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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG6
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/README4
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf55
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdfbin306332 -> 306745 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex3
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf39
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdfbin575278 -> 597534 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex146
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdfbin201949 -> 201981 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex16
-rw-r--r--Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf69
11 files changed, 230 insertions, 108 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
index b3bcfd022ec..a162e00951a 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 2020-08-30
+ Changelog of mcf2graph software package by Akira Yamaji 2020-11-03
*******************************************************************************
+[ver. 4.53 / 2020-11-03]
+ -improve inline definition
+ -update MCF manual(add index),example
+
[ver. 4.52 / 2020-08-30]
-improve aux file output,input
-update MCF manual,example
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README
index 7f830cef14d..1946281e8df 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 : 4.52 2020-08-30
+ version : 4.53 2020-11-03
E-mail : mcf2graph@gmail.com
Located at : http://www.ctan.org/pkg/mcf2graph
********************************************************************************
@@ -21,7 +21,7 @@
( 4) mcf_setup.sty Style file for aux file input
( 5) mcf_manual.tex MCF syntax manual(LaTeX file)
( 6) mcf_man_soc.mf Molecular difinition file for mcf_manual.tex
- ( 7) mcf_manual.pdf PDF of (4) (used pdftex(LaTeX))
+ ( 7) mcf_manual.pdf PDF of (4) (used pdftex(LaTeX),makeindex)
( 8) mcf_example.tex LaTeX example,
Make file 'mcf_exa_soc-info.aux' before typeset
>mpost -s ahlength=1 mcf_exa_soc.mf
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 8cbd78defec..dae7e38efab 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
@@ -1,13 +1,13 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2020.08.30
+% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2020.11.03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %%% it must be version 4.52 or later
+input mcf2graph.mf; %%% it must be version 4.53 or later
%-------------------------------------------------------------------------
fsize:=(33mm,24mm);
max_blength:=4.5mm;
%-------------------------------------------------------------------------
%%%%sw_aux_out:=1;
-%%%%sw_fframe:=1;
+%%%%sw_fframe:=4;
%%%%sw_aframe:=1;
%%%%sw_mframe:=1;
%%%%sw_expand:=1;
@@ -28,11 +28,12 @@ tag1:="F"; tag2:="C"; tag3:="fm"; tag4:="mw"; tag5:="EN"; tag6:="MW";
%%%% for i=nA step nA until h: draw(0,i)--(w,i); endfor );
%***************************************************************************
beginfont("EN:Imidacloprid","MW:255.662")
- MC(<30,Ph,1:N,6:/Cl,3:\,!,|,?5,2=dl,1:N,3:N,2:\,NH,!,NO2)
+ MC(<30,Ph,1:N,6:/Cl,3:\,!,|,?5,2=dl,1:N,3:N,2:/'(NH,!,NO2))
endfont
%***************************************************************************
beginfont("EN:Thiamethoxam","MW:291.71")
- MC(<30,?6,{4,6}:N,2:O,6:/_,5:\\,N,!,NO2,4:\,!,|,?5,{1,3}=dl,3:N,5:S,4:/Cl)
+ MC(<30,?6,{4,6}:N,2:O,6:/_,5://'(N,!,NO2),
+ 4:\,!,|,?5,{1,3}=dl,3:N,5:S,4:/Cl)
endfont
%***************************************************************************
beginfont("EN:Pyridaphenthion","MW:340.334")
@@ -40,17 +41,17 @@ beginfont("EN:Pyridaphenthion","MW:340.334")
endfont
%***************************************************************************
beginfont("EN:Permethrin","MW:391.288")
- MC(<-30,?3,2^-35:*/_,2^35:/*_,1:\,!!,/Cl,!,Cl,
+ MC(<-30,?3,2^-35:*/_,2^35:/*_,1:/'(!!,/Cl,!,Cl),
3:\,//O,!,O,!2,|,Ph,3:\,O,-60,Ph)
endfont
%***************************************************************************
beginfont("EN:Isoprothiolane","MW:290.392")
- MC(<-30,!,/_,!,O,!,//O,|,!2,//O,!,O,!,/_,!,2:\\,|,?5,{2,5}:S)
+ MC(<-30,!,/_,!,O,!,//O,!,//'(?5,2:S,5:S),!,//O,!,O,!,/_,!)
endfont
%***************************************************************************
beginfont("EN:Oxine-Copper","MW:351.852")
- MC(Ph,4:N,5=Ph,-4:\,O,-60,<90,Cu,-90,O,60,|,Ph,5=Ph,10:N,
- ||,4:@,12~vf:#,23:@,12~vf:#)
+ MC(Ph,4:N,5=Ph,-4:\,O,-60,<90,Cu,-90,O,60,|,Ph,5=Ph,10:N,||,
+ 4:@,12~vf:#,23:@,12~vf:#)
endfont
%***************************************************************************
beginfont("EN:Tetraconazole","MW:372.145")
@@ -65,7 +66,7 @@ beginfont("EN:Endosulfan","MW:406.904");
endfont;
%***************************************************************************
beginfont("EN:Oxadiargyl","MW:341.19")
- MC(<30,Ph,{1,3}:/Cl,4:\,|,?5,2=d,{1,2}:N,4:O,5://O,-3:/tBu,$6:\,O,!2,!!!)
+ MC(<30,Ph,{1,3}:/Cl,6:/'(O,!2,!!!),4:\,|,?5,2=d,{1,2}:N,4:O,5://O,-3:/tBu)
endfont
%***************************************************************************
beginfont("EN:Oxaziclomefone","MW:376.277")
@@ -146,21 +147,21 @@ endfont
beginfont("EN:Cefquinome","MW:627.6903")
MC(<45,?4,-3=?6,-4=dl,2:N,8:S,
3^45:/*H,1://O^15,5:/*COOH,
- 4:*\^15,NH,!,//O,!2,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2,-6:\\,N,-60,O,!,
+ 4:*\^15,NH,!,//O,!,//'(N,!,O,!),!,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2,
6:\,!,Ph,-2=?6,-10:N)
endfont
%***************************************************************************
beginfont("EN:Ceftiofur","MW:523.5626")
MC(<45,?4,-3=?6,-4=dl,2:N,8:S,
3^45:/*H,1://O^15,5:/*COOH,
- 4:*\^15,NH,!,//O,!2,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2,-6:\\,N,-60,O,!,
+ 4:*\^15,NH,!,//O,!,//'(N,!,O,!),!,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2,
6:\,!,S,!,//O,!,?5,{-1,-3}=dl,-4:O)
endfont
%***************************************************************************
beginfont("EN:Cefuroxime","MW:424.3852")
MC(<45,?4,-3=?6,-4=dl,2:N,8:S,
3^45:/*H,1://O^15,5:/*COOH,
- 4:*\^15,NH,!,//O,!2,?5,{-1,-3}=dl,-4:O,-6:\\,N,-60,O,!,
+ 4:*\^15,NH,!,//O,!,//'(N,!,O,!),!,?5,{-1,-3}=dl,-4:O,
6:\,!,O,!,//O,!,NH2)
endfont
%***************************************************************************
@@ -176,8 +177,7 @@ beginfont("EN:Gentamycin","MW:477.596")
MC(<-30,?6,
1:\*,O,0~zb,?6,-5:O,5:\*,O,0~zb,?6,-5:O,
{2,4}:*/NH2,20:/*NH2,6:*/OH,
- 11:*/OH^-35,11:/*_^35,12:*/NH!,13:/*OH,
- 17:\,*/_,!,NH,!)
+ 11:*/OH^-35,11:/*_^35,12:*/NH!,13:/*OH,17:/'(*/_,!NH!))
endfont
%***************************************************************************
beginfont("EN:Kanamycin","MW:484.499")
@@ -206,8 +206,8 @@ endfont
beginfont("EN:Neospiramycin","MW:698.9")
MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|,
{12,14}=dl,2:O,1:/*_,5:/*OH,3://O,10:/*_,6:/*O!>vt,
- -6:\*,O,!~wb,?6`.7,-5:O,-3:/*NMe!,-4:*/_,
- 7:\*,O,0~wb,?6`.7,-5:O,-2:*/NMe!,-1:/*OH,-4:*/_,-3:/*OH,
+ -6:\*,O,!~wb,?6`.7,-5:O,-3:/*N!_,-4:*/_,
+ 7:\*,O,0~wb,?6`.7,-5:O,-2:*/N!_,-1:/*OH,-4:*/_,-3:/*OH,
8:\*,!,!!,O)
endfont
%***************************************************************************
@@ -223,8 +223,8 @@ endfont
beginfont("EN:Spiramycin","MW:843.1")
MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|,
{12,14}=dl,2:O,1:/*_,5:/*OH,3://O,10:/*_,6:/*O!>vt,
- -6:\*,O,!~wb,?6`.7,-5:O,-3:/*NMe!,-4:*/_,
- 7:\*,O,0~wb,?6`.7,-5:O,-2:*/NMe!,-1:/*OH,-4:*/_,
+ -6:\*,O,!~wb,?6`.7,-5:O,-3:/*N!_,-4:*/_,
+ 7:\*,O,0~wb,?6`.7,-5:O,-2:*/N!_,-1:/*OH,-4:*/_,
-3:\*`1,O,60~wb`1.5,?6`.7,-5:O,{-2^35,-3}:*/OH,{-2^-35,-4}:/*_,
8:\*,!,!!,O)
endfont
@@ -233,7 +233,7 @@ beginfont("EN:Tylocin","MW:916.10")
MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|,
{12,14}=dl,2:O,1:/*!,5:/*OH,3://O,10:/*_,6:/*_,-6://O,-3:/_,
-1:*\,-60,O,0~wb,?6`.7,-5:O,-3:/*OH,-4:*/_,{-1,-2}:/*O!,
- 7:\*,O,0~wb,?6`.7,-5:O,-2:*/NMe!,-1:/*OH,-4:*/_,
+ 7:\*,O,0~wb,?6`.7,-5:O,-2:*/N!_,-1:/*OH,-4:*/_,
-3:\*`1,O,60~wb`1.5,?6`.7,-5:O,{-2^35,-3}:*/OH,{-2^-35,-4}:/*_,
8:\*,!,!!,O)
endfont
@@ -242,31 +242,31 @@ beginfont("EN:Tilmicosin","MW:869.133")
MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|,
{12,14}=dl,2:O,1:/*!,5:/*OH,{3,11}://O,{6,10}:/*_,14:/_,
-1:*\,-60,O,0~zb,?6`.7,-5:O,{-1,-2}:*/O!,-3:*/OH,-4:/*_,
- 7:\*,O,0,?6`.7,-5:O,-2:*/NMe!,{-1,-3}:/*OH,-4:*/_,
+ 7:\*,O,0,?6`.7,-5:O,-2:*/N!_,{-1,-3}:/*OH,-4:*/_,
8:\*,!2,?6`.7,-6:N,{-2,-4}:*/_)
endfont
%***************************************************************************
beginfont("EN:Chlortracyclin","MW:478.88")
MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_^-35,2:/Cl,
- {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2
+ {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2
)
endfont
%***************************************************************************
beginfont("EN:Oxytetracyclin","MW:460.434")
MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_^-35,11:*/OH,
- {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2
+ {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2
)
endfont
%***************************************************************************
beginfont("EN:Tetracyclin","MW:444.435")
MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_^-35,
- {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2
+ {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2
)
endfont
%***************************************************************************
beginfont("EN:Doxycyclin","MW:444.43")
MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_,
- {5,13~wf^60,11~wf,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2
+ {5,13~wf^60,11~wf,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2
)
endfont
%***************************************************************************
@@ -430,7 +430,7 @@ MC(<30,|=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,=|,1:#,
14:O,13:/*!,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_,
{6^35,11,12^-35}:*/OH,
$3:\*,O,30,|,?6`.7,2:O,{3,5^35}:/_,4:/OH,5^-35:/O!,
- $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMe!)
+ $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/N!_)
endfont;
%**************************************************************************
beginfont("EN:Paclitaxel","MW:853.918")
@@ -446,8 +446,7 @@ beginfont("EN:Mevastatin","MW:390.52")
endfont
%***************************************************************************
beginfont("EN:Sesamine","MW:354.35")
- MC(<54,?5,1=?5,{4,7}:O,{1^-54,2^54}:*/H,
- $5:*\^-12,Ph,|,-3=?5,{-1,-3}:O,$8:*\^-12,Ph,|,-3=?5,{-1,-3}:O)
+ MC(<54,?5,1=?5,{4,7}:O,{1^-54,2^54}:*/H,{5,8}:*/'(Ph,4=?5,7:O,9:O)^-12)
endfont
%**************************************************************************
beginfont("EN:Morphine","MW:285.343")
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf
index b412a69a436..423db59f667 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 784d2d61a2e..fcda26a9b84 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex
@@ -1,10 +1,11 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2020.08.30
+% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2020.09.22
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage{graphicx}
%---------------------
\usepackage{mcf_setup}
+%%%%\pdfpkresolution=1200
%---------------------
\pagestyle{empty}
\topmargin=-20mm
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 ea8912bda76..cd570b7e8a3 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2020.08.30
+% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2020.11.03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %% it must be version 4.52 or later
+input mcf2graph.mf; %% it must be version 4.53 or later
%------------------------------------------------------------------------
sw_mframe:=0;
sw_expand:=0;
@@ -11,7 +11,7 @@ sw_expand:=0;
%***********************************************************************
fsize:=(40mm,25mm);
blength:=6mm;
-%***********************************************************************
+%***************************************************************************
beginfont("EN:Glycine")
MC(<30,NH2,!2,COOH)
endfont
@@ -25,35 +25,35 @@ beginfont("EN:L-Valine")
endfont
%***********************************************************************
beginfont("EN:L-Leucine")
- MC(<30,NH2,!~wb,!,COOH,2:\,!,/_,!)
+ MC(<30,NH2,!~wb,/!iPr,!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Isoleucine")
- MC(<30,NH2,!~wb,!,COOH,2:\,/*_,!2)
+ MC(<30,NH2,!~wb,/'(/*_,!2),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Serine")
- MC(<30,NH2,!~wb,!,COOH,2:/!OH)
+ MC(<30,NH2,!~wb,/!OH,!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Threonine")
- MC(<30,NH2,!~wb,!,COOH,2:\,/_,!~wf,OH)
+ MC(<30,NH2,!~wb,/'(/_,!~wf,OH),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Cysteine")
- MC(<30,NH2,!~wb,!,COOH,2:/!SH)
+ MC(<30,NH2,!~wb,/!SH,!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Methionine")
- MC(<30,NH2,!~wb,!,COOH,2:\,!2,SMe)
+ MC(<30,NH2,!~wb,/'(!2,SMe),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Phenylalanine")
- MC(<30,NH2,!~wb,!,COOH,2:/!Ph)
+ MC(<30,NH2,!~wb,/!Ph,!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Tyrosine")
- MC(<30,NH2,!~wb,!,COOH,2:\,!,Ph,-3:/OH)
+ MC(<30,NH2,!~wb,/'(!Ph,-3:/OH),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Triptophan")
@@ -69,7 +69,7 @@ beginfont("EN:L-Glutamine")
endfont
%***********************************************************************
beginfont("EN:L-Asparagine")
- MC(<30,NH2,!~wb,!,COOH,2:\,!,//O,!,NH2)
+ MC(<30,NH2,!~wb,/'(!,//O,!,NH2),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Aspartic acid")
@@ -77,11 +77,11 @@ beginfont("EN:L-Aspartic acid")
endfont
%***********************************************************************
beginfont("EN:L-Glutamic acid")
- MC(<30,NH2,!~wb,!,COOH,2:\,!2,COOH)
+ MC(<30,NH2,!~wb,/'(!2,COOH),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Lysine")
- MC(<30,NH2,!~wb,!,COOH,2:\,!4,NH2)
+ MC(<30,NH2,!~wb,/'(!4,NH2),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Arginine")
@@ -97,11 +97,11 @@ beginfont("EN:L-DOPA")
endfont
%***********************************************************************
beginfont("EN:Ornithine")
- MC(<30,NH2,!~wb,!,COOH,2:\,!3,NH2)
+ MC(<30,NH2,!~wb,/'(!3,NH2),!,COOH)
endfont
%***********************************************************************
beginfont("EN:Citrulline")
- MC(<30,NH2,!~wb,!,COOH,2:\,!3,NH,!,//O,!,NH2)
+ MC(<30,NH2,!~wb,/'(!3,NH,!,//O,!,NH2),!,COOH)
endfont
%***********************************************************************
beginfont("EN:GABA")
@@ -117,7 +117,7 @@ beginfont("EN:4-amino benzoic acid")
endfont
%***********************************************************************
beginfont("EN:L-Carboxyl glutamic acid")
- MC(<30,NH2,!~wb,!,COOH,2:\,!,/COOH,!,COOH)
+ MC(<30,NH2,!~wb,/'(!,/COOH,!,COOH),!,COOH)
endfont
%***********************************************************************
beginfont("EN:L-Hydroxy Prorine")
@@ -1108,9 +1108,8 @@ 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,-2://O,-3:/O!,
- $9:\,NH,!,//O,!
+ <30,Ph,{1,2,6}:/O!,-4=?7,-5=?7,{-1,-4,-6}=dl,-2://O,-3:/O!,
+ 9:\,NH,!,//O,!
)
endfont
%***************************************************************************
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf
index 233e70eecd7..a3582e5ba83 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 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}
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 314b6cbe23f..ed6e3e605b8 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/doc/metapost/mcf2graph/mcf_mplib_exa.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex
index d35a55eed20..17d23cd4cb0 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2020.08.30
+% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2020.11.03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% mcf2graph.mf it must be version 4.52 or later
+%%% mcf2graph.mf it must be version 4.53 or later
\documentclass{article}
%------------------------------------------------------------------------------
\usepackage{luamplib}%
@@ -174,7 +174,7 @@ beginfont("NO:5","EN:Erythromycin","MW:733.93");
14:O,13:/*Et,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_,
{6^35,11,12^-35}:*/OH,
$3:\*,O,30,|,?6`.7,2:O,{3,5^35}:/_,4:/OH,5^-35:/O!,
- $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMeMe
+ $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/N!_
)
endfont;
\end{verbatim}
@@ -187,7 +187,7 @@ beginfont("NO:5","EN:Erythromycin","MW:733.93");
14:O,13:/*Et,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_,
{6^35,11,12^-35}:*/OH,
$3:\*,O,30,|,?6`.7,2:O,{3,5^35}:/_,4:/OH,5^-35:/O!,
- $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMeMe
+ $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/N!_
)
ext(
defaultscale:=0.8;
@@ -206,8 +206,8 @@ beginfont("EN:Paclitaxel","MW:853.918")
MC(
?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}:/_,{3^-60,15}:*/OH,8:/*H^-60,9:*/_^60,10://O,
- $1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph,
- $7:\*,O,-45,//O,60,Ph,$11:*\,O,-60,//O,60,$12:\*^-15,O,60,//O,-60
+ 1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph,
+ 7:\*,O,-45,//O,60,Ph,11:*\,O,-60,//O,60,12:\*^-15,O,60,//O,-60
)
endfont
\end{verbatim}
@@ -218,8 +218,8 @@ beginfont("EN:Paclitaxel","MW:853.918")
MC(
?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}:/_,{3^-60,15}:*/OH,8:/*H^-60,9:*/_^60,10://O,
- $1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph,
- $7:\*,O,-45,//O,60,Ph,$11:*\,O,-60,//O,60,$12:\*^-15,O,60,//O,-60
+ 1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph,
+ 7:\*,O,-45,//O,60,Ph,11:*\,O,-60,//O,60,12:\*^-15,O,60,//O,-60
)
ext(
defaultscale:=0.8;
diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
index e28af21d625..9314283dea8 100644
--- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
+++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% mcf2graph ver 4.52 Copyright (c) 2013-2020 Akira Yamaji
+% mcf2graph ver 4.53 Copyright (c) 2013-2020 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,
@@ -37,6 +37,9 @@
% Set to use plain.mp (label,arrow,atom) : mpost -s labeloffset=2 FILENAME
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tracingstats:=1;
+message "---------------------------------------------";
+message "This is mcf2graph ver 4.53 2020.11";
+message "---------------------------------------------";
%-------------------------------------------------------------------------------------------------
newinternal com,par,nA,nB,nC,nD,nE,nF,nP;
numeric save_num[],comD[][],parD[][],adrD[][],cntD[],tbl_atom[],tbl_group[][],f_char[],
@@ -125,8 +128,6 @@ else: f_MP:=0;
fi
clearit;
%--------------------------------------------------------------------------------------------------
-message "---------------------------------------------";
-message "This is mcf2graph ver 4.52 2020.08";
if f_MP=1:
if bboxmargin=0: message "output no image file";
elseif bboxmargin=1: message "output first font only";
@@ -149,8 +150,8 @@ if f_MP=1:
message "outputtemplate="&outputtemplate;
message "atomfont="&atomfont;
message "defaultfont="&defaultfont;
+ message "---------------------------------------------";
fi
-message "---------------------------------------------";
%--------------------------------------------------------------------------------------------------
let DIV= /; let MUL= *; let LT= <; let GT= >; let AND= &; let :: = : ; let == = =; let ef=elseif;
%--------------------------------------------------------------------------------------------------
@@ -160,15 +161,14 @@ def ext(text TXT)= sw_ext_all:=1; def EXT_ALL = TXT enddef; enddef;
def ext_clear= sw_ext_all:=0; def EXT_ALL = enddef; enddef;
%--------------------------------------------------------------------------------------------------
?3:=?20:=Ph:=Ph1:=Ph2:=hz:=0; vt:=1;
-ratio_chain_ring:= 0.66; ratio_atom_bond:=0.36;
-ratio_thickness_bond:=0.015; ratio_thickness_char:=0.1;
-ratio_char_bond:=1.5; ratio_bondgap_bond:=0.15; ratio_zebragap_bond:=0.12;
-ratio_zebra_black:=0.4; ratio_wedge_bond:=0.12; ratio_atomgap_atom:=0.040;
+ratio_chain_ring:=0.66; ratio_atom_bond:=0.36; ratio_thickness_bond:=0.015;
+ratio_thickness_char:=0.1; ratio_char_bond:=1.5; ratio_bondgap_bond:=0.15;
+ratio_zebragap_bond:=0.12; ratio_zebra_black:=0.4; ratio_wedge_bond:=0.12;
+ratio_atomgap_atom:=0.040;
offset_thickness:=0.2bp; offset_bond_gap:=0.3bp; offset_zebra_gap:=0.1bp;
-offset_atom:=0.8pt; offset_wedge:=0.4bp; max_labelsize:=20mm;
+offset_atom:=0.8pt; offset_wedge:=0.4bp;
thickness_fframe:=0.2bp; thickness_mframe:=0.2bp; thickness_aframe:=0.1bp;
-max_blength:=10mm; blength:=0; mangle:=0;
-dottedline_gap:=1.5bp;
+max_blength:=10mm; blength:=mangle:=0; max_labelsize:=20mm; dottedline_gap:=1.5bp;
%--------------------------------------------------------------------------------------------------
fsize:=(30mm,20mm); fmargin:=(0.4mm,0.4mm); msize:=(1,1); mposition:=(0.5,0.5);
%==================================================================================================
@@ -190,7 +190,7 @@ def_com(-4090)(_com,_jp_atom,_jp_absA,_jp_bond,_cyc,_cyc_sB,_cyc_eB,_set_line,_d
_chg_len,_get_len,_ring_len,_tmp_len,_rot_ang,_adj_ang,_chg_env,_tmp_env,_set_colorA,_set_colorB,
_group_si,_set_adr,_mk_bond,_set_atom,_arg_ang,_chg_atom,_tmp_rot,_fuse,_size_atom,_numeric,
_jump_at,_connect_at,_set_and,_chg_charge,_nop,_mark,_moff,_term,_len_s,_len_e,_len_ss,_len_ee,
- _group_s,_group_e,si,dl,dr,db,dm,tm,wf,wb,bd,bz,zf,zb,dt,wv,nl,vf,vb,nb,si_,wf_,wb_,bd_);
+ _group_s,_group_e,_rest,si,dl,dr,db,dm,tm,wf,wb,bd,bz,zf,zb,dt,wv,nl,vf,vb,nb,si_,wf_,wb_,bd_);
%--------------------------------------------------------------------------------------------------
def parameter_list=
sw_rep_out,sw_numberA,sw_numberB,sw_mframe,sw_aux_out,sw_expand,sw_mol_out,sw_calc,sw_single,
@@ -313,7 +313,7 @@ def endfont=
enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def set_def_MC=
- save /,//,/*,*/,**,*/*,~,^,`,``,<,>,&,:,=,\,\\,*\,\*,*\*,@,#,@#,$,
+ save /,//,/*,*/,**,*/*,~,^,',`,``,<,>,&,:,=,\,\\,*\,\*,*\*,@,#,@#,$,
{,},|,||,|||,|=,=|,|<,>|,|:,:|,_,d,w,z,inside_def_MC;
inside_def_MC:=1;
_:=Me; d:=db; w:=wf; z:=zf;
@@ -332,13 +332,14 @@ def set_def_MC=
def \ == @,0 enddef; def \\ == \~dm enddef;
def *\ == \~wf enddef; def \* == \~zf enddef; def *\* == \~wv enddef;
def | == (_com,_mark) enddef; def || == (_com,_moff) enddef; def ||| == (_com,_term) enddef;
- def |< == (_com,_len_s) enddef; def >| == (_com,_len_e) enddef;
+ def |< == (_com,_len_s) enddef; def >| == (_com,_len_e) enddef;
def |: == (_com,_len_ss) enddef; def :| == (_com,_len_ee) enddef;
def |=primary n == |<,(_chg_len,n) enddef; def =| == >| enddef;
def /secondary n == if known n:: (_group_si,n) else:: _nop fi enddef;
def //secondary n == /n~dm enddef; def */secondary n == /n~wf enddef;
def /*secondary n == /n~zf enddef; def */*secondary n == /n~wv enddef;
def **secondary n == /n~nb enddef;
+ vardef '(text TXT)== read_mcf(incr parts_usr)(|,TXT,(_com,_rest)); parts_usr enddef;
enddef;
%=================================================================================================
vardef '(text TXT)= read_mcf(incr parts_usr)(TXT); parts_usr enddef;
@@ -743,8 +744,8 @@ enddef;
%-------------------------------------------------------------------------------------------------
def MC(text TXT)=
begingroup
- save markA,markB,f_bra,envT,envB,lenT,lineT,strAT,cnt_group,bondL,temp_lenE,temp_lenF,
- temp_cntB,f_end,f_term,rotT,f_at,f_lineT,f_rotT,f_lenT,f_envT,angT,
+ save markA,markB,saveA,saveB,f_bra,envT,envB,lenT,lineT,strAT,cnt_group,bondL,temp_lenE,
+ temp_lenF,temp_cntB,f_end,f_term,rotT,f_at,f_lineT,f_rotT,f_lenT,f_envT,angT,
maxX,maxY,sA,sC,sD,pA,pB,factor,m_wd,m_ht,crR,CP,CPe,CPx,defaultsize,defaultscale;
%-----------------------------------------------------------------------------------------------
def CP= com_par enddef;
@@ -972,12 +973,13 @@ enddef;
def proc_bond_atom(expr a)(expr n)=
f_bra:=f_end:=f_term:=rotT:=f_lineT:=f_rotT:=f_lenT:=f_envT:=envT:=envB:=strAT:=f_at:=0;
bondL:=crR; lenT:=crR; sB[0]:=0; eB[0]:=1; lineT:=si;
- andAT:=markA:=markB:=0;
+ andAT:=markA:=markB:=saveA:=saveB:=0;
%-----------------------------------------------------------------------------------------------
for i=n upto cntD[a]: com:=comD[a][i]; par:=parD[a][i];
if com=_mk_bond: if (par=0)and(rotT<>0): rotT:=0; fi add_atom;
ef com=_set_adr: adrT:=par;
- ef com=_com: if par=_mark: markA:=cntA; markB:=cntB;
+ ef com=_com: if par=_mark: saveA:=markA; saveB:=markB; markA:=cntA; markB:=saveB:=cntB;
+ ef par=_rest: markA:=saveA; markB:=saveB;
ef par=_moff: markA:=markB:=0;
ef par=_term: termA;
ef par=_len_s: temp_lenE:=bondL; ef par=_len_e: bondL:=temp_lenE;
@@ -1097,10 +1099,10 @@ def add_bond(expr ROT)=
fi
cntB:=cntB+1; posBs:=posBe;
enddef;
-%==================================================================================================
+%=================================================================================================
vardef getA(expr n)= if n>=0: markA+n ef n>=-999: cntA+n+1 else: n+4095 fi enddef;
vardef getB(expr n)= if n>=0: markB+n ef n>=-999: cntB+n+1 else: n+4095 fi enddef;
-%--------------------------------------------------------------------------------------------------
+%-------------------------------------------------------------------------------------------------
def termA=
if f_term=0:
if f_bra=0:
@@ -1171,17 +1173,17 @@ def draw_atom(expr NUM)=
endfor
endgroup
enddef;
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def draw_bond(expr NUM)=
begingroup
save ww,ap,am,ang,col,len,Ls,Le,nL,nS,nE,pA,zA,zL,wpcs;
pair pA,Ls,Le;
path zA,zL;
def wpcs expr n= withpen pencircle scaled n enddef;
- %------------------------------------------------------------------------------------------------
+ %-----------------------------------------------------------------------------------------------
nL:=lineB[NUM]; ang:=angB[NUM]; nS:=sB[NUM]; nE:=eB[NUM]; col:=colorB[NUM];
zL:=posA[nS]--posA[nE]; ww:=wedge_wd; ap:=ang+90; am:=ang-90;
- %------------------------------------------------------------------------------------------------
+ %-----------------------------------------------------------------------------------------------
if (numS[nS]=0)and(numS[nE]=0)or(sw_numberA=1)or(sw_numberB=1):
Ls:=posA[nS]; Le:=posA[nE]; pA:=(.1,.9);
ef numS[nS]=0: Le:=zL intersectionpoint frame_str(nE); Ls:=posA[nS]; pA:=(.15,1);
@@ -1189,7 +1191,7 @@ def draw_bond(expr NUM)=
else: Ls:=zL intersectionpoint frame_str(nS); Le:=zL intersectionpoint frame_str(nE); pA:=(0,1);
fi
zA:=Ls--Le; len:=length(Le-Ls);
- %------------------------------------------------------------------------------------------------
+ %-----------------------------------------------------------------------------------------------
pickup pencircle scaled bond_pen_wd;
if (nL=si)or(sw_single=1): draw zA Cp(col);
ef nL=dl: draw zA Cp(col); draw sfB(subpath pA of zA,bondgap,ap) Cp(col);
@@ -1259,7 +1261,7 @@ Me:='(); Et:='(!); Pr:='(!,!); Bu:='(!,!,!);
for i=4,5,6: for j=2 upto i-2: ?[i][j]:='((_fuse,i),(j,0)); endfor endfor
for i=5,6,7,8: for j=11 upto 15: ?[i][j]:='((_fuse,i),(j,0)); endfor endfor
%=================================================================================================
-H :='("H");C:='("C");N:='("N");O:='("O");S:='("S");P:='("P");F:='("F");I:='("I");K:='("K");
+H :='("H");C:='("C");N:='("N");O:='("O");S:='("S");P:='("P");F:='("F");I:='("I"); K:='("K");
Si:='("{Si}");Al:='("{Al}");Mg:='("{Mg}");Zn:='("{Zn}");As:='("{As}");Co:='("{Co}");Cu:='("{Cu}");
Ag:='("{Ag}");Au:='("{Au}");Sn:='("{Sn}");Cl:='("{Cl}");Br:='("{Br}");Li:='("{Li}");Cr:='("{Cr}");
Na:='("{Na}");Ca:='("{Ca}");Hg:='("{Hg}");Ni:='("{Ni}");Ti:='("{Ti}");U:='("U");
@@ -1269,29 +1271,32 @@ O[1]:= '("{O^+^}"); O[-1]:='("{O^-^}"); N[1]:='("{N^+^}"); N[-1]:='("{N^-^}
S[1]:= '("{S^+^}"); S[-1]:='("{S^-^}"); P[1]:='("{P^+^}"); P[-1]:='("{P^-^}");
Li[1]:='("{Li^+^}"); Na[1]:='("{Na^+^}"); Cl[-1]:='("{Cl^-^}"); Br[-1]:='("{Br^-^}");
%-------------------------------------------------------------------------------------------------
-R:='("R"); R1:='("{R^1^}"); R2:='("{R^2^}"); R3:='("{R^3^}"); R4:='("R^4^"); R5:='("{R^5^}");
+R:='("R"); R1:='("{R^1^}"); R2:='("{R^2^}"); R3:='("{R^3^}"); R4:='("R^4^"); R5:='("{R^5^}");
R6:='("R6"); R7:='("{R^7^}"); R8:='("{R^8^}"); R9:='("{R^9^}"); R10:='("R^10^"); R11:='("{R^11^}");
%-------------------------------------------------------------------------------------------------
CHO:='("CHO"); OH:='("OH"); COOH:='("COOH"); CH2:='("C{H_2_}"); CH3:='("C{H_3_}"); CN:='("CN");
NH2:='("N{H_2_}"); NO2:='("N{O_2_}"); SH:='("SH"); SO3:='("S{O_3_}"); NH:='(N,/H~nl);
%-------------------------------------------------------------------------------------------------
-NMe:=N!:='(N,/_); iPr:=Me!:='(/_,60); tBu:='(/_,/_^60,60); SO:='(S,//O); SOO :='(S,//O^-35,//O^35);
+NMe:=N!:='(N,/_); iPr:=Me!:='(/_,60); tBu:='(/_,/_^60,60); SO:='(S,//O); SOO:='(S,//O^-35,//O^35);
OMe:=O!:='(O,!); OEt:=O!2:='(O,!,!); OPr:=O!3:='(O,!,!,!); OiPr:=OMe!:='(O,!,iPr);
SMe:=S!:='(S,!); SEt:=S!2:='(S,!,!); SPr:=S!3:='(S,!,!,!); SiPr:=SMe!:='(S,!,iPr);
%-------------------------------------------------------------------------------------------------
COO:='(//O,!,O); COOMe:=COO!:='(COO,!); COOEt:=COO!2:='(COO,!,!); COOiPr:=COOMe!:='(COO,!,iPr);
COOPr:=COO!3:='(COO,!,!,!); COOtBu:='(COO,!,tBu);
COMe:=CO!:='(//O,!); COEt:=CO!2:='(//O,!,!); COPr:=CO!3:='(//O,!,!,!);
-OCOMe:=OCO!:='(O,!,//O,!); NMeMe:=NMe!:='(N!,!); NMeEt:=NMe!2:='(N!,!,!); NMePr:=NMe!3:='(N!,!,!,!);
-NHCOMe:=NHCO!:='(NH,!,//O,!); NHiPr:=NHMe!:='(NH,!,iPr); NHtBu:='(NH,!,tBu); NHMe:=NH!:='(NH,!);
-NHEt:=NH!2:='(NH,!,!); NHPr:=NH!3:='(NH,!,!,!);
+OCOMe:=OCO!:='(O,!,//O,!); NMeMe:=NMe!:=N!_:='(N!,!); NMeEt:=NMe!2:=N!2_:='(N!,!,!);
+NMePr:=NMe!3:='(N!,!,!,!);
+NHCOMe:=NHCO!:='(NH,!,//O,!); NHiPr:=NHMe!:='(NH,!,iPr); NHtBu:='(NH,!,tBu);
+NHMe:=NH!:='(NH,!); NHEt:=NH!2:='(NH,!,!); NHPr:=NH!3:='(NH,!,!,!);
%-------------------------------------------------------------------------------------------------
!OH:='(!,OH); !SH:='(!,SH); !NH2:='(!,NH2);
!COMe:=!CO!:='(!,//O,!); !COEt:=!CO!2:='(!,CO!2); !COPr:=!CO!3:='(!,CO!3);
!OMe:=!O!:='(!,O!); !OEt:=!O!2:='(!,O!2); !OPr:=!O!3:='(!,O!3); !OiPr:=!OMe!:='(!,OMe!);
!SMe:=!S!:='(!,S!); !SEt:=!S!2:='(!,S!2); !SPr:=!S!3:='(!,S!3); !SiPr:=!SMe!:='(!,SMe!);
-!NHMe:=!NH!:='(!,NH!); !NHEt:=!NH!2:='(!,NH!2); !NHPr:=!NH!3:='(!,NH!3); !NHiPr:=!NHMe!:='(!,NHMe!);
-!COOH:='(!,COOH); !COOMe:=!COO!:='(!,COO!); !COOEt:=!COO!2:='(!,COO!2); !COOPr:=!COO!3:='(!,COO!3);
+!NHMe:=!NH!:='(!,NH!); !NHEt:=!NH!2:='(!,NH!2); !NHPr:=!NH!3:='(!,NH!3);
+!NHiPr:=!NHMe!:='(!,NHMe!);
+!COOH:='(!,COOH); !COOMe:=!COO!:='(!,COO!); !COOEt:=!COO!2:='(!,COO!2);
+!COOPr:=!COO!3:='(!,COO!3);
!COOtBu:='(!,COOtBu); !OCOMe:=!OCO!:='(!,OCO!); !NMeMe:=!NMe!:='(!,NMe!);
!NMeEt:=!NMe!2:='(!,NMe!2); !NMePr:=!NMe!3:='(!,NMe!3);
!CH3:='(!,CH3); !CN:='(!,CN); !iPr:=!Me!:='(!,iPr); !tBu:='(!,tBu);
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-05 11:17:26 +0000