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authorKarl Berry <karl@freefriends.org>2016-07-10 21:52:35 +0000
committerKarl Berry <karl@freefriends.org>2016-07-10 21:52:35 +0000
commit50db036c4ba61b0a354745f3fc62555afd46b76c (patch)
tree2a7727db43bebeb9f0fab6100d6b4f60472ea165
parent0448ce7927c7bc44875fa237b862a7ac7bc4811d (diff)
mcf2graph (10jul16)
git-svn-id: svn://tug.org/texlive/trunk@41674 c570f23f-e606-0410-a88d-b1316a301751
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG6
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/README6
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf17
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdfbin247779 -> 241608 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex14
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-031.eps77
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-035.eps77
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf43
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdfbin426998 -> 430115 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex63
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdfbin123534 -> 123678 bytes
-rw-r--r--Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf20
12 files changed, 165 insertions, 158 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
index 0b559cd94c8..d214c28b950 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
@@ -1,6 +1,10 @@
*******************************************************************************
- Changelog of mcf2graph software package by Akira Yamaji 2016-06-19
+ Changelog of mcf2graph software package by Akira Yamaji 2016-07-10
*******************************************************************************
+[ver. 3.95 / 2016-07-10]
+ -improve bond type 'ov'
+ -update MCF syntax manual and example
+
[ver. 3.94 / 2016-06-19]
-set maximum ratio atom size / bond length to 0.8
for avoid error when font size is very small
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README
index 6a03f94c432..45491fa57d8 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 : 3.94 2016-06-19
+ version : 3.95 2016-07-10
E-mail : mcf2graph@gmail.com
Located at : http://www.ctan.org/pkg/mcf2graph
********************************************************************************
@@ -19,14 +19,14 @@
( 3) mcf2graph.mf Macro of Metafont / Metapost
( 4) mcf_manual.tex MCF syntax manual(LaTeX file)
( 5) mcf_man_soc.mf Molecular difinition file for mcf_manual.tex
- ( 6) mcf_man_soc-031.eps No.31 EPS(with color) file of (4)
+ ( 6) mcf_man_soc-035.eps No.31 EPS(with color) file of (4)
( 7) mcf_manual.pdf PDF of (4) (used LaTeX,dvipdfmx)
( 8) mcf_example.tex LaTeX example,
Make file 'mcf_exa_soc-info.aux' before typeset
>mpost -s ahangle=0 mcf_exa_soc.mf
( 9) mcf_exa_soc.mf Molecular difinition file for mcf_example.tex
(10) mcf_example.pdf PDF of (8) (used LaTeX,dvipdfmx)
- (11) mcf_mplib_exa.tex luamplib v2.11(LuaLaTeX) example
+ (11) mcf_mplib_exa.tex luamplib(LuaLaTeX) example
(12) mcf_example.pdf PDF of (11) typeset with LuaTeX(LuaLaTeX)
3. How to use mcf2graph with Metapost
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 72c2aef5a87..dcc3ebbcdb0 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
@@ -3,8 +3,8 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
input mcf2graph.mf;
%-------------------------------------------------------------------------
-font_wd#:=35mm#;
-font_ht#:=25mm#;
+font_wd#:=33mm#;
+font_ht#:=24mm#;
max_bond_width:=0.15;
%-------------------------------------------------------------------------
sw_auxout:=1;
@@ -12,6 +12,9 @@ sw_font_frame:=0;
sw_atom_frame:=0;
sw_expand:=0;
sw_start_vector:=0;
+var3:="cal_FM"; tag3:="cFM";
+var4:="cal_MW"; tag4:="cMW";
+%%%% outputtemplate:="%3c-%j.png";
%%%% sw_auxfix:=1;
%%%% var3:="len_x"; tag3:="Lx";
%%%% var4:="len_y"; tag4:="Ly";
@@ -189,7 +192,7 @@ endfont
beginfont("EN:Ampicillin")
MCf(<45,?4,-3=?5,2:N,7:S,
@(3^45,4^-45)/*H,1://O^15,5:/*COOH^-18,@(6^35,6^-35)/Me,
- ,4\^75,NH,!,//O,!,NH,!,Ph)
+ ,4*\^75,NH,!,//O,!,/*NH2,!,Ph)
endfont
%***************************************************************************
beginfont("EN:Validamycin")
@@ -272,8 +275,8 @@ beginfont("EN:Emetine")
endfont
%***************************************************************************
beginfont("EN:Colchicine")
- MCf(<30,Ph,@(1,2,6)/OMe,|,-4=?7,|,-5=?7,$(-1,-4,-6)dl,-2://O,-3:/OMe,
- #9\,NH,!,//O,!)
+ MCf(<30,Ph,@(1,2,6)/OMe,-4=?7,-5=?7,$(-1,-4,-6)dl,-2://O,-3:/OH,
+ 9\,NH,!,//O,!)
endfont
%***************************************************************************
beginfont("EN:Caffeine")
@@ -309,7 +312,7 @@ beginfont("EN:Podophyllotoxin");
endfont;
%***************************************************************************
beginfont("EN:Warfarin");
- MCf(<30,Ph,3=?6,10:O,7:/OH,9://O,8\,/Ph`1,60,!,//O,!)
+ MCf(<30,Ph,3=?6,8=dl,10:O,7:/OH,9://O,8\,/Ph`1,60,!,//O,!)
endfont;
%***************************************************************************
beginfont("EN:Genistein");
@@ -387,3 +390,5 @@ beginfont("EN:Atoropin")
endfont
%***************************************************************************
bye
+*****
+bye
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf
index 85414e94da6..4d1aeb8c6d0 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_example.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex
index 5ebaf163b5c..26e298caed9 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2016.4.28
+% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2016.7.10
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage{graphicx}
@@ -26,13 +26,13 @@
\ifx\@tag\@Lx\edef\MOLlenx{\@var}\fi \ifx\@tag\@Ly\edef\MOLleny{\@var}\fi%
\ifx\@tag\@EN\edef\MOLnameE{\@var}\fi \ifx\@tag\@JN\edef\MOLnameJ{\@var}\fi%
\ifx\@tag\@CAS\edef\MOLcas{\@var}\fi \ifx\@tag\@USE\edef\MOLuse{\@var}\fi%
- \ifx\@tag\@FM\edef\MOLfm{\@var}\fi \ifx\@tag\@FMc\edef\CALfm{\@var}\fi%
- \ifx\@tag\@MW\edef\MOLmw{\@var}\fi \ifx\@tag\@MWc\edef\CALmw{\@var}\fi%
+ \ifx\@tag\@FM\edef\MOLfm{\@var}\fi \ifx\@tag\@cFM\edef\CALfm{\@var}\fi%
+ \ifx\@tag\@MW\edef\MOLmw{\@var}\fi \ifx\@tag\@cMW\edef\CALmw{\@var}\fi%
\ifx\@tag\@logP\edef\MOLlogP{\@var}\fi \ifx\@tag\@EXA\edef\MOLextA{\@var}\fi%
\ifx\@tag\@EXB\edef\MOLextB{\@var}\fi \ifx\@tag\@NO\edef\MOLnum{\@var}\fi\fi}%
%-------------------------------------------------------------------------------
\def\@F{F}\def\@C{C}\def\@EN{EN}\def\@JN{JN}\def\@CAS{CAS}%
-\def\@MW{MW}\def\@MWc{MWc}\def\@FM{FM}\def\@FMc{FMc}\def\@Lx{Lx}\def\@Ly{Ly}%
+\def\@MW{MW}\def\@cMW{cMW}\def\@FM{FM}\def\@cFM{cFM}\def\@Lx{Lx}\def\@Ly{Ly}%
\def\@NO{NO}\def\@USE{USE}\def\@logP{logP}\def\@EXA{EXA}\def\@EXB{EXB}%
%-------------------------------------------------------------------------------
\def\@fst@param#1:#2;{#1}\def\@sec@param#1:#2;{#2}%
@@ -43,6 +43,8 @@
\begin{picture}(\@tempcntb,\@tempcnta)%
\advance\@tempcnta -300\relax%
\put(20,\@tempcnta){\tiny\bf [\the\fontnum] \MOLnameE}%
+ \advance\@tempcnta -250\relax%
+ \put(20,\@tempcnta){\tiny\tt FM:\CALfm { / }MW:\CALmw}%
\put( 0,0){\makebox(\@tempcntb,\@tempcnta){\@stru{\MOLfile}[\MOLchar]}}%
\end{picture}%
\advance\fontnum\@ne\relax\advance\tnum\@ne\relax%
@@ -68,8 +70,10 @@
\begin{center}
{\LARGE\bf Molecular Coding Format examples}\vspace{5mm}\\
Author : Akira Yamaji \quad Date : \today\\
- Located at : http://www.ctan.org/pkg/mcf2graph\vspace{7mm}\\
+ Located at : http://www.ctan.org/pkg/mcf2graph\vspace{3mm}\\
\end{center}
+{\footnotesize ** FM:Molecular formula calculated by mcf2graph \quad
+ ** MW:Molecular weight calculated by mcf2graph}\vspace{3mm}\\
\fontnum=1%
\noindent%
%------------------------------------------------------------------------
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-031.eps b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-031.eps
deleted file mode 100644
index eaab8f569eb..00000000000
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-031.eps
+++ /dev/null
@@ -1,77 +0,0 @@
-%!PS
-%%BoundingBox: 47 13 112 86
-%%HiResBoundingBox: 47.18906 13.67542 111.88002 85.53699
-%%Creator: MetaPost 1.999
-%%CreationDate: 2016.01.16:0956
-%%Pages: 1
-%%BeginProlog
-%%EndProlog
-%%Page: 1 1
- 0 0 0 setrgbcolor 0 0.65842 dtransform truncate idtransform setlinewidth pop
- [] 0 setdash 1 setlinecap 1 setlinejoin 10 setmiterlimit
-newpath 58.52762 34.29977 moveto
-78.5395 22.74597 lineto stroke
-newpath 63.62425 37.00446 moveto
-80.98482 26.98138 lineto stroke
-newpath 91.53891 22.74586 moveto
-111.55081 34.29977 lineto stroke
- 0 1 0 setrgbcolor 0.65842
- 0 dtransform exch truncate exch idtransform pop setlinewidth
-newpath 111.55081 34.29977 moveto
-111.55081 64.91264 lineto stroke
-newpath 106.66019 37.36125 moveto
-106.66019 61.85117 lineto stroke
- 0 0 0 setrgbcolor 0 0.65842 dtransform truncate idtransform setlinewidth pop
-newpath 111.55081 64.91264 moveto
-91.53891 76.46645 lineto stroke
-newpath 78.5395 76.46654 moveto
-58.52762 64.91264 lineto stroke
-newpath 80.98482 72.23112 moveto
-63.62425 62.20796 lineto stroke
- 0.65842 0 dtransform exch truncate exch idtransform pop setlinewidth
-newpath 58.52762 64.91264 moveto
-58.52762 34.29977 lineto stroke
- 1 0 0 setrgbcolor
-newpath 79.7213 13.67542 moveto
-80.70894 13.67542 lineto
-80.70894 24.31123 lineto
-79.7213 24.31123 lineto
- closepath fill
-newpath 89.36948 13.67542 moveto
-90.35712 13.67542 lineto
-90.35712 24.31123 lineto
-89.36948 24.31123 lineto
- closepath fill
-newpath 81.10399 24.31123 moveto
-79.7213 24.31123 lineto
-88.97443 13.67542 lineto
-90.35712 13.67542 lineto
- closepath fill
- 0 0 1 setrgbcolor
-newpath 79.7213 74.90117 moveto
-80.70894 74.90117 lineto
-80.70894 85.53699 lineto
-79.7213 85.53699 lineto
- closepath fill
-newpath 89.36948 74.90117 moveto
-90.35712 74.90117 lineto
-90.35712 85.53699 lineto
-89.36948 85.53699 lineto
- closepath fill
-newpath 81.10399 85.53699 moveto
-79.7213 85.53699 lineto
-88.97443 74.90117 lineto
-90.35712 74.90117 lineto
- closepath fill
- 0 0 0 setrgbcolor
-newpath 55.69298 33.16591 moveto
-55.69298 35.43364 lineto
-47.18906 35.43364 lineto
-47.18906 33.16591 lineto
- closepath fill
-newpath 52.85834 31.46513 moveto
-58.52762 34.29977 lineto
-52.85834 37.13441 lineto
- closepath fill
-showpage
-%%EOF
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-035.eps b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-035.eps
new file mode 100644
index 00000000000..f307e5d2162
--- /dev/null
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-035.eps
@@ -0,0 +1,77 @@
+%!PS
+%%BoundingBox: 47 20 112 93
+%%HiResBoundingBox: 47.18906 20.76202 111.88002 92.6236
+%%Creator: MetaPost 1.9991
+%%CreationDate: 2016.07.10:0747
+%%Pages: 1
+%%BeginProlog
+%%EndProlog
+%%Page: 1 1
+ 0 0 0 setrgbcolor 0 0.65842 dtransform truncate idtransform setlinewidth pop
+ [] 0 setdash 1 setlinecap 1 setlinejoin 10 setmiterlimit
+newpath 58.52762 41.38638 moveto
+78.5395 29.83258 lineto stroke
+newpath 63.62425 44.09106 moveto
+80.98482 34.068 lineto stroke
+newpath 91.53891 29.83247 moveto
+111.55081 41.38638 lineto stroke
+ 0 1 0 setrgbcolor 0.65842
+ 0 dtransform exch truncate exch idtransform pop setlinewidth
+newpath 111.55081 41.38638 moveto
+111.55081 71.99925 lineto stroke
+newpath 106.66019 44.44786 moveto
+106.66019 68.93777 lineto stroke
+ 0 0 0 setrgbcolor 0 0.65842 dtransform truncate idtransform setlinewidth pop
+newpath 111.55081 71.99925 moveto
+91.53891 83.55305 lineto stroke
+newpath 78.5395 83.55315 moveto
+58.52762 71.99925 lineto stroke
+newpath 80.98482 79.31773 moveto
+63.62425 69.29457 lineto stroke
+ 0.65842 0 dtransform exch truncate exch idtransform pop setlinewidth
+newpath 58.52762 71.99925 moveto
+58.52762 41.38638 lineto stroke
+ 1 0 0 setrgbcolor
+newpath 79.7213 20.76202 moveto
+80.70894 20.76202 lineto
+80.70894 31.39784 lineto
+79.7213 31.39784 lineto
+ closepath fill
+newpath 89.36948 20.76202 moveto
+90.35712 20.76202 lineto
+90.35712 31.39784 lineto
+89.36948 31.39784 lineto
+ closepath fill
+newpath 81.10399 31.39784 moveto
+79.7213 31.39784 lineto
+88.97443 20.76202 lineto
+90.35712 20.76202 lineto
+ closepath fill
+ 0 0 1 setrgbcolor
+newpath 79.7213 81.98778 moveto
+80.70894 81.98778 lineto
+80.70894 92.6236 lineto
+79.7213 92.6236 lineto
+ closepath fill
+newpath 89.36948 81.98778 moveto
+90.35712 81.98778 lineto
+90.35712 92.6236 lineto
+89.36948 92.6236 lineto
+ closepath fill
+newpath 81.10399 92.6236 moveto
+79.7213 92.6236 lineto
+88.97443 81.98778 lineto
+90.35712 81.98778 lineto
+ closepath fill
+ 0 0 0 setrgbcolor
+newpath 55.69298 40.25252 moveto
+55.69298 42.52025 lineto
+47.18906 42.52025 lineto
+47.18906 40.25252 lineto
+ closepath fill
+newpath 52.85834 38.55174 moveto
+58.52762 41.38638 lineto
+52.85834 44.22102 lineto
+ closepath fill
+showpage
+%%EOF
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 7669ddb210e..e36123c5a99 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2016.04.10
+% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2016.07.10
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
input mcf2graph.mf;
%------------------------------------------------------------------------
@@ -13,19 +13,6 @@ sw_expand:=0;
sw_start_vector:=0;
%%%%%sw_checklist:=1;
%***********************************************************************
-beginfont("NO:1","EN:Chlorophyll a","MW:893.49","FM:C55H72MgN4O5")
- font_wd#:=80mm#;
- font_ht#:=30mm#;
- MCf(<54,
- {,``1,?5,3\,54,?5,-2\,54,?5,-2\,54,,?5,-2\,&5,
- -1*,24,/*COOMe^15,72,//O,&1,},
- 4\`1.48,Mg,&17,-1*,&11~vb,-1*,&23~vb,
- $(2,5,7,9,11,14,16,20,26,27)dl,@(4,11,17,23)N,
- @(2,9,15,20~zf)/Me,8:/Et,14\,!~dr,
- 21*,-6~wf,!2,//O,!,O,!2,!~dl,|,!13,@(1,5,9,13)/Me,
- )
-endfont
-%***********************************************************************
beginfont("EN:Chain 1")
sw_numberB:=1;
numberB_end:=6;
@@ -83,7 +70,7 @@ endfont
%***********************************************************************
beginfont("EN:change bond 3")
ratio_chain_ring:=1;
- MCf(<30,!5,1=bz,$(2,4)dr,@(3~bd^-45`2,5~ov^45`2)/Me)
+ MCf(<30,!3,!`2,!,$(2,4)dr,@(3~bd`2^-30,5~ov^85`3,3~bz`3^-70)/Me)
endfont
%***********************************************************************
beginfont("EN:change bond length1")
@@ -505,25 +492,25 @@ MCf(<30,?6,-4=?5,$(3,8)dl,@(2,6,7,9)N,@(2,6,9)/Me,@(1,5)//O)
endfont
%***********************************************************************
%% Output additional infomation
-beginfont("EN:Tocopherol","CAS:59-02-9")
+beginfont("EN:Tocopherol","CAS:59-02-9","FM:C29H50O2","MW:430.71")
sw_logout:=1;
MCf(<30,Ph,3=?6,7:O,@(1,2,5)/Me,8:/*Me^60,6:/OH,8\,|,!12,@(4,8)/*Me,12:/Me)
endfont
%***********************************************************************
%% Change infomation separater
-beginfont("EN:Warfarin","CAS:81-81-2")
-MCf(<30,Ph,3=?6,10:O,7:/OH,9://O,8\,/Ph`1,60,!,//O,!)
+beginfont("EN:Warfarin","CAS:81-81-2","FM:C19H16O4","MW:308.33")
+MCf(<30,Ph,3=?6,8=dl,10:O,7:/OH,9://O,8\,/Ph`1,60,!,//O,!)
endfont
%***********************************************************************
-beginfont("EN:Ampicillin")
+beginfont("EN:Ampicillin","CAS:69-53-4","FM:C16H19N3O4S","MW:349.40")
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,!,NH,!,Ph
+ 4*\^75,NH,!,//O,!,/*NH2,!,Ph
)
endfont
%***********************************************************************
-beginfont("EN:Cholesterol")
+beginfont("EN:Cholesterol","CAS:57-88-5","FM:C27H46O","MW:386.65")
MCf(
<30,?6,$(-4,-2)?6,-4=?5,7=dl,
1:*/OH,@(4,12)*/Me^60,9:*/H^60,
@@ -532,20 +519,20 @@ beginfont("EN:Cholesterol")
)
endfont
%***************************************************************************
-beginfont("EN:Colchicine")
+beginfont("EN:Colchicine","CAS:477-27-0","FM:C21H23NO6","MW:385.41")
MCf(<30,Ph,@(1,2,6)/OMe,|,-4=?7,
- |,-5=?7,$(-1,-4,-6)dl,-2://O,-3:/OMe,
+ |,-5=?7,$(-1,-4,-6)dl,-2://O,-3:/OH,
#9\,NH,!,//O,!)
endfont
%***************************************************************************
-beginfont("EN:Lycorine")
+beginfont("EN:Lycorine","CAS:476-28-8","FM:C16H17NO4","MW:287.31")
MCf(<30,
Ph,-4=?6,-2=?6,6=?5,(9,12)=?5[3],13=dl,8:N,@(15,17)O,
9:/*H^180,10:*/H^60,13:*/OH,14:/*OH
)
endfont
%***********************************************************************
-beginfont("EN:Gibberellin A3");
+beginfont("EN:Gibberellin A3","CAS:77-06-5","FM:C19H22O6","MW:346.37");
MCf(
<12,?6`1.3,3=?5,9=?7,12\^160`1.6,&8,
4\^155~zf`1.2,O,55,//O^180`1,&2~zb,
@@ -554,17 +541,17 @@ beginfont("EN:Gibberellin A3");
)
endfont
%***************************************************************************
-beginfont("EN:Quinine")
+beginfont("EN:Quinine","CAS:130-95-0","FM:C20H24N2O2","MW:324.42")
MCf(<30,Ph,3=Ph,7:N,6:/OMe,
10\,*/OH,/H~zf^-60,!,|,?6,2:N,1:*/H^60,4*\,!~dr,2*,165~zf,60,&5~zb)
endfont
%***************************************************************************
-beginfont("EN:Atoropin")
+beginfont("EN:Atoropin","CAS:51-55-8","FM:C17H23NO3","MW:289.37")
MCf(<-30,O,!,//O,!,!,Ph,
#1\~zb^-120,|,?7`1.1,6*\^190`1.25,N,/Me,&3~wb,#3\~wv,!,OH)
endfont
%***************************************************************************
-beginfont("EN:Paclitaxel")
+beginfont("EN:Paclitaxel","CAS:33069-62-4","FM:C47H51NO14","MW:853.91")
MCf(?6,5=d,3*,{,``1,36,45,45,45,45,},
&#5,-4=?6,-4=?4,-1=wb,-3=wf,-1:O,||,
@(4^35,4^-35,6)/Me,@(3^-60,15)*/OH,8:/*H^-60,9:*/Me^60,10://O,
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf
index 497483dd58b..dbb8d181986 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 bea273959d1..567ca20244c 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex
@@ -1,8 +1,9 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format manual by Akira Yamaji 2016.06.11
+% Molecular Coding Format manual by Akira Yamaji 2016.07.10
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
-\usepackage[dvipdfmx]{graphicx}
+\usepackage{graphicx}
+%%%%\usepackage[dvipdfmx]{graphicx}
%%%%\usepackage[pdftex]{graphicx}
%%%%\usepackage{epstopdf}
\topmargin=-18mm
@@ -18,7 +19,7 @@
\newdimen \gpman%
\htman=47mm%
\gpman=4mm%
-\fontnum=1%
+\fontnum=0%
\tempnum=1%
%----------------------------------------------------------------------------
\font\@strufont=mcf_man_soc\relax%
@@ -47,11 +48,10 @@
\ifx\@tag\@cFM\edef\CALfm{\@var}\fi
\fi}%
\def\put@char{%
- \begin{picture}(120,42)%
- \put(0,35){\bf [\MOLnum] \MOLnameE}%
- \put(6,30){\tt MW:\CALmw}%
- \put(6,25){\tt FM:\CALfm}%
- \put(40,0){\font\@strufont=\MOLfile\relax%
+ \begin{picture}(84,50)%
+ \put(0,45){\bf [\MOLnum]\MOLnameE}%
+ \put(5,40){\small\tt FM:\CALfm{ }MW:\CALmw}%
+ \put(10,0){\font\@strufont=\MOLfile\relax%
\hbox{\@strufont\char\MOLchar}}%
\end{picture}%
}
@@ -107,28 +107,37 @@ beginfont("NO:2","EN:Cholesterol") > begin font(information)
endfont > end font
%------------------------------------------------------------------------
bye
+
\end{verbatim}
-%----------------------------------------------------------------------------
+%------------------------------------------------------------------------
+{\bf (Molecular structure output)}\vspace{5mm}\\
+\INFO{F:mcf_man_soc,C:84,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
+\INFO{F:mcf_man_soc,C:85,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
+\newpage
+%------------------------------------------------------------------------
\noindent%
-{\bf (Molecular information output)}\\
+{\bf (Molecular information output)}\vspace{2mm}\\
'filename'-info.aux : for use in \TeX, it takes over filename,
char number, molecular information,etc.
\begin{verbatim}
(sw_auxfix=0)
-F:mcf_man_soc;C:85;cMW:335.37805;cFM:C15H17N3O4S;EN:Ampicillin
+F:mcf_man_soc;C:85;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin
F:mcf_man_soc;C:86;cMW:386.6532;cFM:C27H46O;EN:Cholesterol
.....................................................
+ .....................................................
(sw_auxfix=1)
F;C;cMW;cFM;EN
-mcf_man_soc;85;335.37805;C15H17N3O4S;Ampicillin
+mcf_man_soc;85;349.40462;C16H19N3O4S;Ampicillin
mcf_man_soc;86;386.6532;C27H46O;Cholesterol
......................................
+ ......................................
( tag : variable )
F : filename C : char number NO : serial number EN : english name
cMW : molecular weight calculated cFM : molecular formula calculated
MW : molecular weight from literature data
+
\end{verbatim}
%----------------------------------------------------------------------------
{\bf (LaTeX file example)}
@@ -154,28 +163,22 @@ MW : molecular weight from literature data
\ifx\@tag\@FMc\edef\CALfm{\@var}\fi
\fi}%
\def\put@char{%
- \begin{picture}(120,45)%
- \put(10,35){\bf [\MOLnum] \MOLnameE}%
- \put(16,30){\sf MW:\CALmw}%
- \put(16,25){\sf FM:\CALfm}%
- \put(20,0){\font\@strufont=\MOLfile\relax%
+ \begin{picture}(84,42)%
+ \put(0,38){\bf [\MOLnum]\MOLnameE{ }\small\tt/FM:\CALfm/MW:\CALmw}%
+ \put(10,0){\font\@strufont=\MOLfile\relax%
\hbox{\@strufont\char\MOLchar}}%
- \end{picture}}%
+ \end{picture}%
\def\INFO#1{\@for\@temp:=#1\do{\mol@sel\@temp}\put@char}%
\makeatother
%--------------------------------------------------------------------
\begin{document}
\unitlength=1mm%
-\INFO{F:mcf_man_soc,C:85,NO:1,cMW:335.37805,cFM:C15H17N3O4S,EN:Ampicillin}\\%
+\INFO{F:mcf_man_soc,C:85,NO:1,cMW:349.40462,cFM:C16H19N3O4S,EN:Ampicillin}%
\INFO{F:mcf_man_soc,C:86,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
\end{document}
%--------------------------------------------------------------------
\end{verbatim}\vspace{5mm}%
%############################################################################
-{\bf (Molecular structure output)}\\
-\INFO{F:mcf_man_soc,C:85,NO:1,cMW:335.37805,cFM:C15H17N3O4S,EN:Ampicillin}\\%
-\INFO{F:mcf_man_soc,C:86,NO:2,cMW:386.6532,cFM:C27H46O,EN:Cholesterol}%
-\newpage
%----------------------------------------------------------------------------
\noindent
%-----------------------------------------------------------------------------
@@ -299,8 +302,8 @@ bz : broad dotted
ov : over line
$(2,4)dr : 2=dr,4=dr
- <30,!5,1=bz,$(2,4)dr,
- @(3~bd^-45`2,5~ov^45`2)/Me
+<30,!3,!`2,!,$(2,4)dr,
+ @(3~bd`2^-30,5~ov`3^85,3~bz`3^-70)/Me
** 3~bd^-45`2 : ~~bd,^^-45,'`2,3
\end{verbatim}
@@ -669,8 +672,8 @@ $(3)red : change color of B3 red
\end{minipage}
%%%%\MCFstructure % for Metafont
\makebox(72,3.5)[t]{\frame{\makebox(68,42.3)%
-{\includegraphics{mcf_man_soc-031.eps}}}}% for dvipdfmx
-%%%%{\includegraphics[width=30mm]{mcf_man_soc-031.png}}}}% for pdfLaTeX
+{\includegraphics{mcf_man_soc-035.eps}}}}% for dvipdfmx
+%%%%{\includegraphics[width=30mm]{mcf_man_soc-035.png}}}}% for pdfLaTeX
\advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
\vspace{\gpman}\\
%-----------------------------------------------------------------------------
@@ -1245,9 +1248,9 @@ mcf_man_soc;88;1;Ampicillin
\begin{minipage}[t][\htman]{90mm}
\MCFtitle{Example(2) Colchicine}
\begin{verbatim}
- <30,Ph,@(1,2,6)/OMe,|,-4=?7,
- |,-5=?7,$(-1,-4,-6)dl,-2://O,-3:/OMe,
- #9\,NH,!,//O,!
+ <30,Ph,@(1,2,6)/OMe,-4=?7,-5=?7,
+ $(-1,-4,-6)dl,-2://O,-3:/OH,
+ 9\,NH,!,//O,!
\end{verbatim}
\end{minipage}
\MCFstructure
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 f10f5040e36..39f0f2fe7ec 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 ccff8ecd160..06e221df212 100644
--- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
+++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% mcf2graph ver 3.94 Copyright (c) 2013-2016 Akira Yamaji
+% mcf2graph ver 3.95 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,
@@ -30,7 +30,7 @@
% Set output checklist : mpost -s ahlength=2 FILENAME
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tracingstats:=1;
-message " This is mcf2graph ver 3.9 2016.6";
+message " This is mcf2graph ver 3.9 2016.7";
%-------------------------------------------------------------------------------------------------
pair posB[],posA[],pairT,Ls,Le,pairA;
numeric angB[],angA[],br_ang[],sB[],eB[],f_FON[],atom_w[],atom_h[],atom_d[],strA[],stkB[],stkA[],
@@ -50,6 +50,7 @@ aux_delimiter:=";"; var1:="jobname"; tag1:="F"; var2:="char_num"; tag2:="C";
for i=3 upto aux_max: var[i]:=tag[i]:=""; endfor
%-------------------------------------------------------------------------------------------------
if known green: f_MP:=1;
+ color color_list[];
mp_log_name:=jobname&"-info.aux";
if ahlength=1: proc_end:=1; fi % first molecular only
if ahlength=2: sw_checklist:=1; def shipit = enddef; fi % checklist on
@@ -59,15 +60,17 @@ if known green: f_MP:=1;
elseif ahangle=3: sw_MOLout:=1; def shipit = enddef; % MDL Molefile on
fi
outputtemplate:="%j-%3c."&outputformat;
- def beginchar(text s)= beginfig(char_num) enddef; def endchar = endfig enddef;
- vardef mp_filename = jobname&"-"&fit_zero(char_num)&decimal(char_num)&"."&outputformat enddef;
+ def beginchar(text s)= beginfig(char_num) enddef;
+ def endchar = endfig enddef;
def printf expr s= write s to mp_log_name enddef;
- ahangle:=45; ahlength:=4; def # = enddef; color color_list[];
+ def # = enddef;
def Cp(expr s) = if known s: if s<>0: withcolor color_list[s] fi fi enddef;
def define_pixels(text s) = enddef;
else: f_MP:=0;
def Cp(expr s) = enddef; def color = transform enddef;
- mode_setup; def printf expr s= message s enddef; def mp_filename= "" enddef; fi
+ mode_setup; def printf expr s= message s enddef;
+fi
+ahangle:=45; ahlength:=4;
clearit; chem_structure:=currentpicture;
%-------------------------------------------------------------------------------------------------
let DIV= /; let MUL= *; let LT= <; let GT= >; let AND= &; let :: = : ; let == = =;
@@ -351,7 +354,8 @@ def MCd(expr RW,RH)(expr FW,FH)(text s)=
else: for i=1 upto 4: proc_skeleton; scaling; resize(RW,RH); size_setup; endfor fi fi
font_setup;
if sw_subst_off=1: cntA:=cntA_skeleton; cntB:=cntB_skeleton; fi
- for i=1 upto cntB: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); endfor
+ for i=1 upto cntB: if lineB[i]<>ov: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
+ for i=1 upto cntB: if lineB[i]=ov: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
for i=1 upto cntA:
if (sw_numberA>=1)and(i>=numberA_start)and(i<=numberA_end):
if sw_numberA=2: nA:=i-numberA_start+1;
@@ -792,7 +796,7 @@ def mol_check=
if com_str[strA[i]]="": com_str[strA[i]]:="C"; fi
if com_str[strA[i]]="C": if nA<4: hide_H:=hide_H+(4-nA); 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);
+ 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]]=tblA[j]:
if tblN[j]=0: sumA[j]:=sumA[j]+1;