf(<30,Ph,4:/Cl,3:/F)
+ endfont
\end{verbatim}
\MCFstructure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\newpage
-\section{MCF draw function}
-\subsection{Function MCd (draw)}
+\section{Function}
+\subsection{Function MCd()}
\begin{verbatim}
+ (Draw molecular structure)
+
MCd(a,b)(c,d)(...)
a: ratio molecular width/font width
b: ratio molecular hight/font hight
c: x axis position
d: y axis position
- MCd(1,0.8)(0.2,0.9)(<30,Ph,3:/F,4:/Cl)
- MCd(1,0.8)(0.8,0.1)(<30,Ph,3:/F,4:/Cl)
+ beginfont()
+ MCd(1,0.8)(0.2,0.9)(<30,Ph,3:/F,4:/Cl)
+ MCd(1,0.8)(0.8,0.1)(<30,Ph,3:/F,4:/Cl)
+ endfont
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Function MCf (fit draw)}
+\subsection{Function MCf()}
\begin{verbatim}
+ (Draw fit to font size)
+
MCf(...) : MCd(1,1)(0.5,0.5)(...)
- sw_font_frame:=1;
+ beginfont()
+ MCf(<30,Ph,3:/F,4:/Cl)
+ endfont
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\newpage
+\subsection{Function EXT()}
+\begin{verbatim}
+ (Extra graphic to font)
+
+ w: font width
+ h: font height
+ wd: font width-margin_left_right*2
+ ht: font height-margin_top_bottom*2
+ p0: x=margin_left_right
+ y=margin_top_bottom
+ n: molecular number
+ p[m]: molecular origin position
+ (1<=m<=molecular count)
+
+ beginfont()
sw_mol_frame:=1;
- MCf(<30,Ph,3:/F,4:/Cl)
+ MCd(1,1)(0,0.5)(<30,Ph,2:/OH,5:/OH)
+ MCd(1,1)(1,0.5)
+ (<30,?6,$(3,6)dl,@(2,5)//O)
+ EXT(
+ draw ((0,0)--(26mm,0)--(22mm,2mm))
+ shifted (0.3w,0.5h);
+ drawdot p1 withpen pencircle scaled 2mm;
+ drawdot p2 withpen pensquare scaled 2mm;
+ )
+ endfont
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\subsection{Function ext()}
+\begin{verbatim}
+ (Extra graphic to molecule)
+
+ wd: molecular width
+ ht: molecular height
+ p0: origin of molecular structure
+ n: atom number
+ p[m]: atom position of A[m]
+ a[m]: branch angle of A[m]
+ (1<=m<=atom count)
+ draw_vector(pos,ang,len) :
+ pos:position ang:angle len:length
+
+ beginfont()
+ MCf(<30,Ph,3:/F,4:/Cl)
+ ext(draw p0--(p0+(wd,0))
+ --(p0+(wd,ht);
+ draw_vector(p6,a6-180,8mm);
+ )
+ endfont
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Local setting}
+\subsection{Local parameter setting}
\begin{verbatim}
beginfont() MCf(Ph) endfont
beginfont()
@@ -844,16 +916,18 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
endfont
beginfont() MCf(Ph) endfont
\end{verbatim}
-\MCFstructure
+\MCFstructure\MCFstructure\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Global setting}
+\subsection{Global parameter setting}
\begin{verbatim}
ratio_thickness_bond:=0.05;
beginfont() MCf(Ph) endfont
beginfont() MCf(Ph) endfont
beginfont() MCf(Ph) endfont
\end{verbatim}
-\MCFstructure
+\MCFstructure\MCFstructure\MCFstructure
+%-----------------------------------------------------------------------------
+\section{Output infomation}
%-----------------------------------------------------------------------------
\subsection{Output molecular information}
\begin{verbatim}
@@ -870,10 +944,14 @@ cFM:calculated molecular formula
\subsection{Output additional information}
\begin{verbatim}
beginfont("EN:Tocopherol","CAS:59-02-9")
- MCf(...) endfont
+ MCf(<30,Ph,3=?6,
+ 7:O,@(1,2,5)/Me,8:/*Me^60,6:/OH,
+ 8\,|,!12,@(4,8)/*Me,12:/Me)
+endfont
%% Output to mcf_man_soc-info.aux %%
F:mcf_man_soc;C:86;EN:Tocopherol;CAS:59-02-9
+............................................
*F:filename *C:char number EN:molecular name
CAS:CAS number *:default output
@@ -884,10 +962,19 @@ CAS:CAS number *:default output
\begin{verbatim}
aux_delimiter:="/";
beginfont("EN:Ampicillin","CAS:69-53-4")
- MCf(...) endfont
+ MCf(<45,?4,2:N,2=?5,-1:S,
+ @(3^45,4^-45)/*H,1://O^15,
+ 5:/*COOH^-18,@(6^35,6^-35)/Me,
+ 4*\^75,NH,!,//O,!,/*NH2,!,Ph)
+endfont
+beginfont(......)
+ ...........
+endfont
+..............
%% Output to mcf_man_soc-info.aux %%
F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
+............................................
**default aux_delimiter=";"
\end{verbatim}
@@ -899,11 +986,21 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
tag4:="EN"; var4:="inf_EN";
sw_auxfix:=1; auxtag_out;
beginfont("EN:Cholesterol","NO:1")
- ..... endfont
+ MCf(<30,?6,$(-4,-2)?6,-4=?5,7=dl,
+ 1:*/OH,@(4,12)*/Me^60,9:*/H^60,
+ 10:/*H^180,11:/*H^-60,17:/*H^-54,
+ -1\^18,/*Me,-60,!3,/Me,!)
+ endfont
+ beginfont(......)
+ ...........
+ endfont
+ ..............
%% Output to mcf_man_soc-info.aux %%
F;C;NO;EN
mcf_man_soc;91;1;Ampicillin
+ ...........................
+
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
@@ -1203,7 +1300,7 @@ M END
\end{verbatim}%
\newpage
%----------------------------------------------------------------------------
-\subsection{\LaTeX file example}
+\subsection{LaTeX file example}
%############################################################################
\begin{verbatim}
%--------------------------------------------------------------------
@@ -1243,7 +1340,7 @@ M END
\end{verbatim}%
%############################################################################
%------------------------------------------------------------------------
-\INFO{F:mcf_man_soc,C:103,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
-\INFO{F:mcf_man_soc,C:104,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+\INFO{F:mcf_man_soc,C:113,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:114,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
%------------------------------------------------------------------------
\end{document}
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf
index c7ab56140a7..8d127fc8104 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf
Binary files differ
diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
index b3461a03db1..60b82397391 100644
--- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
+++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% mcf2graph ver 4.01 Copyright (c) 2013-2016 Akira Yamaji
+% mcf2graph ver 4.02 Copyright (c) 2013-2016 Akira Yamaji
%
% Permission is hereby granted, free of charge, to any person obtaining a copy of this software
% and associated documentation files (the "Software"), to deal in the Software without restriction,
@@ -32,17 +32,17 @@
tracingstats:=1;
message " This is mcf2graph ver 4.0 2016.10";
%-------------------------------------------------------------------------------------------------
-newinternal nA,nB,nC,nD,nE,nF,cntA,cntB,cntP,minX,minY,def_num,def_int,tbl_cnt;
-pair posB[],posA[];
-numeric lineB[],sB[],eB[],angB[],angA[],strA[],str_wd[],lenB[],ang_br[],stock_para[],
+newinternal nA,nB,nC,nD,nE,nF,cntA,cntB,cntM,minX,minY,def_num,def_int,tbl_cnt;
+pair posB[],posA[],posM[];
+numeric lineB[],sB[],eB[],angB[],angA[],strA[],str_wd[],lenB[],ang_br[],save_para[],
tbl_char_wd[],tbl_char_ht[],tbl_char_dp[],tbl_atom[],tbl_subst[][],tbl_atom_wt[],
- comMC[][],parMC[][],cntMC[];
-string info[],tbl_atom_str[],com_str[],var[],tag[],mp_log_name,aux_delimiter;
+ comD[][],parD[][],cntD[];
+string info[],tbl_atom_str[],strD[],var[],tag[],mp_log_name,aux_delimiter;
picture atom_font[],chem_structure;
%-------------------------------------------------------------------------------------------------
-sw_numberA:=sw_numberB:=sw_mol_frame:=sw_auxout:=sw_solid:=sw_expand:=sw_start_vector:=0;
-char_num:=str_cnt:=proc_end:=sw_font_frame:=sw_atom_frame:=sw_checklist:=0;
-sw_MOLout:=sw_subst_off:=sw_bond_single:=sw_auxfix:=sw_clip:=0;
+char_num:=str_cnt:=proc_end:=sw_numberA:=sw_numberB:=sw_mol_frame:=sw_auxout:=sw_solid:=0;
+sw_expand:=sw_font_frame:=sw_atom_frame:=sw_checklist:=sw_MOLout:=sw_subst_off:=sw_bond_single:=0;
+sw_auxfix:=sw_clip:=0;
numberA_start:=numberB_start:=1; numberA_end:=numberB_end:=4095; aux_max:=20;
aux_delimiter:=";"; var1:="jobname"; tag1:="F"; var2:="char_num"; tag2:="C";
for i=3 upto aux_max: var[i]:=tag[i]:=""; endfor
@@ -85,8 +85,8 @@ max_bond_length#:=10mm; bond_len#:=8mm#;
max_inf_num:=12; for i:=1 upto max_inf_num: info[i]:=":"; endfor
%--------------------------------------------------------------------------------------------------
def_emb_start:=500; % 500 => 2499 for embedded definition (max 2000)
-def_usr_start:=2500; % 2500 => 2999 for user definition (max 500)
-def_int_start:=3000; % 3000 => 4000 for internal definition (max 1000)
+def_usr_start:=2500; % 2500 => 2999 for user definition (max 500)
+def_int_start:=3000; % 3000 => 4000 for internal definition (max 1000)
%--------------------------------------------------------------------------------------------------
def def_com(expr n)(text tx)= nA:=n; forsuffixes list=tx:: list:=nA; nA:=nA+1; endfor enddef;
def_com(-4000)(_term,_jp_atom,_jp_atom_abs,_jp_bond,_cyc,_cyc_sB,_cyc_eB,_set_line,_chg_line,
@@ -97,7 +97,7 @@ def_com(1)(si,dl,dr,dm,tm,wf,wb,bd,bz,zf,zb,dt,no,ar,vf,vb,wv,nl,si_,wf_,wb_,bd_
%--------------------------------------------------------------------------------------------------
def parameter_list=
sw_checklist,sw_numberA,sw_numberB,sw_mol_frame,sw_auxout,sw_solid,sw_expand,sw_MOLout,
- sw_start_vector,sw_atom_frame,sw_font_frame,sw_subst_off,sw_bond_single,sw_clip,
+ sw_atom_frame,sw_font_frame,sw_subst_off,sw_bond_single,sw_clip,
margin_left_right,margin_top_bottom,ratio_atom_bond,ratio_thickness_bond,ratio_char_bond,
ratio_chain_ring,max_bond_width,ratio_bondgap_bond,ratio_zebra_black,ratio_zebragap_bond,
ratio_wedge_bond,ratio_atomgap_atom,ratio_bond_width,
@@ -107,24 +107,22 @@ enddef;
%--------------------------------------------------------------------------------------------------
vardef pic_c(expr i,s)= substring(i,i+1) of s enddef;
%--------------------------------------------------------------------------------------------------
-nA:=0; for list=parameter_list: stock_para[incr nA]:=list; endfor
+nA:=0; for list=parameter_list: save_para[incr nA]:=list; endfor
def store_par(text t)=
- nA:=0; for list=t: if stock_para[incr nA]<>list: stock_para[nA]:=list; fi endfor enddef;
+ nA:=0; for list=t: if save_para[incr nA]<>list: save_para[nA]:=list; fi endfor enddef;
def restore_par(text t)= nA:=0;
- forsuffixes list=t: if list<>stock_para[incr nA]: list:=stock_para[nA]; fi endfor enddef;
+ forsuffixes list=t: if list<>save_para[incr nA]: list:=save_para[nA]; fi endfor enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def beginfont(text s)=
store_par(parameter_list); save_wd#:=font_wd#; save_ht#:=font_ht#;
- f_beginchar:=inf_num:=0;
+ f_beginchar:=inf_num:=cntM:=0;
for list=s: info[incr inf_num]:=list; endfor
enddef;
%--------------------------------------------------------------------------------------------------
def endfont=
- if (sw_font_frame=1)or(sw_font_frame=3): AUX(0,0)(draw_frame(w,h,(0,0),thickness_font_frame);) fi
- if (sw_font_frame=2)or(sw_font_frame=3):
- AUX(0,0)(draw_frame(w-2margin_left_right,h-2margin_top_bottom,
- (margin_left_right,margin_top_bottom),thickness_font_frame);) fi
- if sw_font_frame=4: AUX(0,0)(draw_corner(w,h,thickness_font_frame);) fi
+ if (sw_font_frame=1)or(sw_font_frame=3): EXT(draw_frame((0,0),w,h,thickness_font_frame);) fi
+ if (sw_font_frame=2)or(sw_font_frame=3): EXT(draw_frame(p0,wd,ht,thickness_font_frame);) fi
+ if sw_font_frame=4: EXT(draw_corner(w,h,thickness_font_frame);) fi
if (sw_auxout=1)or(sw_checklist=1)or(sw_MOLout=1): proc_calc_out; fi
char_num:=char_num+1; currentpicture:=chem_structure; chem_structure:=nullpicture; endchar;
clearit;
@@ -155,24 +153,27 @@ def set_def_MC=
def */secondary n == (_postC,n) enddef; def /*secondary n == (_postD,n) enddef;
def **secondary n == (_postE,n) enddef; def */*secondary n == (_postF,n) enddef;
enddef;
-%-------------------------------------------------------------------------------------------------
+%=================================================================================================
vardef '(text s)= ''(incr def_num)(s); def_num enddef;
+%-------------------------------------------------------------------------------------------------
def ''(expr k)(text s)=
begingroup
if unknown inside_def_MC:: set_def_MC fi
- cntMC[k]:=0;
+ cntD[k]:=0;
for list==s::
if known list::
- if pair list:: comMC[k][incr cntMC[k]]:=xpart(list); parMC[k][cntMC[k]]:=ypart(list);
+ if pair list:: comD[k][incr cntD[k]]:=xpart(list); parD[k][cntD[k]]:=ypart(list);
elseif numeric list::
if list>=def_emb_start::
- for i==1 upto cntMC[list]::
- comMC[k][incr cntMC[k]]:=comMC[list][i]; parMC[k][cntMC[k]]:=parMC[list][i];
+ for i==1 upto cntD[list]::
+ comD[k][incr cntD[k]]:=comD[list][i]; parD[k][cntD[k]]:=parD[list][i];
endfor
- else:: comMC[k][incr cntMC[k]]:=_mk_bond; parMC[k][cntMC[k]]:=list; fi
- elseif string list:: com_str[incr str_cnt]:=list;
- comMC[k][incr cntMC[k]]:=_set_atom; parMC[k][cntMC[k]]:=str_cnt;
- if pic_c(0,list)=="{":: str_wd[str_cnt]:=1.7; else:: str_wd[str_cnt]:=1; fi fi fi
+ else:: comD[k][incr cntD[k]]:=_mk_bond; parD[k][cntD[k]]:=list; fi
+ elseif string list:: strD[incr str_cnt]:=list;
+ comD[k][incr cntD[k]]:=_set_atom; parD[k][cntD[k]]:=str_cnt;
+ if pic_c(0,list)=="{":: str_wd[str_cnt]:=1.6; else:: str_wd[str_cnt]:=1; fi
+ fi
+ fi
endfor
endgroup
enddef;
@@ -222,16 +223,16 @@ vardef $$(text t)(expr e) =
elseif (e>=?3)and(e<=?20):: for list==t:: !?(list)(e-?3+3) endfor
elseif e==Ph1:: !?(t)(6) PA(_dl,-2) PA(_dl,-4)
elseif e==Ph2:: !?(t)(6) PA(_dl,-1) PA(_dl,-3) PA(_dl,-5)
- elseif comMC[e][1]==_fuse::
- if comMC[e][2]<=6:: for list==t:: !!?(list)(parMC[e][1])(comMC[e][2]) endfor
- elseif (comMC[e][2]>=11)and(comMC[e][2]<=15)::
- for list==t:: !??(list)(parMC[e][1])(comMC[e][2]) endfor
+ elseif comD[e][1]==_fuse::
+ if comD[e][2]<=6:: for list==t:: !!?(list)(parD[e][1])(comD[e][2]) endfor
+ elseif (comD[e][2]>=11)and(comD[e][2]<=15)::
+ for list==t:: !??(list)(parD[e][1])(comD[e][2]) endfor
fi
fi
elseif color e:: color_list[incr cntC]:=e;
for list==t:: PA(_set_adr,list) PA(_set_colorB,cntC) endfor
fi fi
- cntMC[def_int]:=nA;
+ cntD[def_int]:=nA;
def_int %------- Retern value -------
enddef;
%-------------------------------------------------------------------------------------------------
@@ -262,37 +263,56 @@ vardef @@(text t)(expr s)=
PA(_set_clr,0)
elseif color s:: color_list[incr cntC]:=s;
for list==t:: PA(_set_adr,list) PA(_set_colorA,cntC) endfor fi fi
- cntMC[def_int]:=nA;
+ cntD[def_int]:=nA;
def_int %------- Retern value -------
enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-def AUX(expr a,b)(text s)=s addto chem_structure also currentpicture shifted(a,b); clearit; enddef;
-def MCf(text s)= MCd(1,1)(.5,.5)(s); enddef; % MC fill draw
-def MCd(expr RW,RH)(expr FW,FH)(text s)= proc_drawing(RW,RH)(FW,FH)(s); enddef;
+def EXT(text s)=
+ begingroup
+ save wd,ht,n,p; pair p[]; wd:=w-2margin_left_right; ht:=h-2margin_top_bottom;
+ p0:=(margin_left_right,margin_top_bottom); n:=cntM; for i=1 upto n: p[i]:=posM[i]; endfor
+ s addto chem_structure also currentpicture; clearit;
+ endgroup;
+enddef;
+%--------------------------------------------------------------------------------------------------
+def ext(text s)=
+ begingroup
+ save wd,ht,n,a,p; numeric a[]; pair p[]; wd:=mol_wd; ht:=mol_ht;
+ p0:=(minX,minY); n:=cntA; for i=1 upto n: p[i]:=posA[i]; a[i]:=ang_br[i]; endfor
+ s addto chem_structure also currentpicture shifted (sftX,sftY); clearit;
+ endgroup;
+enddef;
+%=================================================================================================
+def MCf(text s)= MCd(1,1)(.5,.5)(s) enddef; % MC fill draw
%-------------------------------------------------------------------------------------------------
-def proc_drawing(expr RW,RH)(expr FW,FH)(text s)=
+def MCd(expr RW,RH)(expr FW,FH)(text TX)=
begingroup
- save com,par,adrA,adrB,f_bra,envT,envB,lenT,lineT,strAT,stkA,stkB,stkL,stkM,bondL,temp_len,
- temp_cntB,f_end,f_term,rotT,adrS,f_lineT,f_rotT,f_lenT,f_envT,PP,angT,tempB,glu,sftX,sftY,
- xpos,ypos,str_len,max_x,max_y,par_s,par_e,score_u,hat,f_char,lenB,ps_adr,ps_com,op_com,
- op_par,op_cnt,crR,colorA,colorB,PA,PAs,PP,PG;
- %-----------------------------------------------------------------------------------------------
- def PA(expr a,b)= comMC[def_int][incr nA]:=a; parMC[def_int][nA]:=b; enddef;
- def PAs(text t)= for list==t:: PA(xpart(list),ypart(list)) endfor enddef;
- def PP(expr a,b)= op_com[cntP][incr op_cnt[cntP]]:=a; op_par[cntP][op_cnt[cntP]]:=b; enddef;
- def PG(expr a,b)= comMC[0][incr cntMC[0]]:=a; parMC[0][cntMC[0]]:=b; enddef;
+ save com,par,adrA,adrB,f_bra,envT,envB,lenT,lineT,strAT,stkA,stkB,stkL,stkM,cntP,
+ bondL,temp_len,temp_cntB,f_end,f_term,rotT,adrS,f_lineT,f_rotT,f_lenT,f_envT,angT,tempB,
+ glu,sftX,sftY,xpos,ypos,str_len,max_x,max_y,par_s,par_e,score_u,hat,f_char,lenB,
+ ps_adr,ps_com,op_com,op_par,op_cnt,crR,colorA,colorB;
%-----------------------------------------------------------------------------------------------
numeric stkB[],stkA[],stkL[],stkM[],f_char[],ps_adr[],ps_com[],colorA[],colorB[],
op_com[][],op_par[][],op_cnt[];
%-----------------------------------------------------------------------------------------------
+ save ww,ap,am,hpt,pA,pB,pC,pT,Ls,Le,dx,j,u,pairA,pairT;
+ pair Ls,Le,pairA,pairT;
+ path pA,pB,pC,pT;
+ %-----------------------------------------------------------------------------------------------
+ save PA,PAs,PP,PG;
+ def PA(expr a,b)= comD[def_int][incr nA]:=a; parD[def_int][nA]:=b; enddef;
+ def PAs(text t)= for list==t:: PA(xpart(list),ypart(list)) endfor enddef;
+ def PP(expr a,b)= op_com[cntP][incr op_cnt[cntP]]:=a; op_par[cntP][op_cnt[cntP]]:=b; enddef;
+ def PG(expr a,b)= comD[0][incr cntD[0]]:=a; parD[0][cntD[0]]:=b; enddef;
+ %-----------------------------------------------------------------------------------------------
if (sw_numberA>=1)or(sw_numberB>=1): ratio_atom_bond:=0.25; fi
if (sw_expand=1)or(sw_MOLout=1): expand_set; fi
def_num:=def_usr_start;
def_int:=def_int_start;
par_s=ASCII("{"); par_e=ASCII("}"); score_u=ASCII("_"); hat=ASCII("^");
- cntA:=cntB:=cntP:=cntC:=0; com_str[0]:=""; str_cnt:=2000; crR:=-ratio_chain_ring;
- %-----------------------------------------------------------------------------------------------
- ''(0)(s,(_term,0)); proc_bond_atom(1); if (cntP>0)and(sw_subst_off=0): ps_get(1); fi
+ cntA:=cntB:=cntP:=cntC:=0; strD[0]:=""; str_cnt:=2000; crR:=-ratio_chain_ring;
+ %===============================================================================================
+ ''(0)(TX,(_term,0)); proc_bond_atom(1); if (cntP>0)and(sw_subst_off=0): ps_get(1); fi
define_pixels(font_wd,font_ht,thickness_font_frame);
char_use_check;
if sw_solid=1: bond_len#:=font_wd#*ratio_bond_width;
@@ -309,7 +329,8 @@ def proc_drawing(expr RW,RH)(expr FW,FH)(text s)=
if bond_len#>max_bond_length#:
bond_len#:=max_bond_length#; proc_size_setup; proc_skeleton; proc_scaling; fi
fi
- proc_char_setup(char_pen_wd);
+ proc_char_setup;
+ %-----------------------------------------------------------------------------------------------
if f_beginchar=0:
if sw_clip=1: font_wd#:=font_wd#*((mol_wd+2margin_left_right)/font_wd);
font_ht#:=font_ht#*((mol_ht+2margin_top_bottom)/font_ht); fi
@@ -325,15 +346,15 @@ def proc_drawing(expr RW,RH)(expr FW,FH)(text s)=
if i<10: draw_atom(i,posA[i],0,decimal(nA),1);
else: draw_atom(i,posA[i]+(-.2atom_wd,0),0,decimal(nA),1); fi
elseif sw_numberB>=1:
- else: draw_atom(i,posA[i],ang_br[i],com_str[strA[i]],str_wd[strA[i]]); fi
+ else: draw_atom(i,posA[i],ang_br[i],strD[strA[i]],str_wd[strA[i]]); fi
endfor
sftX:=margin_left_right-minX+(w-mol_wd-2margin_left_right)*FW;
sftY:=margin_top_bottom-minY+(h-mol_ht-2margin_top_bottom)*FH;
- if sw_mol_frame=1: AUX(sftX,sftY)(draw_frame(mol_wd,mol_ht,(minX,minY),0.2pt);) fi
- if sw_start_vector=1: AUX(sftX,sftY)(start_vector) fi
+ posM[incr cntM]:=(minX+sftX,minY+sftY);
+ if sw_mol_frame=1: ext(draw_frame(p0,wd,ht,0.2pt);) fi
addto chem_structure also currentpicture shifted (sftX,sftY);
clearit;
- endgroup
+ endgroup; % <=added ";"
enddef;
%-------------------------------------------------------------------------------------------------
def ps_put(expr n,p)=
@@ -346,17 +367,17 @@ def ps_put(expr n,p)=
enddef;
%-------------------------------------------------------------------------------------------------
def ps_get(expr n)=
- nA:=cntP; nB:=cntMC[0];
+ nA:=cntP; nB:=cntD[0];
for i=n upto cntP:
PG(_jp_atom_abs,ps_adr[i]) PG(_push,1)
for j=1 upto op_cnt[i]: PG(op_com[i][j],op_par[i][j]) endfor
- for j=1 upto cntMC[ps_com[i]]: PG(comMC[ps_com[i]][j],parMC[ps_com[i]][j]) endfor
+ for j=1 upto cntD[ps_com[i]]: PG(comD[ps_com[i]][j],parD[ps_com[i]][j]) endfor
PG(_pop,1) PG(_term,0)
endfor
proc_bond_atom(nB+1); if cntP>nA: ps_get(nA+1); fi
enddef;
%-------------------------------------------------------------------------------------------------
-def draw_frame(expr LX,LY,PS,PN)=
+def draw_frame(expr PS,LX,LY,PN)=
draw ((PN/2,PN/2)--(LX-PN/2,PN/2)--(LX-PN/2,LY-PN/2)--(PN/2,LY-PN/2)--cycle) shifted PS wpss PN;
enddef;
%-------------------------------------------------------------------------------------------------
@@ -365,9 +386,9 @@ def draw_corner(expr LX,LY,PN)=
drawdot (LX-PN/2,LY-PN/2) wpss PN; drawdot (PN/2,LY-PN/2) wpss PN;
enddef;
%-------------------------------------------------------------------------------------------------
-def start_vector= draw (posA[1] shifted (-1mm,0))--(posA[1] shifted (-4mm,0))
- withpen penrazor rotated 90 scaled .8mm;
- fill (posA[1] shifted (-2mm,-1mm))--posA[1]--(posA[1] shifted (-2mm,1mm))--cycle;
+def draw_vector(expr POS,ROT,LEN)=
+ fill (-2mm,-1mm)--(0,0)--(-2mm,1mm)--(-2mm,.4mm)--(-LEN,.4mm)--
+ (-LEN,-.4mm)--(-2mm,-.4mm)--cycle rotated ROT shifted POS;
enddef;
%-------------------------------------------------------------------------------------------------
def proc_size_setup=
@@ -384,10 +405,11 @@ enddef;
%-------------------------------------------------------------------------------------------------
def proc_scaling=
minX:=minY:=4095.999; max_x:=max_y:=-4095.999;
- for i=1 upto cntA: xpos:=xpart(posA[i]); ypos:=ypart(posA[i]);
+ for i=1 upto cntA:
+ xpos:=xpart(posA[i]); ypos:=ypart(posA[i]);
if strA[i]<>0: str_len:=nC:=nD:=0;
- for j=0 upto length(com_str[strA[i]])-1:
- nA:=ASCII(pic_c(j,com_str[strA[i]]));
+ for j=0 upto length(strD[strA[i]])-1:
+ nA:=ASCII(pic_c(j,strD[strA[i]]));
if (nA=score_u)or(nA=hat)or(nA=par_s)or(nA=par_e):
if (nA=hat)and(nC<.5atom_wd): nC:=.5atom_wd; fi;
if (nA=score_u)and(nD<.5atom_wd): nD:=.5atom_wd; fi;
@@ -408,15 +430,17 @@ enddef;
def char_use_check=
for i=1 upto 128: f_char[i]:=0; endfor
if (sw_numberA>0)or(sw_numberB>0): for j=ASCII("0") upto ASCII("9"): f_char[j]:=1; endfor
- else: for i=1 upto cntA: if strA[i]<>0: for j=0 upto length(com_str[strA[i]])-1:
- f_char[ASCII(pic_c(j,com_str[strA[i]]))]:=1; endfor fi endfor fi
+ else: for i=1 upto cntA: if strA[i]<>0: for j=0 upto length(strD[strA[i]])-1:
+ f_char[ASCII(pic_c(j,strD[strA[i]]))]:=1; endfor fi endfor fi
enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def proc_bond_atom(expr n)=
f_bra:=f_end:=f_term:=rotT:=adrS:=f_lineT:=f_rotT:=f_lenT:=f_envT:=envT:=envB:=strAT:=0;
stkL[0]:=bondL:=crR; lenT:=crR; sB[0]:=0; eB[0]:=1; lineT:=si;
for i=0 upto 5: stkA[i]:=stkB[i]:=0; endfor
- for i=n upto cntMC[0]: com:=comMC[0][i]; par:=parMC[0][i];
+ %-----------------------------------------------------------------------------------------------
+ for i=n upto cntD[0]:
+ com:=comD[0][i]; par:=parD[0][i];
if com=_push:
if par=1: stkL[adrS]:=bondL; stkA[incr adrS]:=adrA:=cntA; stkB[adrS]:=adrB:=cntB;
elseif par=0: temp_len:=bondL; fi
@@ -433,10 +457,10 @@ def proc_bond_atom(expr n)=
elseif com=_jp_bond: tempB:=getB(par); sB[cntB+1]:=sB[tempB]; f_bra:=1;
elseif com=0or_jp_atom: termA; sB[cntB+1]:=getA(par); f_bra:=1;
elseif com=_jp_atom_abs: sB[cntB+1]:=par; f_bra:=1; temp_cntB:=cntB;
- elseif com=_chg_atom: strA[getA(adrT)]:=parMC[par][1];
- elseif com=_N: strA[getA(par)]:=parMC[N][1];
- elseif com=_O: strA[getA(par)]:=parMC[O][1];
- elseif com=_S: strA[getA(par)]:=parMC[S][1];
+ elseif com=_chg_atom: strA[getA(adrT)]:=parD[par][1];
+ elseif com=_N: strA[getA(par)]:=parD[N][1];
+ elseif com=_O: strA[getA(par)]:=parD[O][1];
+ elseif com=_S: strA[getA(par)]:=parD[S][1];
elseif com=_H: ps_put(getA(par),H);
elseif com=_chg_len: if par=_ring_len: bondL:=ringL;
elseif par=0: if lenT<>crR: bondL:=lenT; else: if bondL<0: bondL:=1; fi fi
@@ -477,7 +501,9 @@ def proc_skeleton=
envT:=envB:=f_lineT:=f_rotT:=f_lenT:=f_envT:=stkM[0]:=0; lineT:=si;
angA[0]:=angB[0]:=ang_br[0]:=0; posA[0]:=posB[0]:=posB[1]:=(0,0);
for i=0 upto 5: stkA[i]:=stkB[i]:=0; endfor
- for i=1 upto cntMC[0]: com:=comMC[0][i]; par:=parMC[0][i];
+ %----------------------------------------------------------------------------------------------
+ for i=1 upto cntD[0]:
+ com:=comD[0][i]; par:=parD[0][i];
if com=_push: if par=1: stkM[adrS]:=envB; adrS:=adrS+1; stkA[adrS]:=adrA:=cntA;
stkB[adrS]:=adrB:=cntB;
elseif par=0: temp_len:=bondL; fi
@@ -535,27 +561,24 @@ def glu_c(expr n)= if strA[n]<>0: nB:=angT mod 180; nC:=.5str_wd[strA[n]]*atom_
else :glu:=glu+((cosd(nB)*.5atom_wd)++.5atom_wd) fi fi
enddef;
vardef proc_env(expr n,m,a,b)= r:=(n mod 360);
- if m>=def_emb_start: parMC[m][cntB-temp_cntB-1] else:
+ if m>=def_emb_start: parD[m][cntB-temp_cntB-1] else:
if m=hz:if r=0:a elseif r<=90:b elseif r<=180:a elseif r<270:b else:a fi
elseif m=vt:if r=0:b elseif r<90:a elseif r<=180:b elseif r<=271:a else:b fi
elseif (m>=-180)and(m<=180): m fi fi
enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-def draw_atom(expr n,p,r,s,w)=
- begingroup
- save dx,u,j,pairA,pairT,par_s,par_e,score_u,hat; pair pairA,pairT;
- par_s=ASCII("{"); par_e=ASCII("}"); score_u=ASCII("_"); hat=ASCII("^");
- %---------------------------------------------------------------------------------------
+def draw_atom(expr n,p,r,s,WD)=
if ((r mod 360)<=90+1)or((r mod 360)>=270-1): dx:=1; else: dx:=-1; fi
- pairT:=p-(.5atom_wd*w*dx,.5atom_wd); u:=j:=0;
- for i=0 upto length(s)-1: nB:=ASCII(pic_c(i,s));
+ pairT:=p-(.5atom_wd*dx*WD,.5atom_wd); u:=j:=0;
+ for i=0 upto length(s)-1:
+ nB:=ASCII(pic_c(i,s));
if dx<0: if nB=par_s:k:=i+1;j:=1;forever:exitif pic_c(i+(incr j),s)="}";endfor fi
if j>0: nB:=ASCII(pic_c(k+(decr j),s)); fi fi
if nB=score_u: if u=0: u:=-.5; else:u:=0; fi;
elseif nB=hat: if u=0: u:= .5; else:u:=0; fi;
elseif (nB<>par_s)and(nB<>par_e):
nA:=atom_wd*tbl_char_wd[nB]; pairA:=pairT+(.5*((dx-1)*nA),u*atom_wd);
- if sw_atom_frame=1: draw_frame(nA,atom_wd,pairA,0.1pt); fi
+ if sw_atom_frame=1: draw_frame(pairA,nA,atom_wd,0.1pt); fi
if (sw_numberA>=1)or(sw_numberB>=1):
erase fill unitsquare xscaled nA yscaled atom_wd shifted pairA wpcs 0.01pt; fi
addto currentpicture also atom_font[nB]
@@ -563,15 +586,9 @@ def draw_atom(expr n,p,r,s,w)=
pairT:=pairT+(nA*dx,0);
fi
endfor
- endgroup
enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def draw_bond(expr n,BP,EP,ANG,LN)=
- begingroup
- save ww,ap,am,hpt,pA,pB,pC,pT,Ls,Le;
- pair Ls,Le;
- path pA,pB,pC,pT;
- %--------------------------------------------------------------------------------------------
nC:=length(posA[EP]-posA[BP]);
if (nC>0)and(LN<>0):
ww:=wedge_wd; hpt:=.5bond_pen_wd; ap:=ANG+90; am:=ANG-90;
@@ -579,6 +596,7 @@ def draw_bond(expr n,BP,EP,ANG,LN)=
else: clipping(strA[BP],strA[EP],posA[BP],posA[EP],nC); fi
pickup pencircle scaled bond_pen_wd;
if known colorB[n]: nB:=colorB[n]; fi
+ %---------------------------------------------------------------------------------------------
if (LN=si)or(sw_bond_single=1): draw pA Cp(nB);
elseif LN=dl:draw pA Cp(nB); draw sfB(pC,bondgap,ap) Cp(nB);
elseif LN=dr:draw pA Cp(nB); draw sfB(pC,bondgap,am) Cp(nB);
@@ -610,7 +628,6 @@ def draw_bond(expr n,BP,EP,ANG,LN)=
else: nB:=n; fi
draw_atom(n,.5[posA[BP],posA[EP]],0,decimal(nB),1); fi
fi
- endgroup
enddef;
%-------------------------------------------------------------------------------------------------
def draw_wv= nB:=3bond_pen_wd; nA:=nB/length(Le-Ls);
@@ -632,7 +649,7 @@ def bz_put(expr PA,PB,PC,PD,CL)= nC:=length(Le-Ls);
nA:=zebra_gap*i/nC; nD:=(zebra_gap*i+ratio_zebra_black*zebra_gap)/nC;
fill nA[PB,PA]--nA[PD,PC]--nD[PD,PC]--nD[PB,PA]--cycle Cp(CL); endfor enddef;
def cut_off(expr p,w,h,s)=
- p intersectionpoint sqr(1.1w,1.1h) shifted (s-(.5(1.1w),.5(1.1h))); enddef;
+ p intersectionpoint sqr(w+.1h,1.1h) shifted (s-(.5(w+.1h),.5(1.1h))); enddef;
def clipping(expr SA,SB,PA,PB,LEN)=
pT:=PA--PB; nA:=0.6atom_wd/LEN;
if (SA=0)and(SB=0): Ls:=PA; Le:=PB; pA:=pB:=pT; pC:=0.1[PA,PB]--0.1[PB,PA];
@@ -681,8 +698,6 @@ S_H:='(S,!,H); N_H:='(N,/H); C_HHH:='(/H,/H^60,60,H);
def expand_set= save CH,NH,NO,OH,CHO,COOH,CN,SH;
CH3:=C_HHH; NH:=N_H; NH2:=N_HH; NO2:=N_OO; OH:=O_H; CHO:=CO_H; COOH:=CO_OH; CN:=C_N; SH:=S_H;
enddef;
-%==================================================================================================
-message "-- total "&decimal(def_num)&" embedded definition --";
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def char_size_set(expr a)(expr b)(expr c)(expr s)=
for j=0 upto length(s)-1: nA:=ASCII(pic_c(j,s));
@@ -696,8 +711,8 @@ char_size_set(.7)( 1)( 0)(" ()0123456789nhj=*bdiltf");
char_size_set(.7)( 1)(.15)("pqg");
char_size_set(.7)(.8)( 0)("acekosuvxzwry");
char_size_set(.4)( 1)( 0)(".,:;'`");
-%------------------------------------------------------------------------------------------------
-def proc_char_setup(expr a)=
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+def proc_char_setup=
begingroup
save Z,aW,aH,fW,hW,hW,hH,fP,hP,vL,hL,PO,POh,sH,FD;
pair Z[];
@@ -727,7 +742,9 @@ def POh= (hP,.25aH)..Z19..(fW,.25aH)..Z20..cycle enddef;
def sH expr n= shifted (0,n) enddef;
def SP(expr m,n)expr p=subpath(m*length(p),n*length(p)) of p enddef;
%==================================================================================================
-pickup pencircle scaled a; fP:=a; hP:=.5a;
+pickup pencircle scaled char_pen_wd;
+fP:=char_pen_wd; hP:=.5char_pen_wd;
+%------------------------------------------------------------------------------------------
FD(" ")();
FD(".")(drawdot Z19 wpcs fP);
FD(",")(drawdot Z19 wpcs fP; draw (hW+.5fP,hP)..(hW+.3fP,-fP)..(hW-.5fP,hP-2fP));
@@ -818,26 +835,11 @@ vardef fixed_l(expr n)(expr s)= s&(substring(0,n-length(s)) of blank_str) enddef
vardef fdr(expr n)(expr s)=fixed_r(n)(decimal(s)) enddef;
def warning(expr s)= message "% "&decimal(char_num)&fdr(3)(incr warning_cnt)&")"&s&" !!!"; enddef;
def B_check(expr s)(expr t)(expr n)=
- if com_str[strA[s]]=t: if bond_cnt>n:
- warning(fdr(4)(s)&" ["&com_str[strA[s]]&"] has "&fdr(3)(bond_cnt)&" bonds"); fi fi
+ if strD[strA[s]]=t: if bond_cnt>n:
+ warning(fdr(4)(s)&" ["&strD[strA[s]]&"] has "&fdr(3)(bond_cnt)&" bonds"); fi fi
enddef;
vardef stripP(expr a)=if length(a)=4: substring (1,3) of a else: a fi enddef;
%==================================================================================================
-def proc_get_info=
- for j=1 upto inf_num:
- nA:=0; for i=0 upto length(info[j]): if pic_c(i,info[j])=":": nA:=i; fi exitif nA>0; endfor
- if nA>0:
- s_tag:=substring (0,nA) of info[j];
- s_var:=substring (nA+1,length(info[j])) of info[j];
- if s_tag="NO": inf_NO:=s_var; elseif s_tag="MW": inf_MW:=s_var;
- elseif s_tag="EN": inf_EN:=s_var; elseif s_tag="JN": inf_JN:=s_var;
- elseif s_tag="FM": inf_FM:=s_var; elseif s_tag="CAS": inf_CAS:=s_var;
- elseif s_tag="USE": inf_USE:=s_var; elseif s_tag="EXA": inf_EXA:=s_var;
- elseif s_tag="EXB": inf_EXB:=s_var; fi
- fi
- endfor
-enddef;
-%==================================================================================================
def STa(expr a,b)=
tbl_atom_str[incr tbl_cnt]:=a; tbl_atom[tbl_cnt]:=0; tbl_atom_wt[tbl_cnt]:=b;
enddef;
@@ -865,6 +867,17 @@ STb("N{H_2_}")("N","H","H");
STb("S{O_3_}")("S","O","O","O"); STb("COOH")("C","O","O","H");
STb("C{H_3_}")("C","H","H","H"); STb("C{F_3_}")("C","F","F","F");
%==================================================================================================
+def proc_get_info=
+ for j=1 upto inf_num:
+ nA:=0; for i=0 upto length(info[j]): if pic_c(i,info[j])=":": nA:=i; fi exitif nA>0; endfor
+ if nA>0:
+ s_tag:=substring (0,nA) of info[j];
+ s_var:=substring (nA+1,length(info[j])) of info[j];
+ if known scantokens("inf_"&s_tag): scantokens("inf_"&s_tag):=s_var; fi
+ fi
+ endfor
+enddef;
+%==================================================================================================
def proc_calc_out=
begingroup
save warning_cnt,cal_MW,cal_MWp,knownA,cal_FM,bondC,tmp_wtp,bond_cnt,hide_H,
@@ -874,6 +887,7 @@ def proc_calc_out=
inf_NO,inf_EN,inf_JN,inf_FM,inf_CAS,inf_USE,inf_EXA,inf_EXB,inf_MW;
inf_NO:=inf_EN:=inf_JN:=inf_FM:=inf_CAS:=inf_USE:=inf_EXA:=inf_EXB:=inf_MW:="";
cal_MW_str:=cal_FM:=""; hide_H:=warning_cnt:=cal_MW:=cal_MWp:=0;
+ %------------------------------------------------------------------------------------------
proc_get_info;
for i=1 upto tbl_cnt: sumA[i]:=0; endfor
for i=1 upto cntA: knownA:=bond_cnt:=0;
@@ -882,16 +896,16 @@ def proc_calc_out=
elseif lineB[j]=0: bondC[j]:=0; else: bondC[j]:=1; fi
if (sB[j]=i)or(eB[j]=i): bond_cnt:=bond_cnt+bondC[j]; fi endfor
Bcnt[i]:=bond_cnt;
- if com_str[strA[i]]="": com_str[strA[i]]:="C"; fi
- if com_str[strA[i]]="C": if bond_cnt<4: hide_H:=hide_H+(4-bond_cnt); fi fi
+ if strD[strA[i]]="": strD[strA[i]]:="C"; fi
+ if strD[strA[i]]="C": if bond_cnt<4: hide_H:=hide_H+(4-bond_cnt); fi fi
B_check(i)("C")(4); B_check(i)("H")(1); B_check(i)("O")(2);
B_check(i)("F")(1); B_check(i)("{Cl}")(1); B_check(i)("Br}")(1);
for j=1 upto tbl_cnt:
- if com_str[strA[i]]=tbl_atom_str[j]:
+ if strD[strA[i]]=tbl_atom_str[j]:
if tbl_atom[j]=0: sumA[j]:=sumA[j]+1;
else: for k=1 upto tbl_atom[j]: sumA[tbl_subst[j][k]]:=sumA[tbl_subst[j][k]]+1; endfor fi
knownA:=1; fi endfor
- if knownA=0: warning(" Unknown Str("&com_str[strA[i]]&") is used "&decimal(i)); fi
+ if knownA=0: warning(" Unknown Str("&strD[strA[i]]&") is used "&decimal(i)); fi
endfor
sumA[2]:=sumA[2]+hide_H;
for i=1 upto tbl_cnt:
@@ -924,8 +938,7 @@ enddef;
%==================================================================================================
def proc_checklist_out= nA:=0;
message "% Molecular name = "& inf_EN;
- message "% There were "&fdr(3)(warning_cnt)&
- " warnings / Expanded command count= "&decimal(cntMC[0]);
+ message "% warnings = "&fdr(3)(warning_cnt)&" / Expanded command = "&decimal(cntD[0]);
message "% width * height = " & fdr(8)(mol_wd)&" * "&fdr(8)(mol_ht);
message "% Shift width * height = "& fdr(8)(minX)&" * "&fdr(8)(minY);
message "% Bond length = "&fdr(3)(bond_len)&" Atom size = "&fdr(3)(atom_wd);
@@ -933,15 +946,14 @@ def proc_checklist_out= nA:=0;
" Ring count="&fdr(3)(cntB-cntA+1)&" Hide H ="&fdr(3)(hide_H);
message "%-----------------------------------< atom >< bond >-------";
for i=1 upto cntA: message "% "&fdr(3)(i)&" ("&fdr(10)(xpart(posA[i])/bond_len)&" ) ("&
- fdr(10)(ypart(posA[i])/bond_len)&" ) "&fixed_l(8)(com_str[strA[i]])&" "&fdr(3)(Bcnt[i]);
+ fdr(10)(ypart(posA[i])/bond_len)&" ) "&fixed_l(8)(strD[strA[i]])&" "&fdr(3)(Bcnt[i]);
endfor
message "%Bond list---------------------------------------------------------";
for i=1 upto cntB: if lineB[i]<>0: message "% "&fdr(3)(incr nA)&" "&fdr(3)(sB[i])&
" -> "&fdr(3)(eB[i])&" ("&fdr(3)(bondC[i]-si+1)&")"; fi
endfor
message "%Fomula / Molecular weight ---------------------------------------";
- if cal_MWp<=40: cal_MW_str:=fdr(10)(cal_MW);
- else: cal_MW_str:=fdr(10)(cal_MWp)&" * 100"; fi
+ if cal_MWp<=40: cal_MW_str:=fdr(10)(cal_MW); else: cal_MW_str:=fdr(10)(cal_MWp)&" * 100"; fi
for i=1 upto tbl_cnt:
if sumA[i]>=1:
message "% "&fixed_l(4)(stripP(tbl_atom_str[i]))&"("&fdr(9)(tbl_atom_wt[i])&
@@ -960,7 +972,7 @@ def proc_MOLfile_out=
printf ""; printf " -MCFtoMOL- "&fixed_l(20)(info[1]); printf "";
printf fdr(3)(cntA)&fdr(3)(cntB)&" 0 0 0 0 0 0 0 0999 V2000";
for i=1 upto cntA: printf fdr(10)(xpart(posA[i])/bond_len)& fdr(10)(ypart(posA[i])/bond_len)&
- fdr(10)(0)&" "&fixed_l(2)(stripP(com_str[strA[i]]))&" 0 0 0 0"; endfor
+ fdr(10)(0)&" "&fixed_l(2)(stripP(strD[strA[i]]))&" 0 0 0 0"; endfor
for i=1 upto cntB: if lineB[i]<>0:
if (lineB[i]=dl)or(lineB[i]=dr)or(lineB[i]=dm): nA:=2;
elseif lineB[i]=tm: nA:=3;
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-02 10:18:05 +0000