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-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG11
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/README6
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf7
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdfbin235860 -> 235841 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex2
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-060.eps100
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.eps100
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf79
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdfbin440033 -> 462405 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex298
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdfbin122289 -> 122254 bytes
-rw-r--r--Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex4
-rw-r--r--Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf110
13 files changed, 468 insertions, 249 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
index b827c211c0d..a3bee0be47d 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG
@@ -1,6 +1,15 @@
*******************************************************************************
- Changelog of mcf2graph software package by Akira Yamaji 2017-01-15
+ Changelog of mcf2graph software package by Akira Yamaji 2017-01-29
*******************************************************************************
+[ver. 4.09 / 2017-01-29]
+ -add new function puts()
+ put string in EXT(),ext()
+ -add new function use_font()
+ make font for puts()
+ -change option parameter name
+ sw_checklist => sw_report
+ -update MCF syntax manual
+
[ver. 4.08 / 2017-01-15]
-add monoisotopic mass calculation
-update MCF syntax manual
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README
index bcd344c9b18..15ae275aa52 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 : 4.08 2017-01-15
+ version : 4.09 2017-01-29
E-mail : mcf2graph@gmail.com
Located at : http://www.ctan.org/pkg/mcf2graph
********************************************************************************
@@ -19,7 +19,7 @@
( 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-060.eps No.60 EPS(with color) file of (4)
+ ( 6) mcf_man_soc-064.eps No.64 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
@@ -36,7 +36,7 @@
( 3) >mpost -s ahangle=2 FILENAME => output SVG file.
( 4) >mpost -s ahangle=3 FILENAME => output MDL Molfile(V2000)
( 5) >mpost -s ahlength=1 FILENAME => output first definition only (for test)
- ( 6) >mpost -s ahlength=2 FILENAME => output checklist.
+ ( 6) >mpost -s ahlength=2 FILENAME => output report.
4. License
Permission is hereby granted, free of charge, to any person obtaining a copy
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 97a01bf0236..3cb3c1facd0 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf
@@ -1,12 +1,13 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2017.01.13
+% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2017.01.29
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %%% it must be version 4.08 or later
+input mcf2graph.mf; %%% it must be version 4.09 or later
%-------------------------------------------------------------------------
font_wd#:=33mm#;
font_ht#:=24mm#;
max_bond_length#:=4.5mm#;
%-------------------------------------------------------------------------
+sw_select:=1;
sw_auxout:=1;
sw_font_frame:=0;
sw_atom_frame:=0;
@@ -23,7 +24,7 @@ var4:="cal_MW"; tag4:="cMW";
%%%% var8:="inf_USE"; tag8:="USE";
%%%% var9:="inf_EXA"; tag9:="EXA";
%%%% auxtag_out;
-%%%% sw_checklist:=1;
+%%%% sw_report:=1;
%%%% sw_MOLout:=1;
%%%% outputformat:="png"; hppp:=vppp:=0.1; outputtemplate:="%j-%3c.png";
%***************************************************************************
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf
index 162df6cac38..641c2fab99e 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 07a44728a79..2486b6f94b7 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 2017.01.15
+% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2017.01.29
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
\usepackage{graphicx}
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-060.eps b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-060.eps
deleted file mode 100644
index 254fc84ed15..00000000000
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-060.eps
+++ /dev/null
@@ -1,100 +0,0 @@
-%!PS-Adobe-3.0 EPSF-3.0
-%%BoundingBox: 0 0 66 57
-%%HiResBoundingBox: 0 0 65.2089 56.69304
-%%Creator: MetaPost 1.9991
-%%CreationDate: 2016.10.08:2245
-%%Pages: 1
-%%DocumentResources: procset mpost-minimal
-%%DocumentSuppliedResources: procset mpost-minimal
-%%EndComments
-%%BeginProlog
-%%BeginResource: procset mpost-minimal
-/bd{bind def}bind def/fshow {exch findfont exch scalefont setfont show}bd
-/fcp{findfont dup length dict begin{1 index/FID ne{def}{pop pop}ifelse}forall}bd
-/fmc{FontMatrix dup length array copy dup dup}bd/fmd{/FontMatrix exch def}bd
-/Amul{4 -1 roll exch mul 1000 div}bd/ExtendFont{fmc 0 get Amul 0 exch put fmd}bd
-/ScaleFont{dup fmc 0 get Amul 0 exch put dup dup 3 get Amul 3 exch put fmd}bd
-/SlantFont{fmc 2 get dup 0 eq{pop 1}if Amul FontMatrix 0 get mul 2 exch put fmd}bd
-%%EndResource
-%%EndProlog
-%%BeginSetup
-%%EndSetup
-%%Page: 1 1
- 0 0 0 setrgbcolor 0 0.51848 dtransform truncate idtransform setlinewidth pop
- [] 0 setdash 1 setlinecap 1 setlinejoin 10 setmiterlimit
-newpath 14.1732 17.70572 moveto
-27.95258 9.75023 lineto stroke
-newpath 17.7621 19.66498 moveto
-29.69818 12.77371 lineto stroke
-newpath 37.25743 9.75015 moveto
-51.03682 17.70572 lineto stroke
- 0 1 0 setrgbcolor 0.51848
- 0 dtransform exch truncate exch idtransform pop setlinewidth
-newpath 51.03682 17.70572 moveto
-51.03682 38.98888 lineto stroke
-newpath 47.54561 19.83417 moveto
-47.54561 36.86043 lineto stroke
- 0 0 0 setrgbcolor 0 0.51848 dtransform truncate idtransform setlinewidth pop
-newpath 51.03682 38.98888 moveto
-37.25743 46.94435 lineto stroke
-newpath 27.95258 46.94443 moveto
-14.1732 38.98888 lineto stroke
-newpath 29.69818 43.92094 moveto
-17.7621 37.02962 lineto stroke
- 0.51848 0 dtransform exch truncate exch idtransform pop setlinewidth
-newpath 14.1732 38.98888 moveto
-14.1732 17.70572 lineto stroke
- 1 0 0 setrgbcolor
-newpath 28.7985 3.25761 moveto
-29.57623 3.25761 lineto
-29.57623 10.87064 lineto
-28.7985 10.87064 lineto
- closepath fill
-newpath 35.63377 3.25761 moveto
-36.41151 3.25761 lineto
-36.41151 10.87064 lineto
-35.63377 10.87064 lineto
- closepath fill
-newpath 29.88733 10.87064 moveto
-28.7985 10.87064 lineto
-35.32268 3.25761 lineto
-36.41151 3.25761 lineto
- closepath fill
- 0 0 1 setrgbcolor
-newpath 28.7985 45.82394 moveto
-29.57623 45.82394 lineto
-29.57623 53.43697 lineto
-28.7985 53.43697 lineto
- closepath fill
-newpath 35.63377 45.82394 moveto
-36.41151 45.82394 lineto
-36.41151 53.43697 lineto
-35.63377 53.43697 lineto
- closepath fill
-newpath 29.88733 53.43697 moveto
-28.7985 53.43697 lineto
-35.32268 45.82394 lineto
-36.41151 45.82394 lineto
- closepath fill
- 0 0 0 setrgbcolor
-newpath 0 0.19925 moveto
-0 0 lineto
-0.19925 0 lineto
-65.2089 0 lineto
-65.2089 0.19925 lineto
-65.2089 56.69304 lineto
-65.00964 56.69304 lineto
-0 56.69304 lineto
-0 56.49379 lineto
-0 0 lineto
-0.19925 0 lineto
-0.19925 0.19925 lineto
-0.19925 56.69304 lineto
-0.19925 56.49379 lineto
-65.2089 56.49379 lineto
-65.00964 56.49379 lineto
-65.00964 0 lineto
-65.00964 0.19925 lineto
- closepath fill
-showpage
-%%EOF
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.eps b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.eps
new file mode 100644
index 00000000000..e1776150793
--- /dev/null
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.eps
@@ -0,0 +1,100 @@
+%!PS-Adobe-3.0 EPSF-3.0
+%%BoundingBox: -1 -1 66 57
+%%HiResBoundingBox: -0.09962 -0.09962 65.06522 56.58049
+%%Creator: MetaPost 1.9991
+%%CreationDate: 2017.01.29:2040
+%%Pages: 1
+%%DocumentResources: procset mpost-minimal
+%%DocumentSuppliedResources: procset mpost-minimal
+%%EndComments
+%%BeginProlog
+%%BeginResource: procset mpost-minimal
+/bd{bind def}bind def/fshow {exch findfont exch scalefont setfont show}bd
+/fcp{findfont dup length dict begin{1 index/FID ne{def}{pop pop}ifelse}forall}bd
+/fmc{FontMatrix dup length array copy dup dup}bd/fmd{/FontMatrix exch def}bd
+/Amul{4 -1 roll exch mul 1000 div}bd/ExtendFont{fmc 0 get Amul 0 exch put fmd}bd
+/ScaleFont{dup fmc 0 get Amul 0 exch put dup dup 3 get Amul 3 exch put fmd}bd
+/SlantFont{fmc 2 get dup 0 eq{pop 1}if Amul FontMatrix 0 get mul 2 exch put fmd}bd
+%%EndResource
+%%EndProlog
+%%BeginSetup
+%%EndSetup
+%%Page: 1 1
+ 0 0 0 setrgbcolor
+newpath -0.09962 0.09962 moveto
+-0.09962 -0.09962 lineto
+0.09962 -0.09962 lineto
+65.06522 -0.09962 lineto
+65.06522 0.09962 lineto
+65.06522 56.58049 lineto
+64.86597 56.58049 lineto
+-0.09962 56.58049 lineto
+-0.09962 56.38124 lineto
+-0.09962 -0.09962 lineto
+0.09962 -0.09962 lineto
+0.09962 0.09962 lineto
+0.09962 56.58049 lineto
+0.09962 56.38124 lineto
+65.06522 56.38124 lineto
+64.86597 56.38124 lineto
+64.86597 -0.09962 lineto
+64.86597 0.09962 lineto
+ closepath fill
+ 0 0.51848 dtransform truncate idtransform setlinewidth pop [] 0 setdash
+ 1 setlinecap 1 setlinejoin 10 setmiterlimit
+newpath 14.1732 17.70528 moveto
+27.95216 9.75003 lineto stroke
+newpath 17.762 19.66449 moveto
+29.69772 12.77344 lineto stroke
+newpath 37.25676 9.74995 moveto
+51.03572 17.70528 lineto stroke
+ 0 1 0 setrgbcolor 0.51848
+ 0 dtransform exch truncate exch idtransform pop setlinewidth
+newpath 51.03572 17.70528 moveto
+51.03572 38.98781 lineto stroke
+newpath 47.5446 19.83366 moveto
+47.5446 36.85942 lineto stroke
+ 0 0 0 setrgbcolor 0 0.51848 dtransform truncate idtransform setlinewidth pop
+newpath 51.03572 38.98781 moveto
+37.25676 46.94304 lineto stroke
+newpath 27.95216 46.94312 moveto
+14.1732 38.98781 lineto stroke
+newpath 29.69772 43.91971 moveto
+17.762 37.0286 lineto stroke
+ 0.51848 0 dtransform exch truncate exch idtransform pop setlinewidth
+newpath 14.1732 38.98781 moveto
+14.1732 17.70528 lineto stroke
+ 1 0 0 setrgbcolor
+newpath 28.79805 3.2576 moveto
+29.57579 3.2576 lineto
+29.57579 10.8704 lineto
+28.79805 10.8704 lineto
+ closepath fill
+newpath 35.63312 3.2576 moveto
+36.41086 3.2576 lineto
+36.41086 10.8704 lineto
+35.63312 10.8704 lineto
+ closepath fill
+newpath 29.88689 10.8704 moveto
+28.79805 10.8704 lineto
+35.32202 3.2576 lineto
+36.41086 3.2576 lineto
+ closepath fill
+ 0 0 1 setrgbcolor
+newpath 28.79805 45.82266 moveto
+29.57579 45.82266 lineto
+29.57579 53.43547 lineto
+28.79805 53.43547 lineto
+ closepath fill
+newpath 35.63312 45.82266 moveto
+36.41086 45.82266 lineto
+36.41086 53.43547 lineto
+35.63312 53.43547 lineto
+ closepath fill
+newpath 29.88689 53.43547 moveto
+28.79805 53.43547 lineto
+35.32202 45.82266 lineto
+36.41086 45.82266 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 0cace2ff00d..bf9e92058d3 100644
--- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
+++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf
@@ -1,13 +1,13 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2017.01.15
+% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2017.01.29
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-input mcf2graph.mf; %% it must be version 4.08 or later
+input mcf2graph.mf; %% it must be version 4.09 or later
%------------------------------------------------------------------------
sw_auxout:=0;
sw_mol_frame:=0;
sw_expand:=0;
sw_solid:=2;
-%%%%%sw_checklist:=1;
+%%%%%sw_report:=1;
%***********************************************************************
font_wd#:=35mm#;
font_ht#:=25mm#;
@@ -786,9 +786,9 @@ beginfont("EN:Switwch molecular frame")
endfont
%***********************************************************************
beginfont("EN:Switwch atom frame")
- font_ht#:=15mm#;
+ font_ht#:=12mm#;
sw_atom_frame:=1;
- MCf(<30,Ph,1:/Cl,4:/COOH,3:/OH)
+ MCf(<30,COOH,!0,COOH)
endfont
%***********************************************************************
beginfont("EN:MCd()")
@@ -818,25 +818,40 @@ beginfont("EN:MCf() vt")
endfont
%***********************************************************************
beginfont("EN:EXT()")
- font_ht#:=26mm#;
+ margin_left_right:=margin_top_bottom:=3mm;
+ font_wd#:=70mm#;
+ font_ht#:=35mm#;
bond_len#:=8mm#;
sw_font_frame:=3;
- sw_mol_frame:=1;
MCd(1,0.8)(0.1,0.5)(<30,Ph,2:/OH,5:/OH)
MCd(1,0.8)(0.9,0.5)(<30,?6,$(3,6)dl,@(2,5)//O)
- EXT(draw ((0,0)--(25mm,0)--(21mm,2mm)) shifted (0.3w,0.5h);
- drawdot p0 withpen pencircle scaled 2mm;
- drawdot p1 withpen pensquare scaled 2mm;
- drawdot p2 withpen pensquare scaled 2mm;)
+ EXT(
+ draw ((0,0)--(25mm,0)--(21mm,2mm)) shifted (0.3w,0.52h);
+ draw ((4mm,-2mm)--(0,0)--(25mm,0)) shifted (0.3w,0.48h);
+ draw fullcircle scaled 3mm shifted p0;
+ drawdot p1 withpen pencircle scaled 2mm;
+ drawdot p2 withpen pensquare scaled 2mm;
+ use_font(5pt#);
+ puts((0.4w,0.6h))("Oxidation");
+ puts((0.4w,0.35h))("Reduction");
+ )
endfont
%***********************************************************************
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,l);
+ margin_left_right:=margin_top_bottom:=3mm;
+ font_wd#:=70mm#;
+ font_ht#:=25mm#;
+ sw_solid:=0;
+ MCd(1,0.9)(0.1,0.5)(<30,Ph,3:/F,4:/Cl)
+ ext(
+ drawdot p0 withpen pencircle scaled 2mm;
+ draw p0--(p0+(wd,0))--(p0+(wd,ht));
+ )
+ MCd(1,0.9)(0.9,0.5)(<30,Ph,3:/F,4:/Cl)
+ ext(
+ draw_vector(p6,a6-180,l);
+ drawdot p0 withpen pensquare scaled 2mm;
+ draw p0--(p0+(wd,0))--(p0+(wd,ht));
)
endfont
%***********************************************************************
@@ -911,7 +926,35 @@ beginfont("EN:Cholesterol","CAS:57-88-5","FM:C27H46O","MW:386.65")
-1\^18,/*_,-60,!3,/_,!,
)
endfont
-%***********************************************************************
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%***************************************************************************
+beginfont("EN:Acetamiprid","MW:222.676")
+ font_ht#:=20mm#;
+ MCf(<30,Ph,2:N,1:/Cl,4\,!,N,/_,!,/_,!!,N,!,CN)
+endfont
+%***************************************************************************
+beginfont("EN:Fenitrothion","MW:277.231")
+ font_ht#:=20mm#;
+ MCf(<30,!,O,!,P,//S,/O!^160,!,O,!,|,Ph,3:/_,4:/NO2)
+endfont
+%***************************************************************************
+beginfont("EN:Permethrin","MW:391.288")
+ font_ht#:=25mm#;
+ MCf(<-30,?3,2^-35:*/_,2^35:/*_,1\,!!,/Cl,!,Cl,
+ 3\,//O,!,O,!2,|,Ph,3\,O,-60,Ph)
+endfont
+%***************************************************************************
+beginfont("EN:Endosulfan","MW:406.904");
+ font_ht#:=25mm#;
+ MCf(<26,?7,7=?6[13],11*,208~wf`1.45,&8~wb,10=d,@(3,5)O,4:S,4://O,
+ @(8,9,10,11,12^-210,12^-150)/Cl)
+endfont;
+%***************************************************************************
+beginfont("EN:Luciferin","MW:280.33")
+ MCf(<30,Ph,3=?5,8\,?5,$(9,16)d,
+ @(9,14)N,@(7,11)S,1:/OH,-2:*/COOH)
+endfont
+%***************************************************************************
beginfont("EN:Warfarin","CAS:81-81-2","FM:C19H16O4","MW:308.33")
font_ht#:=25mm#;
MCf(<30,Ph,3=?6,8=dl,10:O,7:/OH,9://O,8\,/Ph`1,60,!,//O,!)
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf
index dfe41477291..656035e1754 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 d3030c9aef9..a3468a88fc1 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 2017.01.15
+% Molecular Coding Format manual by Akira Yamaji 2017.01.29
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper]{article}
%%%%\usepackage{graphicx}
@@ -62,6 +62,7 @@
\maketitle
\begin{center} Located at http://www.ctan.org/pkg/mcf2graph \end{center}
%-----------------------------------------------------------------------------
+\thispagestyle{empty}
\vspace{10mm}
{\@strufont%
\makebox[10mm]{}\char1 \raisebox{10mm}{\char2 }\char3 \raisebox{10mm}{\char4}\\
@@ -71,11 +72,13 @@
\makebox[10mm]{}\char17\raisebox{10mm}{\char18}\char19\raisebox{10mm}{\char20}\\}
%-----------------------------------------------------------------------------
\twocolumn
+\thispagestyle{empty}
\tableofcontents
%-----------------------------------------------------------------------------
\linethickness{0.08mm}%
%----------------------------------------------------------------------------
\newpage
+\setcounter{page}{1}
\section{Introduction}
Molecular Coding Format(MCF) is new linear notation
represent chemical structure diagrams.
@@ -540,7 +543,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
<30,Ph,@(2,5)N,2:red,5:blue,3=green
\end{verbatim}
%%%%\MCFstructure % for Metafont
-\includegraphics{mcf_man_soc-060.eps}% for dvipdfmx
+\includegraphics{mcf_man_soc-064.eps}% for dvipdfmx
\advance\fontnum\@ne\relax\advance\tempnum\@ne\relax%
%-----------------------------------------------------------------------------
\subsubsection{Make block}
@@ -885,7 +888,7 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\subsubsection{Atom frame}
\begin{verbatim}
sw_atom_frame:=1;
- MCf(<30,Ph,1:/Cl,4:/COOH,3:/OH)
+ MCf(<30,COOH,!0,COOH)
** default: sw_atom_frame=0
\end{verbatim}
\MCFstructure
@@ -935,22 +938,46 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
p[m]: molecular origin position
(1<=m<=molecular count)
+(Function)
+ puts(pos)(string):
+ put string at pos
+ use_font(wd#):
+ make string font for puts()
+ (font width = wd#)
+ draw_vector(pos,angle,length):
+ draw vector at pos
+
+ %----------------------------------
beginfont()
- sw_mol_frame:=1;
- MCd(1,0.8)(0.1,0.5)(<30,Ph,2:/OH,5:/OH)
+ sw_font_frame:=3;
+ %----------------------------------
+ MCd(1,0.8)(0.1,0.5)
+ (<30,Ph,2:/OH,5:/OH)
MCd(1,0.8)(0.9,0.5)
(<30,?6,$(3,6)dl,@(2,5)//O)
+ %----------------------------------
EXT(
- draw ((0,0)--(25mm,0)--(21mm,2mm))
- shifted (0.3w,0.5h);
- drawdot p0 withpen pencircle scaled 2mm;
- drawdot p1 withpen pensquare scaled 2mm;
- drawdot p2 withpen pensquare scaled 2mm;
+ draw ((0,0)--(25mm,0)--(21mm,2mm))
+ shifted (0.3w,0.52h);
+ draw ((4mm,-2mm)--(0,0)--(25mm,0))
+ shifted (0.3w,0.48h)
+ draw fullcircle scaled 3mm
+ shifted p0;
+ drawdot p1
+ withpen pencircle scaled 2mm;
+ drawdot p2
+ withpen pensquare scaled 2mm;
+ %----------------------------------
+ use_font(5pt#);
+ puts((0.4w,0.6h))("Oxidation");
+ puts((0.4w,0.35h))("Reduction");
)
+ %----------------------------------
endfont
\end{verbatim}
-\MCFstructure
+\MCFstructure\\
%-----------------------------------------------------------------------------
+\newpage
\subsection{Function ext()}
\begin{verbatim}
(Extra graphic to molecule)
@@ -962,14 +989,22 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
p[m]: atom position of A[m]
a[m]: branch angle of A[m]
(1<=m<=atom count)
- draw_vector(position,angle,length)
beginfont()
- MCf(<30,Ph,3:/F,4:/Cl)
- ext(draw p0--(p0+(wd,0))
- --(p0+(wd,ht);
- draw_vector(p6,a6-180,l);
- )
+ %-------------------------------
+ MCd(1,0.9)(0.1,0.5)(<30,Ph,3:/F,4:/Cl)
+ ext(
+ drawdot p0 withpen pencircle scaled 2mm;
+ draw p0--(p0+(wd,0))--(p0+(wd,ht));
+ )
+ %-------------------------------
+ MCd(1,0.9)(0.9,0.5)(<30,Ph,3:/F,4:/Cl)
+ ext(
+ draw_vector(p6,a6-180,l);
+ drawdot p0 withpen pensquare scaled 2mm;
+ draw p0--(p0+(wd,0))--(p0+(wd,ht));
+ )
+ %-------------------------------
endfont
\end{verbatim}
\MCFstructure
@@ -994,15 +1029,28 @@ pk font,PNG,SVG,EPS or MDL MOL file(V2000).\\
\end{verbatim}
\MCFstructure\MCFstructure\MCFstructure
%-----------------------------------------------------------------------------
+\newpage
\section{Output information}
%-----------------------------------------------------------------------------
\subsection{Output molecular information}
\begin{verbatim}
-var3:="calc_weight"; tag3:="cMW";
-var4:="calc_formula"; tag4:="cFM";
+tag3:="cMW"; var3:="calc_weight";
+tag4:="cFM"; var4:="calc_formula";
+%-----------------------------------------
+beginfont()
+ MCf(<30,?6,3=d,
+ @(2,6)N,@(2,6)/_,@(1,5)//O,
+ |,-4=?5,2=dl,@(1,3)N,3:/_)
+endfont
+%-----------------------------------------
+
%% Output to mcf_man_soc-info.aux %%
..... ;C:85;cMW:194.19174;cFM:C8H10N4O2
+** default value
+ tag1:="F"; var1:="jobname";
+ tag2:="C"; var2:="char_num";
+
cMW:calculated molecular weight
cFM:calculated molecular formula
\end{verbatim}
@@ -1051,29 +1099,77 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\begin{verbatim}
tag3:="NO"; var3:="inf_NO";
tag4:="EN"; var4:="inf_EN";
- sw_auxfix:=1; auxtag_out;
+ sw_auxfix:=1;
+ auxtag_out; % output tag list
+ %--------------------------------------
beginfont("EN:Cholesterol","NO:1")
- MCf(<30,?6,$(-4,-2)?6,-4=?5,7=dl,
+ MCf(
+ <30,?6,$(-4,-2)?6,-4=?5,7=dl,
1:*/OH,@(4,12)*/_^60,9:*/H^60,
10:/*H^180,11:/*H^-60,17:/*H^-54,
- -1\^18,/*_,-60,!3,/_,!)
+ -1\^18,/*_,-60,!3,/_,!
+ )
endfont
+ %--------------------------------------
beginfont(......)
...........
endfont
+ %--------------------------------------
..............
%% Output to mcf_man_soc-info.aux %%
F;C;NO;EN
mcf_man_soc;91;1;Ampicillin
...........................
+ ...........................
+ ** default sw_auxfix=0
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
\newpage
\section{MCF example}
-\subsection{Warfarin}
+%-----------------------------------------------------------------------------
+\subsection*{Acetamiprid}
+\begin{verbatim}
+ <30,Ph,2:N,1:/Cl,
+ 4\,!,N,/_,!,/_,!!,N,!,CN
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\subsection*{Fenitrothion}
+\begin{verbatim}
+ <30,!,O,!,P,//S,/O!^160,!,O,!,
+ |,Ph,3:/_,4:/NO2
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\subsection*{Permethrin}
+\begin{verbatim}
+ <-30,?3,2^-35:*/_,2^35:/*_,
+ 1\,!!,/Cl,!,Cl,
+ 3\,//O,!,O,!2,|,Ph,
+ 3\,O,-60,Ph
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\subsection*{Endosulfan}
+\begin{verbatim}
+ <26,?7,7=?6[13],11*,208~wf`1.45,&8~wb,
+ 10=d,@(3,5)O,4:S,4://O,
+ @(8,9,10,11,12^-210,12^-150)/Cl
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\subsection*{Luciferin}
+\begin{verbatim}
+ <30,Ph,3=?5,8\,?5,$(9,16)d,
+ @(9,14)N,@(7,11)S,
+ 1:/OH,-2:*/COOH
+\end{verbatim}
+\MCFstructure
+%-----------------------------------------------------------------------------
+\subsection*{Warfarin}
\begin{verbatim}
<30,Ph,3=?6,8=dl,
10:O,7:/OH,9://O,
@@ -1081,7 +1177,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Limonin}
+\subsection*{Limonin}
\begin{verbatim}
<30,?6,$(-3,-4)?6,-5=?3,
-2=wf,-1=wb,6=?5,-4=?6,-5=wf,
@@ -1092,7 +1188,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Sesamine}
+\subsection*{Sesamine}
\begin{verbatim}
<54,?5,1=?5,
@(4,7)O,@(1^-54,2^54)*/H,
@@ -1101,7 +1197,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Colchicine}
+\subsection*{Colchicine}
\begin{verbatim}
<30,Ph,@(1,2,6)/O!,
-4=?7,-5=?7,
@@ -1110,7 +1206,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Lycorine}
+\subsection*{Lycorine}
\begin{verbatim}
<30,Ph,
-4=?6,-2=?6,6=?5,(9,12)=?5[3],
@@ -1121,7 +1217,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Gibberellin}
+\subsection*{Gibberellin}
\begin{verbatim}
<18,?5,3=?7,5=?6[12],
8*,160`1.3,&3,
@@ -1132,7 +1228,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Quinine}
+\subsection*{Quinine}
\begin{verbatim}
<30,Ph,3=Ph,7:N,6:/O!,
10\,*/OH,/H~zf^-60,!,
@@ -1142,7 +1238,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Atoropin}
+\subsection*{Atoropin}
\begin{verbatim}
<-30,O,!,//O,!,!,Ph,
#1\~zb^-120,
@@ -1151,7 +1247,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Rotenone}
+\subsection*{Rotenone}
\begin{verbatim}
<-60,?5,$(-3,-2,-3,-4)?6,
$(7,9,-2,-4)dl,$(3,17)dr,
@@ -1160,7 +1256,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Pyrethrin I}
+\subsection*{Pyrethrin I}
\begin{verbatim}
<30,?3,@(3^35~wf,3^-35~zf)/_,
1*\,!!,iPr,2\*,//O,!,O,-36~zb,|,
@@ -1168,7 +1264,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Validamycin}
+\subsection*{Validamycin}
\begin{verbatim}
<30,?6,@(5,6)/OH,3:/!OH>rl,
#4\,O,-60,|,?6,2:O,@(3,4,5)/OH,6:/!OH,
@@ -1176,7 +1272,7 @@ F:mcf_man_soc/C:90/EN:Ampicillin/CAS:69-53-4
\end{verbatim}
\MCFstructure
%-----------------------------------------------------------------------------
-\subsection{Paclitaxel}
+\subsection*{Paclitaxel}
\begin{verbatim}
?6,5=d,3*,{,``1,36,45,45,45,45,},&#5,
-4=?6,-4=?4,-1=wb,-3=wf,-1:O,||,
@@ -1201,6 +1297,8 @@ font_wd#:=60mm#; % font width >
font_ht#:=40mm#; % font height >
var3:="cal_MW"; tag3:="cMW"; > AUX file table
var4:="cal_FM"; tag4:="cFM"; >
+%%%% sw_report:=1; > Report output
+%%%% sw_MOLout:=1; > MOL file output
outputformat:="png"; hppp:=vppp:=0.1; > PNG output
outputtemplate:="%j-%3c.png"; >
%-------------------------------------------------------------------------
@@ -1218,10 +1316,35 @@ beginfont("NO:2","EN:Cholesterol") > begin font(information)
-1\^17,/*_,!4,/_,!) > end MCF
endfont > end font
%------------------------------------------------------------------------
+beginfont("NO:3","EN:Limonin") > begin font(information)
+ MCf(<30,?6,$(-3,-4)?6, > begin MCF (3)
+ -5=?3,-2=wf,-1=wb,6=?5,-4=?6,-5=wf, >
+ @(13,15,17,20)O,@(3,12,21)//O, >
+ @(4~wf^60,8~zf^60,18^35,18^-35)/_, >
+ @(1^60,5^180,16^60)/*H, >
+ 14\*,|,?5,$(1,4)dl,3:O) > end MCF
+endfont > end font
+%------------------------------------------------------------------------
+beginfont("NO:4","EN:beta-carotene) > begin font(information)
+ MCf(<30,?6,3=dl,@(3,5^35,5^-35)/_, > begin MCF (4)
+ 4\,|,!18,$(1,3,5,7,9,11,13,15,17)dr, >
+ @(3,7,12,16)/_, >
+ |,?6,6=dl,@(6,2^35,2^-35)/_) > end MCF
+endfont > end font
+%------------------------------------------------------------------------
+beginfont("NO:5","EN:Gibberellin A3"); > begin font(information)
+ MCf(<18,?5,3=?7,5=?6[12], > begin MCF (5)
+ 8*,160`1.3,&3,13=dl,6=wf,8=wb, >
+ 5*,40~zf`1,O,60,//O^180,&14~zb, >
+ 2:/COOH,7://_,13:*/OH,8:/*OH, >
+ 14:*/_,@(1^60,4^60)*/H) > end MCF
+endfont; > end font
+%------------------------------------------------------------------------
bye
\end{verbatim}
%------------------------------------------------------------------------
\noindent%
+\newpage
\subsection{Information auxfile output}
\paragraph{(Insert option parameter setting)}
\begin{verbatim}
@@ -1235,31 +1358,45 @@ bye
\paragraph{(Output)}
\begin{verbatim}
(sw_auxfix=0)
-F:mcf_man_soc;C:109;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin
-F:mcf_man_soc;C:110;cMW:386.6532;cFM:C27H46O;EN:Cholesterol
+F:mcf_man_soc;C:1;cMW:349.40462;cFM:C16H19N3O4S;EN:Ampicillin
+F:mcf_man_soc;C:2;cMW:386.6532;cFM:C27H46O;EN:Cholesterol
+F:mcf_exa_soc;C:3;cMW:470.5113;cFM:C26H30O8;EN:Limonin
+F:mcf_exa_soc;C:4;cMW:536.8722;cFM:C40H56;EN:beta-Carotene
+F:mcf_exa_soc;C:5;cMW:346.3742;cFM:C19H22O6;EN:Gibberellin A3
.....................................................
.....................................................
(sw_auxfix=1)
F;C;cMW;cFM;EN
-mcf_man_soc;90;349.40462;C16H19N3O4S;Ampicillin
-mcf_man_soc;91;386.6532;C27H46O;Cholesterol
+mcf_man_soc;1;349.40462;C16H19N3O4S;Ampicillin
+mcf_man_soc;2;386.6532;C27H46O;Cholesterol
+mcf_exa_soc;3;470.5113;C26H30O8;Limonin
+mcf_exa_soc;4;536.8722;C40H56;beta-Carotene
+mcf_exa_soc;5;346.3742;C19H22O6;Gibberellin A3
......................................
......................................
-( tag : variable )
-F : filename C : char number NO : serial number EN : english name
-cMW : molecular weight calculated cFM : molecular formula calculated
+( Tag )
+F : filename
+C : char number
+NO : serial number
+EN : english name
+JN : japanese name
+FM : formula from literature data
MW : molecular weight from literature data
+USE : the use
+cMW : molecular weight calculated
+cMI : monoisotopic mass calculated
+cFM : molecular formula calculated
\end{verbatim}
%------------------------------------------------------------------------
\newpage
\noindent%
-\subsection{Checklist output}
+\subsection{Report output}
\paragraph{(Insert option parameter setting)}
\begin{verbatim}
- sw_checklist:=1;
- ** default : sw_checklist=0
+ sw_report:=1;
+ ** default : sw_report=0
\end{verbatim}
\paragraph{(Command line)}
\begin{verbatim}
@@ -1269,51 +1406,52 @@ MW : molecular weight from literature data
\begin{verbatim}
%------------------------------------------------------------------
% Molecular name = Caffeine
-% Warnings = 0 / Expanded command = 75
-% Width * Height = 39.5496 * 36.85023
-% Shift width * height = -9.33653 * -12.77606
-% Bond length = 9.23695 Atom size = 4.12231
+% Warnings = 0 / Expanded command = 80
+% Width * Height = 54.31772 * 50.43338
+% Shift width * height = -12.59462 * -17.49146
+% Bond length = 12.75589 Atom size = 5.38914
% Atom count= 14 Bond count= 15 Ring count= 2 Hide H count= 10
%------------------------------------------------------------------
-%< NO. >< x axis , y axis >< atom >< bond >< hide_H >
-% A1 ( 0 , 0 ) C 4
-% A2 ( 0.866 , -0.5 ) N 3
-% A3 ( 1.732 , 0 ) C 4
-% A4 ( 1.732 , 1 ) C 4
-% A5 ( 0.866 , 1.5 ) C 4
-% A6 ( 0 , 1 ) N 3
-% A7 ( 2.683 , -0.309 ) N 3
-% A8 ( 3.271 , 0.5 ) C 3 1
-% A9 ( 2.683 , 1.309 ) N 3
-% A10 ( 0.866 , -1.383 ) C 1 3
-% A11 ( -0.788 , 1.455 ) C 1 3
-% A12 ( 2.959 , 2.159 ) C 1 3
-% A13 ( -0.788 , -0.455 ) O 2
-% A14 ( 0.866 , 2.383 ) O 2
+%< NO. >( x axis , y axis )< atom >< bond >< hide_H >
+% A1 ( 0 , 0 ) C 4
+% A2 ( 0.866 , -0.5 ) N 3
+% A3 ( 1.732 , 0 ) C 4
+% A4 ( 1.732 , 1 ) C 4
+% A5 ( 0.866 , 1.5 ) C 4
+% A6 ( 0 , 1 ) N 3
+% A7 ( 2.683 , -0.309 ) N 3
+% A8 ( 3.271 , 0.5 ) C 3 1
+% A9 ( 2.683 , 1.309 ) N 3
+% A10 ( 0.866 , -1.371 ) C 1 3
+% A11 ( -0.776 , 1.448 ) C 1 3
+% A12 ( -0.776 , -0.448 ) O 2
+% A13 ( 0.866 , 2.371 ) O 2
+% A14 ( 2.955 , 2.147 ) C 1 3
%------------------------------------------------------------------
%< NO. >< bond (sdt)><angle + ( +- )><length ( pt )>
-% B1 1 -> 2 ( 1) 330 ( -30) 1 ( 9.24)
-% B2 2 -> 3 ( 1) 30 ( 30) 1 ( 9.24)
-% B3 3 -> 4 ( 2) 90 ( 90) 1 ( 9.24)
-% B4 4 -> 5 ( 1) 150 ( 150) 1 ( 9.24)
-% B5 5 -> 6 ( 1) 210 ( -150) 1 ( 9.24)
-% B6 6 -> 1 ( 1) 270 ( -90) 1 ( 9.24)
-% B7 3 -> 7 ( 1) 342 ( -18) 1 ( 9.24)
-% B8 7 -> 8 ( 2) 54 ( 54) 1 ( 9.24)
-% B9 8 -> 9 ( 1) 126 ( 126) 1 ( 9.24)
-% B10 9 -> 4 ( 1) 198 ( -162) 0.66 ( 6.1)
-% B11 2 -> 10 ( 1) 270 ( -90) 0.66 ( 6.1)
-% B12 6 -> 11 ( 1) 150 ( 150) 0.66 ( 6.1)
-% B13 9 -> 12 ( 1) 72 ( 72) 0.66 ( 6.1)
-% B14 1 -> 13 ( 2) 210 ( -150) 0.66 ( 6.1)
-% B15 5 -> 14 ( 2) 90 ( 90) 0.66 ( 6.1)
+% B1 1 -> 2 ( 1) 330 ( -30) 1 ( 12.76)
+% B2 2 -> 3 ( 1) 30 ( 30) 1 ( 12.76)
+% B3 3 -> 4 ( 2) 90 ( 90) 1 ( 12.76)
+% B4 4 -> 5 ( 1) 150 ( 150) 1 ( 12.76)
+% B5 5 -> 6 ( 1) 210 ( -150) 1 ( 12.76)
+% B6 6 -> 1 ( 1) 270 ( -90) 1 ( 12.76)
+% B7 3 -> 7 ( 1) 342 ( -18) 1 ( 12.76)
+% B8 7 -> 8 ( 2) 54 ( 54) 1 ( 12.76)
+% B9 8 -> 9 ( 1) 126 ( 126) 1 ( 12.76)
+% B10 9 -> 4 ( 1) 198 ( -162) 0.66 ( 8.42)
+% B11 2 -> 10 ( 1) 270 ( -90) 0.66 ( 8.42)
+% B12 6 -> 11 ( 1) 150 ( 150) 0.66 ( 8.42)
+% B13 1 -> 12 ( 2) 210 ( -150) 0.66 ( 8.42)
+% B14 5 -> 13 ( 2) 90 ( 90) 0.66 ( 8.42)
+% B15 9 -> 14 ( 1) 72 ( 72) 0.66 ( 8.42)
%------------------------------------------------------------------
% C ( 12.0107) * 8 = 96.08557
% H ( 1.00793) * 10 = 10.07935
% N ( 14.0067) * 4 = 56.0268
% O ( 15.9994) * 2 = 31.99881
-% Weight Calc: 194.19052 / Input: 194.19 / weight gap= 0.00052
-% Fomula Calc: C8H10N4O2 / Input: C8H10N4O2 / MACTCH
+% Monoisotopic mass: 194.08038
+% Weight Calc: 194.1905 / Input: 194.194 / weight gap= -0.00348
+% Fomula Calc: C8H10N4O2 / Input:
%==================================================================
\end{verbatim}%
\newpage
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 2f74ae116c2..9d792f89f10 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 8a72f70b7db..32373b33a9a 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 2017.01.15
+% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2017.01.29
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%% mcf2graph.mf it must be version 4.08 or later
+%%% mcf2graph.mf it must be version 4.09 or later
\documentclass{article}
%------------------------------------------------------------------------------
\usepackage{luamplib}%
diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
index 86aed79aff3..7fa4db15f74 100644
--- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
+++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf
@@ -1,5 +1,5 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% mcf2graph ver 4.08 Copyright (c) 2013-2017 Akira Yamaji
+% mcf2graph ver 4.09 Copyright (c) 2013-2017 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,
@@ -27,7 +27,7 @@
% Set outputformat to "svg" : mpost -s ahangle=2 FILENAME
% Set outputformat to MDL Molfile : mpost -s ahangle=3 FILENAME
% Set first font only (for test) : mpost -s ahlength=1 FILENAME
-% Set output checklist : mpost -s ahlength=2 FILENAME
+% Set output report : mpost -s ahlength=2 FILENAME
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tracingstats:=1;
message " This is mcf2graph ver 4.0 2017.1";
@@ -36,11 +36,11 @@ newinternal nA,nB,nC,nD,nE,nF,char_num,str_cnt,def_num,def_int,tbl_cnt;
numeric save_para[],comD[][],parD[][],cntD[],tbl_str_wd[],tbl_atom[],tbl_subst[][],tbl_atom_wt[],
tbl_atom_mi[],tbl_char_wd[],tbl_char_ht[],tbl_char_dp[];
string tbl_atom_str[],strD[],var[],tag[],mp_log_name,aux_delimiter;
-picture atom_font[],mol_stru[];
+picture atom_font[],str_font[],mol_stru[],save_pict;
%-------------------------------------------------------------------------------------------------
char_num:=str_cnt:=proc_end:=0;
sw_numberA:=sw_numberB:=sw_mol_frame:=sw_auxout:=sw_solid:=sw_expand:=sw_font_frame:=0;
-sw_atom_frame:=sw_checklist:=sw_MOLout:=sw_subst_off:=sw_bond_single:=sw_auxfix:=sw_clip:=0;
+sw_atom_frame:=sw_report:=sw_MOLout:=sw_subst_off:=sw_bond_single:=sw_auxfix:=sw_clip:=0;
numberA_start:=numberB_start:=1; numberA_end:=numberB_end:=4095; aux_max:=max_inf_num:=20;
aux_delimiter:=";"; var1:="jobname"; tag1:="F"; var2:="char_num"; tag2:="C";
for i=3 upto aux_max: var[i]:=tag[i]:=""; endfor
@@ -50,7 +50,7 @@ if (known green)and(known ahlength):
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
+ if ahlength=2: sw_report:=1; def shipit = enddef; fi % report on
if ahangle=0: def shipit = enddef; % No image file
elseif ahangle=1: outputformat:="png"; hppp:=vppp:=0.1; % PNG format
elseif ahangle=2: outputformat:="svg"; % SVG format
@@ -94,7 +94,7 @@ def_com(-4000)(_term,_jp_atom,_jp_atom_abs,_jp_bond,_cyc,_cyc_sB,_cyc_eB,_set_li
def_com(1)(si,dl,dr,db,dm,tm,wf,wb,bd,bz,zf,zb,dt,wv,nl,vf,vb,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_report,sw_numberA,sw_numberB,sw_mol_frame,sw_auxout,sw_solid,sw_expand,sw_MOLout,
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,
@@ -112,6 +112,7 @@ def restore_par(text t)= nA:=0;
forsuffixes list=t: if list<>save_para[incr nA]: list:=save_para[nA]; fi endfor enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def beginfont(text s)=
+ char_num:=char_num+1;
store_par(parameter_list);
begingroup
save cntA,cntB,cntM,minX,minY,f_beginchar,numS,sftX,sftY,f_ext,
@@ -123,7 +124,6 @@ def beginfont(text s)=
for i:=1 upto max_inf_num: info[i]:=":"; endfor
f_ext:=inf_num:=cntM:=0;
for list=s: info[incr inf_num]:=list; endfor
- char_num:=char_num+1;
enddef;
%==================================================================================================
def endfont=
@@ -145,10 +145,11 @@ def endfont=
beginchar(char_num,font_wd#,font_ht#,0)
if (sw_font_frame=1)or(sw_font_frame=3): draw_frame((0,0),w,h,thickness_font_frame); fi
if (sw_font_frame=2)or(sw_font_frame=3):
- nA:=w-2margin_left_right; nB:=h-2margin_top_bottom; pT:=(margin_left_right,margin_top_bottom);
+ nA:=w-2margin_left_right; nB:=h-2margin_top_bottom;
+ pT:=(margin_left_right,margin_top_bottom);
draw_frame(pT,nA,nB,thickness_font_frame); fi
if sw_font_frame=4: draw_corner(w,h,thickness_font_frame); fi
- if (sw_auxout=1)or(sw_checklist=1)or(sw_MOLout=1): proc_calc_out; fi
+ if (sw_auxout=1)or(sw_report=1)or(sw_MOLout=1): proc_calc_out; fi
for i=1 upto cntM:
addto currentpicture also mol_stru[i] shifted posM[0][i]; mol_stru[i]:=nullpicture;
endfor
@@ -316,6 +317,27 @@ def ext(text s)=
s addto mol_stru[cntM] also currentpicture; clearit;
endgroup;
enddef;
+%--------------------------------------------------------------------------------------------------
+def use_font(expr WD)=
+ save_pict:=currentpicture;
+ for i=1 upto 128: f_char[i]:=1; endfor
+ proc_char_setup(str_font)(WD);
+ str_wd#:=WD;
+ define_pixels(str_wd);
+ currentpicture:=save_pict;
+enddef;
+%--------------------------------------------------------------------------------------------------
+def puts(expr PA)(expr STR)=
+ begingroup
+ save cp; pair cp;
+ cp:=PA;
+ for i=0 upto length(STR)-1:
+ nA:=ASCII(pic_c(i,STR));
+ addto currentpicture also str_font[nA] shifted (cp-(0,str_wd*tbl_char_dp[nA]));
+ cp:=cp+(str_wd*tbl_char_wd[nA],0);
+ endfor
+ endgroup;
+enddef;
%=================================================================================================
def MCf(text s)= MCd(1,1)(.5,.5)(s) enddef; % MC fill draw
%-------------------------------------------------------------------------------------------------
@@ -359,7 +381,7 @@ def MCd(expr RW,RH)(expr FW,FH)(text TX)=
if bond_len#>max_bond_length#:
bond_len#:=max_bond_length#; proc_size_setup; proc_skeleton; proc_scaling; fi
fi
- proc_char_setup;
+ proc_char_setup(atom_font)(atom_wd#);
%-----------------------------------------------------------------------------------------------
for i=1 upto cntB: if lineB[i]<si_ : draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
for i=1 upto cntB: if lineB[i]>=si_: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor
@@ -462,9 +484,15 @@ 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 numS[i]<>0: for j=0 upto length(strD[numS[i]])-1:
- f_char[ASCII(pic_c(j,strD[numS[i]]))]:=1; endfor fi endfor fi
+ 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 numS[i]<>0:
+ for j=0 upto length(strD[numS[i]])-1: f_char[ASCII(pic_c(j,strD[numS[i]]))]:=1; endfor
+ fi
+ endfor
+ fi
enddef;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def proc_bond_atom(expr n)=
@@ -747,7 +775,7 @@ CH3:='("C{H_3_}"); CN:='("CN"); NH2:='("N{H_2_}"); NO2:='("N{O_2_}"); SH:='("SH"
SO3:='("S{O_3_}"); NMe:=N!:='(N,/Me); iPr:=Me!:='(60,-2\); tBu:='(60,-2\,-3*,60);
OMe:=O!:='(O,!); OEt:=O!2:='(O,!2); OPr:=O!3:='(O,!3); OiPr:=OMe!:='(O,!,iPr);
SMe:=S!:='(S,!); SEt:=S!2:='(S,!2); SPr:=S!3:='(S,!3); SiPr:=SMe!:='(S,!,iPr);
-COOMe:=COO!:='(//O,!,O,!); COMe:=CO!:='(//O,!);
+COOMe:=COO!:='(//O,!,O,!); COMe:=CO!:='(//O,!); COEt:=CO!2:='(//O,!2);
OCOMe:=OCO!:='(O,!,//O,!); COOEt:=COO!2:='(//O,!,O,!2);
COOiPr:=COOMe!:='(//O,!,O,!,iPr); COOPr:=COO!3:='(//O,!,O,!3);
COOtBu:='(//O,!,O,!,tBu); NMeMe:=NMe!:='(N,/Me,!); NHCOMe:=NHCO!:='(NH,!,//O,!);
@@ -780,15 +808,15 @@ char_size_set(.7)( 1)(.15)("pqg");
char_size_set(.7)(.8)( 0)("acekosuvxzwry");
char_size_set(.4)( 1)( 0)(".,:;'`");
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-def proc_char_setup=
+def proc_char_setup(suffix FONT)(expr SIZE)=
begingroup
save Z,aW,aH,fW,hW,hW,hH,fP,hP,vL,hL,PO,POh,sH,FD;
pair Z[];
%---------------------------------------------------------------
def FD(expr c)(text s)=
if f_char[ASCII(c)]=1:
- aW#:=atom_wd#*tbl_char_wd[ASCII(c)]*(1-ratio_atomgap_atom*2);
- aH#:=atom_wd#*tbl_char_ht[ASCII(c)]*(1-ratio_atomgap_atom*2);
+ aW#:=SIZE*tbl_char_wd[ASCII(c)]*(1-ratio_atomgap_atom*2);
+ aH#:=SIZE*tbl_char_ht[ASCII(c)]*(1-ratio_atomgap_atom*2);
define_pixels(aW,aH);
fW:=aW-hP; hW:=.5aW; fH:=aH-hP; hH:=.5aH;
Z01:=( 0,hP); Z02:=(hP, 0); Z03:=(hP,hP); Z04:=(aW,hP); Z05:=(fW, 0); Z08:=( 0,hH);
@@ -796,7 +824,7 @@ def FD(expr c)(text s)=
Z18:=(hP,aH); Z19:=(hW,hP); Z20:=(hW,hH); Z06:=(hW,aH); Z07:=(hW, 0); Z11:=(hW,aW);
Z15:=(fW,aH); Z17:=(aW,hH);
s;
- atom_font[ASCII(c)]:=
+ FONT[ASCII(c)]:=
currentpicture shifted (ratio_atomgap_atom*atom_wd,ratio_atomgap_atom*atom_wd);
clearit;
fi
@@ -926,21 +954,21 @@ def STb(expr a)(text s)=
enddef;
%==================================================================================================
tbl_cnt:=0;
-STa("C" ,12.0107, 12.0000000); STa("H" , 1.00794, 1.00782503223);
-STa("{Al}",26.9815, 26.98153853); STa("{As}",74.9216, 74.92159457);
-STa("B" ,10.811, 11.00930536); STa("{Br}",79.904, 78.9183376);
-STa("{Ca}",40.078, 39.962590863); STa("{Cl}",35.453, 34.968852);
-STa("{Co}",58.933194, 58.93319429); STa("{Cr}",51.9961, 51.94050623);
-STa("{Cu}",63.546, 62.92959772); STa("D" ,2.012, 2.01410177812);
-STa("F" ,18.9984, 18.99840316273); STa("{Fe}",55.845, 55.93493633);
-STa("{Hg}",200.59, 201.97064340); STa("I" ,126.90447, 126.9044719);
-STa("K" ,39.0983, 38.9637064864); STa("{Li}",6.941, 7.0160034366);
-STa("{Mg}",24.305, 23.985041697); STa("{Mn}",54.938044, 54.93804391);
-STa("N" ,14.0067, 14.00307400443); STa("{Na}",22.98977, 22.9897692820);
-STa("{Ni}",58.693, 57.93534241); STa("O" ,15.9994, 15.99491461957);
-STa("P" ,30.973762, 30.97376199842); STa("S" ,32.065, 31.9720711744);
-STa("{Se}",78.971, 79.9165218); STa("{Si}",28.0855, 27.97692653465);
-STa("{Sn}",118.71, 119.90220163); STa("{Ti}",47.867, 47.94794198);
+STa("C" ,12.0107, 12.0000000); STa("H" , 1.00794, 1.00782503223);
+STa("{Al}",26.9815, 26.98153853); STa("{As}",74.9216, 74.92159457);
+STa("B" ,10.811, 11.00930536); STa("{Br}",79.904, 78.9183376);
+STa("{Ca}",40.078, 39.962590863); STa("{Cl}",35.453, 34.968852);
+STa("{Co}",58.933194, 58.93319429); STa("{Cr}",51.9961, 51.94050623);
+STa("{Cu}",63.546, 62.92959772); STa("D" ,2.012, 2.01410177812);
+STa("F" ,18.9984, 18.99840316273); STa("{Fe}",55.845, 55.93493633);
+STa("{Hg}",200.59, 201.97064340); STa("I" ,126.90447,126.9044719);
+STa("K" ,39.0983, 38.9637064864); STa("{Li}",6.941, 7.0160034366);
+STa("{Mg}",24.305, 23.985041697); STa("{Mn}",54.938044, 54.93804391);
+STa("N" ,14.0067, 14.00307400443); STa("{Na}",22.98977, 22.9897692820);
+STa("{Ni}",58.693, 57.93534241); STa("O" ,15.9994, 15.99491461957);
+STa("P" ,30.973762, 30.97376199842); STa("S" ,32.065, 31.9720711744);
+STa("{Se}",78.971, 79.9165218); STa("{Si}",28.0855, 27.97692653465);
+STa("{Sn}",118.71, 119.90220163); STa("{Ti}",47.867, 47.94794198);
STa("{Zn}",65.409, 63.92914201);
%--------------------------------------------------------------------------------------------------
STb("{H_2_}")("H","H"); STb("OH")("O","H"); STb("O{Na}")("O","{Na}"); STb("CN")("C","N");
@@ -1020,7 +1048,7 @@ def proc_calc_out=
cal_MI:=substring (0,10) of decimal(MI_num);
cal_MW:=substring (0,8) of decimal(MW_num);
if sw_auxout=1: proc_auxfile_out; fi
- if sw_checklist=1: proc_checklist_out; fi
+ if sw_report=1: proc_report_out; fi
if sw_MOLout=1: proc_MOLfile_out; fi
endgroup
enddef;
@@ -1045,20 +1073,20 @@ vardef round_auto(expr n)=
elseif (n<400)and(n>-400): round(n*10)/10 else: round(n) fi
enddef;
%--------------------------------------------------------------------------------------------------
-def proc_checklist_out=
+def proc_report_out=
message "%------------------------------------------------------------------";
message "% Molecular name = "& inf_EN;
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 "% Width * Height = " & fdr(10)(mol_wd)&" * "&fdr(10)(mol_ht);
+ message "% Shift width * height = "& fdr(10)(minX)&" * "&fdr(10)(minY);
message "% Bond length = "&fdr(3)(bond_len)&" Atom size = "&fdr(3)(atom_wd);
message "% Atom count="&fdr(3)(cntA)&" Bond count="&fdr(3)(cntB)&
" Ring count="&fdr(3)(cntB-cntA+1)&" Hide H count="&fdr(3)(cnt_hide_H);
message "%------------------------------------------------------------------";
- message "%< NO. >< x axis , y axis >< atom >< bond >< hide_H >";
+ message "%< NO. >( x axis , y axis )< atom >< bond >< hide_H >";
for i=1 upto cntA:
- message "% A"&fdl(4)(i)&" ("&fdr(7)(round_auto(xpart(posA[i])/bond_len))&" , "&
- fdr(7)(round_auto(ypart(posA[i])/bond_len))&" ) "&fixed_l(8)(strD[numS[i]])&
+ message "% A"&fdl(4)(i)&" ("&fdr(10)(round_auto(xpart(posA[i])/bond_len))&" , "&
+ fdr(10)(round_auto(ypart(posA[i])/bond_len))&" ) "&fixed_l(8)(strD[numS[i]])&
" "&fdr(3)(Bcnt[i]) if hideH[i]>0: &fdr(8)(hideH[i]) fi;
endfor
message "%------------------------------------------------------------------";
@@ -1084,7 +1112,7 @@ def proc_checklist_out=
if nA<40: &fdr(12)(tbl_atom_wt[i]*sumA[i]); else: &fdr(12)(nA)&" * 100"; fi
fi
endfor
- message "% Mono isotopic:" &cal_MI_str;
+ message "% Monoisotopic mass: "&cal_MI_str;
message "% Weight Calc: " &cal_MW_str &" / Input: "
if inf_MW<>"": &inf_MW &" / weight gap= " &decimal(MW_num-scantokens(inf_MW)) fi;
message "% Fomula Calc: "&cal_FM&" / Input: "