From 1f17918f6a9af739d984a5ea165dcbbe1c78f0b6 Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Sat, 11 May 2019 21:31:07 +0000 Subject: mcf2graph (11may19) git-svn-id: svn://tug.org/texlive/trunk@51090 c570f23f-e606-0410-a88d-b1316a301751 --- Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG | 9 +- Master/texmf-dist/doc/metapost/mcf2graph/README | 2 +- .../doc/metapost/mcf2graph/mcf_exa_soc.mf | 30 +- .../doc/metapost/mcf2graph/mcf_example.pdf | Bin 279915 -> 281005 bytes .../doc/metapost/mcf2graph/mcf_example.tex | 2 +- .../doc/metapost/mcf2graph/mcf_man_soc-064.mps | 429 +++++++-------------- .../doc/metapost/mcf2graph/mcf_man_soc.mf | 80 ++-- .../doc/metapost/mcf2graph/mcf_manual.pdf | Bin 584030 -> 588104 bytes .../doc/metapost/mcf2graph/mcf_manual.tex | 122 +++--- .../doc/metapost/mcf2graph/mcf_mplib_exa.pdf | Bin 177927 -> 172010 bytes .../doc/metapost/mcf2graph/mcf_mplib_exa.tex | 74 ++-- Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf | 140 ++++--- 12 files changed, 373 insertions(+), 515 deletions(-) diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG index 8df1b8c52cb..74ba391dbda 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG +++ b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG @@ -1,6 +1,13 @@ ******************************************************************************* - Changelog of mcf2graph software package by Akira Yamaji 2019-03-21 + Changelog of mcf2graph software package by Akira Yamaji 2019-05-11 ******************************************************************************* +[ver. 4.41 / 2019-05-11] + -change syntax + |<=,=>| => |=,=| + ext() => add() + EXT() => ext() + -update MCF manual + [ver. 4.40 / 2019-03-21] -add function MC() -change function name MCa() => MCat() diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README index 9297f9ef02b..3cd62eb060f 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 : 4.40 2019-03-21 + version : 4.41 2019-05-11 E-mail : mcf2graph@gmail.com Located at : http://www.ctan.org/pkg/mcf2graph ******************************************************************************** diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf index d18c965ff88..c225b302cc2 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf @@ -1,7 +1,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2019.03.10 +% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2019.05.11 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph.mf; %%% it must be version 4.40 or later +input mcf2graph.mf; %%% it must be version 4.41 or later %------------------------------------------------------------------------- fsize:=(33mm,24mm); max_blength:=4.5mm; @@ -27,6 +27,8 @@ var4:="cal_MW"; tag4:="cMW"; %%%% sw_rep_out:=1; %%%% sw_mol_out:=1; %%%% outputformat:="png"; hppp:=vppp:=0.1; outputtemplate:="%j-%3c.png"; +%--------------------------------------------------------------------------- +%ext(defaultscale:=.5; label.bot(decimal(char_num)&":"&inf_EN,(.5w,0));) %*************************************************************************** beginfont("EN:Acetamiprid","MW:222.676","FM:C10H11ClN4") MC(<30,Ph,2:N,1:/Cl,4:\,!,N,/_,!,/_,!!,N,!,CN) @@ -67,7 +69,8 @@ endfont %*************************************************************************** beginfont("EN:Isoprothiolane","MW:290.392") MC(<30,!,/_,!,O,!,//O,|,!2,//O,!,O,!,/_,!,2:\\,|,?5,{2,5}:S) -endfont%*************************************************************************** +endfont +%*************************************************************************** beginfont("EN:Etridiazole","MW:247.518") MC(<18,?5,{1,3}=dl,{2,4}:N,5:S,1:/O!2,3:/CCl3) endfont @@ -177,9 +180,9 @@ endfont beginfont("EN:Rifampicin","MW:822.94") MC(<30,Ph,6:/_^30,5:/OH,|,-6=?5,1:O,3://O,2:/*_^60, |,-8=?6,{2,4}=dl,{1,4}:/OH, - |<=1,-2:\,NH,60,//O,-60,/_,60~dl,60,60~dl,-60, + |=1,-2:\,NH,60,//O,-60,/_,60~dl,60,60~dl,-60, */_,60,/*OH,-60,/*_,60,/*OH,60,*/_^30,-60, - 60,/*_^30,-53,66,-53~dl,66`1.2,O,>|,$8:#, + 60,/*_^30,-53,66,-53~dl,66`1.2,O,=|,$8:#, -4:/*O!,-6:@,-30,O,!,//O,!,$11:\,!!,N,!,|,?6,{1,4}:N,4:/_) endfont %*************************************************************************** @@ -211,12 +214,13 @@ beginfont("EN:Luciferin","MW:280.33") endfont %*************************************************************************** beginfont("EN:Chlorophyll a","MW:893.509") -MC(<54,|<=1,?5,{2,5}=dl,4:N,3:\,54~dl,|,?5,{2,4}=dl,5:N, +MC(<54,|=1,?5,{2,5}=dl,4:N,3:\,54~dl,|,?5,{2,4}=dl,5:N, -2:\,54~dl,|,?5,2=d,5:N,-2:\~dl,54,|,?5,5=d,5:N,-2:\~dl,$5:#, - -1:@,24,/*COO!^15,72,//O,$1:#,>|, + -1:@,24,/*COO!^15,72,//O,$1:#,=|,||, {2,9,15,20~zf}:/_,8:/!,14:\,!!, - $4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#, - $21:@,-6~wf,!2,//O,!,O,!2,!!,|,!13,{1,5,9,13}:/_) + 4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#, + 21:@,-6~wf,!2,//O,!,O,!2,!!,|,!13,{1,5,9,13}:/_ + ) endfont %************************************************************************** beginfont("EN:Gibberellin A3","MW:346.379"); @@ -237,8 +241,8 @@ beginfont("EN:Lycorine","MW:287.315") endfont %************************************************************************** beginfont("EN:Tetrodotoxine","MW:319.27") - MC(|<=1,<60,-90,60,-30`1.15,150,60,$1:#,$3:@,-135,60,-30`1.15,150,$4:#, - $10:\,O,60`1.33,60,$3~si_:#,$8:@,-15~si_,O,$12:#,>|, + MC(|=1,<60,-90,60,-30`1.15,150,60,$1:#,$3:@,-135,60,-30`1.15,150,$4:#, + $10:\,O,60`1.33,60,$3~si_:#,$8:@,-15~si_,O,$12:#,=|, $9:@,45,-60,OH,1^120://NH, {5~zf^-15,7,9^-75,12,13~zf}:/OH,{2,6^180}:NH) endfont @@ -346,7 +350,7 @@ beginfont("EN:Pyrethrin I","MW:328.452"); endfont; %*************************************************************************** beginfont("EN:Erythromycin","MW:733.937"); -MC(<30,|<=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,>|,1:#, +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!, @@ -354,7 +358,7 @@ MC(<30,|<=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,>|,1:#, endfont; %************************************************************************** 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, + 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) diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf index 0fc7eccc3e7..ddb0920295e 100644 Binary files a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf and b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf differ diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex index d94488e02ff..8199e247681 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 2019.02.24 +% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2019.05.11 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage{graphicx} diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.mps b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.mps index e5ba95a90bd..70e27e77c68 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.mps +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc-064.mps @@ -2,12 +2,12 @@ %%BoundingBox: -1 -1 213 57 %%HiResBoundingBox: -0.1 -0.1 212.69804 56.79282 %%Creator: MetaPost 2.00 -%%CreationDate: 2019.03.17:0708 +%%CreationDate: 2019.05.11:0740 %%Pages: 1 %%DocumentResources: procset mpost-minimal -%%+ font ICXWUR-CMTT10 ICXWUR-CMR8 +%%+ font JIZCCV-NimbusSanL-Regu IXTKJB-CMR8 %%DocumentSuppliedResources: procset mpost-minimal -%%+ font ICXWUR-CMTT10 ICXWUR-CMR8 +%%+ font JIZCCV-NimbusSanL-Regu IXTKJB-CMR8 %%EndComments %%BeginProlog %%BeginResource: procset mpost-minimal @@ -18,37 +18,34 @@ /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 -%%BeginResource: font ICXWUR-CMTT10 -%!PS-AdobeFont-1.0: CMTT10 003.002 -%%Title: CMTT10 -%Version: 003.002 -%%CreationDate: Mon Jul 13 16:17:00 2009 -%%Creator: David M. 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cleartomark {restore}if %%EndResource -%%BeginResource: font ICXWUR-CMR8 +%%BeginResource: font IXTKJB-CMR8 %!PS-AdobeFont-1.0: CMR8 003.002 %%Title: CMR8 %Version: 003.002 @@ -354,7 +185,7 @@ cleartomark % This license is in the accompanying file OFL.txt, and is also % available with a FAQ at: http://scripts.sil.org/OFL. %%EndComments -FontDirectory/ICXWUR-CMR8 known{/ICXWUR-CMR8 findfont dup/UniqueID known{dup +FontDirectory/IXTKJB-CMR8 known{/IXTKJB-CMR8 findfont dup/UniqueID known{dup /UniqueID get 5000791 eq exch/FontType get 1 eq and}{pop false}ifelse {save true}{false}ifelse}{false}ifelse 11 dict begin @@ -600,7 +431,7 @@ cleartomark %%EndResource %%EndProlog %%BeginSetup - /cmtt10 /ICXWUR-CMTT10 def + /uhvr8r /JXDTPR-NimbusSanL-Regu def /cmr8 /GMTUEE-CMR8 def %%EndSetup %%Page: 1 1 @@ -702,8 +533,8 @@ newpath 40.45374 39.80562 moveto 0 0.50114 dtransform truncate idtransform setlinewidth pop newpath 75.229 19.72816 moveto 86.09601 13.45413 lineto stroke -6.07166 45.71011 moveto -(\(draw\)) cmtt10 9.96265 fshow +9.22984 46.03944 moveto +(\(draw\)) uhvr8r 9.96265 fshow 150.14568 6.07826 moveto (N) cmr8 10.56937 fshow 150.14568 46.23317 moveto @@ -738,8 +569,8 @@ newpath 136.30315 39.80562 moveto 0 0.50114 dtransform truncate idtransform setlinewidth pop newpath 171.07841 19.72816 moveto 181.94542 13.45413 lineto stroke -101.92107 45.71011 moveto -(\(cmr8\)) cmtt10 9.96265 fshow +104.53125 46.03944 moveto +(\(cmr8\)) uhvr8r 9.96265 fshow newpath -0.1 0.1 moveto -0.1 -0.1 lineto 0.1 -0.1 lineto 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 d9fd8811323..f0b051ade6b 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 2019.03.10 +% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2019.05.11 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph.mf; %% it must be version 4.40 or later +input mcf2graph.mf; %% it must be version 4.41 or later %------------------------------------------------------------------------ sw_mframe:=0; sw_expand:=0; @@ -11,6 +11,8 @@ sw_expand:=0; %*********************************************************************** fsize:=(35mm,25mm); blength:=6mm; +%------------------------------------------------------------------------- +%ext(defaultscale:=.5; label.bot(decimal(char_num)&":"&inf_EN,(.5w,0));) %*********************************************************************** beginfont("EN:Glycine") MC(<30,NH2,!0,!,COOH) @@ -109,7 +111,7 @@ beginfont("EN:Chain 1") MC(<10,-30,45,-45,30,-30,60, {1^-75,2^67.5,3^-60,4^75,5^-75,6^60}:/_~dt ) - ext( + add( defaultscale:=0.5; labeloffset:=2bp; drawarrow .7[B7s,B7e]{dir(B7dir-90)}..{dir(B1dir-90)}.7[B1s,B1e]; @@ -136,7 +138,7 @@ beginfont("EN:Chain 2") MC(<30,!6, {1^-60,2^60,3^-60,4^60,5^-60,6^60}:/_~dt ) - ext( + add( defaultscale:=0.5; labeloffset:=2bp; drawarrow .7[B7s,B7e]{dir(B7dir-90)}..{dir(B1dir-90)}.7[B1s,B1e]; @@ -226,7 +228,7 @@ beginfont("EN:rotate 1") labeloffset:=2bp; MC(``1,0,0,<90,0,<-90,0,0,{1,2,3,4,5}=vf, {3,4^180}:/_~dt) - ext( + add( drawarrow .7[B6s,B6e]{dir(B6dir+90)}..{dir(B3dir+90)}.7[B3s,B3e]; label.urt("90",.7[B6s,B6e]); drawarrow .7[B7s,B7e]{dir(B7dir-90)}..{dir(B4dir-90)}.7[B4s,B4e]; @@ -508,10 +510,10 @@ beginfont("EN:Change color,font") defaultsize:=10bp; fmargin:=(3mm,1mm); MCat(0.25,0)(<30,Ph,{2,5}:N,3:/NH2,2:red,5:blue,3=green) - ext(label.lft("(draw)",p0+(0,.9h));) + add(label.lft("(draw)",p0+(0,.9h));) atomfont:="cmr8"; MCat(1,0)(<30,Ph,{2,5}:N,3:/NH2) - ext(label.lft("(cmr8)",p0+(0,.9h));) + add(label.lft("(cmr8)",p0+(0,.9h));) endfont %*********************************************************************** beginfont("EN:Make brock") @@ -552,17 +554,17 @@ beginfont("EN:mangle") blength:=6mm; mangle:=0; MCat(0.2,0.5)(Ph) - ext(drawarrow((A1 shifted (aw,0)) rotated A1dir..A1);) + add(drawarrow((A1 shifted (aw,0)) rotated A1dir..A1);) mangle:=30; MCat(0.8,0.5)(Ph) - ext(drawarrow((A1 shifted (aw,0)) rotated A1dir..A1);) + add(drawarrow((A1 shifted (aw,0)) rotated A1dir..A1);) endfont %*********************************************************************** beginfont("EN:blength=0") sw_fframe:=3; fsize:=(40mm,15mm); MC(<30,Ph) - EXT(pickup pencircle scaled 0.2pt; + ext(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -575,7 +577,7 @@ beginfont("EN:01") fsize:=(40mm,15mm); blength:=8mm; MC(<30,Ph) - EXT(pickup pencircle scaled 0.2pt; + ext(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -602,7 +604,7 @@ beginfont("EN:msize=(1)") fsize:=(40mm,15mm); msize:=(1,1); MC(<30,Ph) - EXT(pickup pencircle scaled 0.2pt; + ext(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -616,7 +618,7 @@ beginfont("EN:msize=(0.25,1)") fsize:=(40mm,15mm); msize:=(0.25,1); MC(<30,Ph) - EXT(pickup pencircle scaled 0.2pt; + ext(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -630,7 +632,7 @@ beginfont("EN:msize=(11mm,11mm)") fsize:=(40mm,15mm); msize:=(11mm,11mm); MC(<30,Ph) - EXT(pickup pencircle scaled 0.2pt; + ext(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -662,7 +664,7 @@ beginfont("EN:mposition") msize:=(1,0.8); mposition:=(10mm,4mm); MC(<30,Ph) - EXT(drawdot p1 withpen pencircle scaled 3pt; + ext(drawdot p1 withpen pencircle scaled 3pt; pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor @@ -675,7 +677,7 @@ beginfont("EN:Font size") fsize:=(40mm,15mm); sw_fframe:=1; MC(<30,Ph) - EXT(pickup pencircle scaled 0.2pt; + ext(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -689,7 +691,7 @@ beginfont("EN:fmargin") sw_mframe:=1; fmargin:=(10mm,3mm); MC(<30,Ph) - EXT(pickup pencircle scaled 0.2pt; + ext(pickup pencircle scaled 0.2pt; for i=0 upto w/mm: draw (i*mm,0)--(i*mm,-.5mm); endfor for i=0 upto h/mm: draw (0,i*mm)--(-.5mm,i*mm); endfor for i=0 upto w/cm: draw (i*cm,0)--(i*cm,-.8mm); endfor @@ -964,7 +966,7 @@ beginfont("EN:MCat()") for i=1 step -0.25 until 0: for j=0 step 0.25 until 1: MCat(j,i)(Ph,4:N) - ext( + add( drawarrow((A1 shifted (aw,0)) rotated A1dir..A1); label(decimal(mangle),p0+(0.5w,0.5h)); ) @@ -973,23 +975,39 @@ beginfont("EN:MCat()") endfor endfont %*********************************************************************** -beginfont("EN:EXT()") +beginfont("EN:add()") + fsize:=(50mm,20mm); + msize:=(1,0.7); MCat(0,0.5)(<30,?6,3=dl,4:/CH3) + add( + label.top("+",A7); + drawarrow B3{dir(B3dir-90)}.. + {dir(B7dir+90)}0.4[B7s,B7e]; + ) + msize:=(1,0.7); MCat(1,0.5)(<30,?6,4://CH3) + add( + labeloffset:=0bp; + label.lrt("+",A3); + ) + ext(drawdblarrow (0.4w,0.5h)..(0.55w,0.5h);) +endfont +%*********************************************************************** +beginfont("EN:ext()") fsize:=(70mm,30mm); blength:=0.065; sw_label_emu:=1; % MCat(0.1,0.5)(<-210,60`1,60`1,60`1,{1,3}=dl,1:/R1,4:/R2^-60) - ext( + add( defaultscale:=0.6; label.bot("Diene",p0+(0.5w,0)); ) MCat(0.4,0.5)(<-30,-60`1,1=dl,1:/R3,2:/R4^60) - ext( + add( defaultscale:=0.6; label.bot("Dienophile",p0+(0.5w,0)); ) MCat(0.9,0.5)(<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1) - EXT( + ext( drawarrow (0.52w,0.5h)..(0.6w,0.5h); defaultscale:=0.7; label("+",(0.25w,0.5h)); @@ -997,22 +1015,6 @@ beginfont("EN:EXT()") label.bot("Diels-Alder Reaction",(0.5w,h)); ) endfont -%*********************************************************************** -beginfont("EN:ext()") - fsize:=(50mm,20mm); - msize:=(1,0.7); MCat(0,0.5)(<30,?6,3=dl,4:/CH3) - ext( - label.top("+",A7); - drawarrow B3{dir(B3dir-90)}.. - {dir(B7dir+90)}0.4[B7s,B7e]; - ) - msize:=(1,0.7); MCat(1,0.5)(<30,?6,4://CH3) - ext( - labeloffset:=0bp; - label.lrt("+",A3); - ) - EXT(drawdblarrow (0.4w,0.5h)..(0.55w,0.5h);) -endfont sw_trimming:=1; %*************************************************************************** beginfont("EN:Acetamiprid","MW:222.676") diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf index 9fd36cb57f6..33067cd995e 100644 Binary files a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf and b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf differ diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex index d6d8bab65b7..d4de4fc7810 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 2019.03.03 +% Molecular Coding Format manual by Akira Yamaji 2019.05.11 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} %%%%\documentclass[a4paper,twoside]{article} @@ -588,10 +588,10 @@ pk font,PNG,SVG,EPS or MDL MOL file. defaultsize:=8bp; MCat(0.25,0)(<30,Ph,{2,5}:N,3:/NH2, 2:red,5:blue,3=green) - ext(label.lft("(draw)",p0+(0,0.9h));) + add(label.lft("(draw)",p0+(0,0.9h));) atomfont:="cmr8"; % default:"draw" MCat(1,0)(<30,Ph,{2,5}:N,3:/NH2) - ext(label.lft("(cmr8)",p0+(0,0.9h));) + add(label.lft("(cmr8)",p0+(0,0.9h));) \end{verbatim} {\MCFformat=0 \MCFgraph} %----------------------------------------------------------------------------- @@ -1039,7 +1039,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) for i=1 step -0.25 until 0: for j=0 step 0.25 until 1: MCat(j,i)(Ph,4:N) - ext( + add( drawarrow((A1 shifted (aw,0)) rotated A1dir..A1); label(decimal(mangle), @@ -1054,61 +1054,9 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) \MCFgraph %=============================================================================== \newpage -\subsection{Function EXT()} +\subsection{Function add()} \begin{verbatim} -(Add extra graphic to font) - - w: font width - h: font height - w0: font width-2xpart(fmargin) - h0: font height-2ypart(fmargin) - aw: atom font size - em: label font size - p0: fmargin - n: molecular number - p[m]: molecular origin position - w[m]: molecular width - h[m]: molecular height - ratio_thickness_char: - pen thickness / char width - -%---------------------------------------- -beginfont() - fsize:=(70mm,30mm;) - ratio_bond_width:=0.065; - sw_solid:=1; - %--------------------------------------- - MCat(0.1,0.5) - (<-210,60`1,60`1,60`1,{1,3}=dl, - 1:/R1,4:/R2^-60) - ext(defaultscale:=0.6; - label.bot("Diene",p0+(0.5w,0));) - %--------------------------------------- - MCat(0.4,0.5) - (<-30,-60`1,1=dl,1:/R3,2:/R4^60) - ext(defaultscale:=0.6; - label.bot("Dienophile",p0+(0.5w,0));) - %--------------------------------------- - MCat(0.9,0.5) - (<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1) - %--------------------------------------- - EXT( - drawarrow (0.52w,0.5h)..(0.6w,0.5h); - defaultscale:=0.7; - label("+",(0.25w,0.5h)); - ratio_thickness_char:=0.125; - label.bot("Diels-Alder Reaction", - (0.5w,h)); - ) - %--------------------------------------- -endfont -\end{verbatim} -\MCFgraph -%----------------------------------------------------------------------------- -\newpage -\subsection{Function ext()} -\begin{verbatim} -(Add extra graphic to molecule) +(Add graphic to molecule) w: molecular width h: molecular height @@ -1131,19 +1079,19 @@ beginfont() %--------------------------------------- msize:=(1,0.7); MCat(0,0.5)(<30,?6,3=dl,4:/CH3) - ext( + add( label.top("+",A7); drawarrow B3{dir(B3dir-90)}.. {dir(B7dir+90)}0.4[B7s,B7e]; ) %--------------------------------------- MCat(1,0.5)(<30,?6,4://CH3) - ext( + add( labeloffset:=0bp; label.lrt("+",A3); ) %--------------------------------------- - EXT( + ext( drawdblarrow (0.4w,0.5h)..(0.55w,0.5h); ) %--------------------------------------- @@ -1163,6 +1111,58 @@ drawarrow & drawdblarrow: \end{verbatim} %----------------------------------------------------------------------------- \newpage +\subsection{Function ext()} +\begin{verbatim} +(Extra graphic to font) + + w: font width + h: font height + w0: font width-2xpart(fmargin) + h0: font height-2ypart(fmargin) + aw: atom font size + em: label font size + p0: fmargin + n: molecular number + p[m]: molecular origin position + w[m]: molecular width + h[m]: molecular height + ratio_thickness_char: + pen thickness / char width + +%======================================== +ext(label(inf_EN,(.5w,0));) => all font +%======================================== +beginfont() + fsize:=(70mm,30mm;); blength:=0.065; + %--------------------------------------- + MCat(0.1,0.5) + (<-210,60`1,60`1,60`1,{1,3}=dl, + 1:/R1,4:/R2^-60) + add(defaultscale:=0.6; + label.bot("Diene",p0+(0.5w,0));) + %--------------------------------------- + MCat(0.4,0.5) + (<-30,-60`1,1=dl,1:/R3,2:/R4^60) + add(defaultscale:=0.6; + label.bot("Dienophile",p0+(0.5w,0));) + %--------------------------------------- + MCat(0.9,0.5) + (<30,?6,6=dl,2:/R2,3:/R4,4:/R3,5:/R1) + %--------------------------------------- + ext( + drawarrow (0.52w,0.5h)..(0.6w,0.5h); + defaultscale:=0.7; + label("+",(0.25w,0.5h)); + ratio_thickness_char:=0.125; + label.bot("Diels-Alder Reaction", + (0.5w,h)); + ) + %--------------------------------------- +endfont +\end{verbatim} +\MCFgraph +%----------------------------------------------------------------------------- +\newpage \section{MCF example} %----------------------------------------------------------------------------- \subsection{Acetamiprid} 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 62d1377278c..d7345f5a1ef 100644 Binary files a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf and b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf 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 9d40f3fbcac..bf4a8e9797e 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 2019.03.17 +% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2019.05.11 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%%% mcf2graph.mf it must be version 4.40 or later +%%% mcf2graph.mf it must be version 4.41 or later \documentclass{article} %------------------------------------------------------------------------------ \usepackage{luamplib}% @@ -12,8 +12,7 @@ \mplibnumbersystem{double}% \everymplib{% if unknown Ph1: input mcf2graph.mf; fi - sw_aux_out:=1; - sw_label_emu:=1; + sw_calc:=1; sw_fframe:=4; max_blength:=4.5mm; defaultfont:="uhvr8r"; @@ -44,14 +43,14 @@ beginfont("NO:1","EN:Chlorophyll a","MW:893.49") msize:=(.9,.9); MCat(0,0.5)(<54, - |<=1,?5,{2,5}=dl,4:N,3:\,54~dl,|,?5,{2,4}=dl,5:N, - -2:\,54~dl,|,?5,2=dl,5:N,-2:\~dl,54,|,?5,5=dl,5:N,-2:\~dl,$5:#, - -1:@,24,/*COO!^15,72,//O,$1:#,>|, - 4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#, + |=1,?5,{2,5}=dl,4:N,3:\,54~dl,|,?5,{2,4}=dl,5:N, + -2:\,54~dl,|,?5,2=d,5:N,-2:\~dl,54,|,?5,5=d,5:N,-2:\~dl,$5:#, + -1:@,24,/*COO!^15,72,//O,$1:#,=|,||, {2,9,15,20~zf}:/_,8:/!,14:\,!!, - 21:@,-6~wf,!2,//O,!,O,!2,!!,|,!13,{1,5,9,13}:/_, + 4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#, + 21:@,-6~wf,!2,//O,!,O,!2,!!,|,!13,{1,5,9,13}:/_ ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -62,15 +61,16 @@ \end{mplibcode} \begin{minipage}[b]{85mm} \begin{verbatim} -|<=1,?5,{2,5}=dl,4:N,3:\,54~dl, +|=1,?5,{2,5}=dl,4:N,3:\,54~dl, |,?5,{2,4}=dl,5:N, --2:\,54~dl,|,?5,2=dl,5:N, --2:\~dl,54,|,?5,5=dl,5:N,-2:\~dl,$5:#, --1:@,24,/*COO!^15,72,//O,$1:#,>|, -4:\`1.45,Mg,17:#,-1:@,11~vb:#,-1:@,23~vb:#, -{2,9,15,20~zf}:/_,8:/!,14:\,!!, -21:@,-6~wf,!2,//O,!,O,!2,!!, -|,!13,{1,5,9,13}:/_, +-2:\,54~dl,|,?5,2=d,5:N,-2:\~dl,54, +|,?5,5=d,5:N,-2:\~dl,$5:#, +-1:@,24,/*COO!^15,72,//O,$1:#,=|,||, + {2,9,15,20~zf}:/_,8:/!,14:\,!!, + 4:\`1.45,Mg,17:#,-1:@,11~vb:#, + -1:@,23~vb:#, + 21:@,-6~wf,!2,//O,!,O,!2,!!, +|,!13,{1,5,9,13}:/_ \end{verbatim} \end{minipage} @@ -85,7 +85,7 @@ beginfont("EN:beta-Carotene","MW:536.888") 4:\,|,!18,{1,3,5,7,9,11,13,15,17}=dr,{3,7,12,16}:/_, |,?6,6=dl,{6,2^35,2^-35}:/_ ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -114,7 +114,7 @@ endfont {4~wf^60,8~zf^60,18^35,18^-35}:/_,{1^60,5^180,16^60}:/*H, 14:\*,|,?5,{1,4}=dl,3:O ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -143,7 +143,7 @@ beginfont("NO:4","EN:Gibberellin A3","MW:346.37"); <18,?5,3=?7,5=?6[12],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:*/_,{1,4}:*/H^60) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -171,7 +171,7 @@ beginfont("EN:Morphine","MW:285.343") 7:@,60~wf`0.75,70~si_`1.3,45,N,/_,9~wb:#, 15=d,6:/OH,8^180:*/H,12:/*OH ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -196,13 +196,13 @@ endfont fsize:=(80mm,35mm); beginfont("NO:5","EN:Erythromycin","MW:733.93"); MCat(0.8,0.5)( - <30,|<=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,>|,1:#, + <30,|=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,=|,1:#, 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 ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -213,8 +213,8 @@ beginfont("NO:5","EN:Erythromycin","MW:733.93"); \end{mplibcode} \begin{minipage}[b]{85mm} \begin{verbatim} -<30,|<=1,<-120,60,60,60,-60,60, -60,-60,60,60,60,-60,60,60,>|,1:#, +<30,|=1,<-120,60,60,60,-60,60, +60,-60,60,60,60,-60,60,60,=|,1:#, 14:O,13:/*Et,{1,9}://O,{2,10}:*/_, {4,6^-35,8,12^35}:/*_, {6^35,11,12^-35}:*/OH, @@ -230,12 +230,12 @@ $5:\*^30`1.7,O,!,|,?6`.7,6:O, fsize:=(80mm,35mm); beginfont("EN:Paclitaxel","MW:853.918") MCat(0.8,0.5)( - ?6,5=d,3:@,|<=1,36,45,45,45,45,>|,$5:#,-4=?6,-4=?4,||,-1=wb,-3=wf,-1:O, + ?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 ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -246,7 +246,7 @@ endfont \end{mplibcode} \begin{minipage}[b]{85mm} \begin{verbatim} -?6,5=d,3:@,|<=1,36,45,45,45,45,>|,$5:#, +?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, @@ -264,10 +264,10 @@ fsize:=(80mm,70mm); beginfont("NO:6","EN:Vancomycin","MW:1449.25"); MCat(0.9,0)( <30, - |<=1,!12,{1,3,12}=zf,7=wf,/H^-60,60,*/OH,60, + |=1,!12,{1,3,12}=zf,7=wf,/H^-60,60,*/OH,60, Ph,-4:/Cl,-3:\,O,!,Ph,-4:\,O,!,Ph,-1^15:/Cl,-3:\,/*OH,*/H^-60,$1:#, $7:@,$26:#,$1:@,120,//O,60,NH,60,/*H,*/COOH^180,-60, - Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,>|, + Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,=|, {3^40,6,9,12}://O,{2,5,8,11}:NH, {1^180,4^180}:*/H,{7^-60,10^60,14^60}:/*H, $10:*\^-60,60,//O,!,NH2, @@ -275,7 +275,7 @@ beginfont("NO:6","EN:Vancomycin","MW:1449.25"); $23:\,O,!,|,?6`.7,2:O,3^10:/!OH,{4,5}:/OH, -1:\,O,!,|,?6`.7,6:O,{3^35,5}:/_,3^-35:/NH2,4:/OH ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,h-5mm)); @@ -286,13 +286,13 @@ endfont; \end{mplibcode} \begin{minipage}[b]{85mm} \begin{verbatim} -<30,|<=1,!12,{1,3,12}=zf,7=wf, +<30,|=1,!12,{1,3,12}=zf,7=wf, /H^-60,60,*/OH,60,Ph,-4:/Cl, -3:\,O,!,Ph,-4:\,O,!,Ph,-1^15:/Cl, -3:\,/*OH,*/H^-60,$1:#, $7:@,$26:#,$1:@,120,//O,60,NH,60, /*H,*/COOH^180,-60, -Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,>|, +Ph,{-2,-4}:/OH,-1:\,Ph,-5:/OH,-2:@,$4:#,=|, {3^40,6,9,12}://O,{2,5,8,11}:NH, {1^180,4^180}:*/H, {7^-60,10^60,14^60}:/*H, @@ -326,7 +326,7 @@ $23:\,O,!,|,?6`.7,2:O,3^10:/!OH,{4,5}:/OH, $36:@,-45~zf,O,30,SOO,30,"O{Na}", $150:\,|,!7,{1,2}:/*OH,4:*/_,5:/*_,7=dl ) - EXT( + ext( label.lrt("("&inf_EN&")",(0,.8h)); defaultscale:=0.8; label.lrt("FM(C): "&cal_FM,(0,.8h-5mm)); @@ -371,7 +371,7 @@ MCat(0, 0.05)(<30,O[-1],!0,//O,!3,//O,!,O[-1]) MCat(0, 0.55)(<30,O[-1],!0,//O,!,!~dr,!,//O,!,O[-1]) MCat(0, 1)(<30,O[-1],!0,//O,!3,//O,!,O[-1],3:/OH) %------------------------------------------------------------------------- -EXT( +ext( defaultfont:="uhvr8r"; defaultscale:=0.75; ext_setup; @@ -429,7 +429,7 @@ MCat(0.33,0.05)(<30,O[-1],!0,//O,!3,//O,!,"{S-CoA}") MCat(0, 0.05)(<30,O[-1],!0,//O,!3,//O,!,O[-1]) MCat(0, 0.55)(<30,O[-1],!0,//O,!,!~dr,!,//O,!,O[-1]) MCat(0, 1)(<30,O[-1],!0,//O,!3,//O,!,O[-1],3:/OH) -EXT( +ext( defaultfont:="uhvr8r"; defaultscale:=0.75; ext_setup; diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf index 75deb69c4d4..12652c004bf 100644 --- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf +++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% mcf2graph ver 4.40 Copyright (c) 2013-2019 Akira Yamaji +% mcf2graph ver 4.41 Copyright (c) 2013-2019 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, @@ -18,10 +18,10 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % mcf2graph is METAFONT/METAPOST macro package convert % Molecular Coding Format(MCF) to font(pk)/eps/sgv/png/mdl molfile -%---------------------------------------------------------------------------------------------- +%-------------------------------------------------------------------------------------------------- % This package is located at : http://www.ctan.org/pkg/mcf2graph % Suggestion or request mail to : mcf2graph@gmail.com -%---------------------------------------------------------------------------------------------- +%-------------------------------------------------------------------------------------------------- % Set output no image file : mpost -s bboxmargin=0 FILENAME % Set output first font only : mpost -s bboxmargin=1 FILENAME % Set outputformat to "eps"(.mps) : mpost -s ahangle=0 FILENAME @@ -36,7 +36,7 @@ % Set to use plain.mp (label,arrow,atom) : mpost -s labeloffset=2 FILENAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% tracingstats:=1; -message " This is mcf2graph ver 4.40 2019.03"; +message " This is mcf2graph ver 4.41 2019.05"; %------------------------------------------------------------------------------------------------- newinternal char_num,str_cnt,sub_usr,sub_int,tbl_cnt,sharp_char; numeric save_num[],comD[][],parD[][],cntD[],tbl_atom[],tbl_subst[][], @@ -47,7 +47,7 @@ pair save_pair[],msize,mposition,fsize,fmargin,save_mposition; picture mol_stru[]; path arrow_path,arrow_head; %------------------------------------------------------------------------------------------------- -char_num:=str_cnt:=proc_end:=mangle:=sw_label_emu:=0; +char_num:=str_cnt:=proc_end:=mangle:=sw_label_emu:=sw_calc:=sw_extall:=0; sw_numberA:=sw_numberB:=sw_mframe:=sw_aux_out:=sw_expand:=sw_fframe:=sw_trimming:=0; sw_aframe:=sw_rep_out:=sw_mol_out:=sw_subst_off:=sw_single:=sw_auxfix:=sw_arrow:=0; numberA_start:=numberB_start:=1; numberA_end:=numberB_end:=4095; aux_max:=max_inf_num:=20; @@ -98,6 +98,7 @@ if (known green)and(known ahlength): def printf expr s= write s to out_file_name enddef; def # = enddef; def Cp(expr s) = if known s: if s<>0: withcolor color_list[s] fi fi enddef; + def ext(text TXT)= sw_extall:=sw_calc:=1; def EXTALL = TXT enddef; enddef; if atomfont="": atomfont:="draw"; fi % default atom font if defaultfont="": defaultfont:="draw"; fi % default label font %----------------------------------------------------------------------------------------- @@ -106,6 +107,7 @@ else: f_MP:=0; dotlabeldiam:=3bp; def Cp(expr s) = enddef; def color = transform enddef; + def ext(text TXT)= enddef; sw_arrow:=0; atomfont:="draw"; defaultfont:="draw"; @@ -125,7 +127,7 @@ ratio_char_bond:=1.5; ratio_bondgap_bond:=0.15; ratio_zebragap_bond:=0. ratio_zebra_black:=0.4; ratio_wedge_bond:=0.12; ratio_atomgap_atom:=0.050; offset_thickness:=0.2bp; offset_bond_gap:=0.3bp; offset_zebra_gap:=0.1bp; offset_atom:=0.8pt; offset_wedge:=0.4bp; -thickness_fframe:=0.2bp; thickness_mframe:=0.2bp; thickness_aframe:=0.1bp; +thickness_fframe:=0.2bp; thickness_mframe:=0.2bp; thickness_aframe:=0.1bp; max_blength:=10mm; blength:=0; mangle:=0; %-------------------------------------------------------------------------------------------------- fsize:=(30mm,20mm); fmargin:=(0.4mm,0.4mm); msize:=(1,1); mposition:=(0.5,0.5); @@ -151,7 +153,7 @@ 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_rep_out,sw_numberA,sw_numberB,sw_mframe,sw_aux_out,sw_expand,sw_mol_out, + sw_rep_out,sw_numberA,sw_numberB,sw_mframe,sw_aux_out,sw_expand,sw_mol_out,sw_calc,sw_extall, sw_aframe,sw_fframe,sw_subst_off,sw_single,sw_trimming,sw_arrow,sw_label_emu, ratio_atom_bond,ratio_thickness_bond,ratio_char_bond, ratio_chain_ring,ratio_bondgap_bond,ratio_zebra_black,ratio_zebragap_bond,ratio_thickness_char, @@ -202,24 +204,41 @@ enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def beginfont(text s)= begingroup - save cntA,cntB,cntM,minX,minY,f_beginchar,numS,sftX,sftY,f_ext,blen, + save cntA,cntB,cntM,minX,minY,f_beginchar,numS,sftX,sftY,f_ext,blen,ext,add, cal_FM,cal_MW,cal_MW_str,cal_MI,cal_MI_str,wdM,htM, inf_NO,inf_EN,inf_JN,inf_FM,inf_CAS,inf_USE,inf_EXA,inf_EXB,inf_MW, posA,posM,lineB,sB,eB,angB,angA,wdA,dxA,lenB,ang_br,info; numeric lineB[],sB[],eB[],angB[],angA[],lenB[],angX[],numS[],wdM[],htM[],wdA[],dxA[],dx_A[]; pair posA[],posM[][]; - string info[],cal_FM,cal_MW,cal_MW_str,cal_MI,cal_MI_str, + string info[],sumA,s_tag,s_var,cal_FM,cal_MW,cal_MW_str,cal_MI,cal_MI_str, inf_NO,inf_EN,inf_JN,inf_FM,inf_CAS,inf_USE,inf_EXA,inf_EXB,inf_MW; %------------------------------------------------------------------------------------------------ + def ext=ext_font enddef; + def add=add_mol enddef; + %------------------------------------------------------------------------------------------------ + inf_NO:=inf_EN:=inf_JN:=inf_FM:=inf_CAS:=inf_USE:=inf_EXA:=inf_EXB:=inf_MW:=""; + cal_MW:=cal_MW_str:=cal_FM:=""; + %------------------------------------------------------------------------------------------------ char_num:=char_num+1; store_par(parameter_list); for i:=1 upto max_inf_num: info[i]:=":"; endfor f_ext:=inf_num:=cntM:=0; for list=s: inf_num:=inf_num+1; info[inf_num]:=list; endfor + %------------------------------------------------------------------------------------------------ + for j=1 upto inf_num: + nA:=0; for i=0 upto length(info[j]): if pic_c(i,info[j])=":": nA:=i; fi exitif nA>0; endfor + if nA>0: + s_tag:=substring (0,nA) of info[j]; + s_var:=substring (nA+1,length(info[j])) of info[j]; + if known scantokens("inf_"&s_tag): scantokens("inf_"&s_tag):=s_var; fi + fi + endfor + %------------------------------------------------------------------------------------------------ mol_stru[0]:=nullpicture; enddef; %================================================================================================== def endfont= + if (f_MP=1)and(sw_extall=1): ext_font(EXTALL); fi if sw_trimming>=1: nA:=nC:=4095; nB:=nD:=-4095; for i=1 upto cntM: @@ -240,12 +259,12 @@ def endfont= if f_MP=0: beginchar(char_num,font_wd/bp*bp#,font_ht/bp*bp#,0) else: beginfig(char_num) w:=charwd:=font_wd; h:=charht:=font_ht; chardp:=0; fi - if (sw_fframe=1)or(sw_fframe=3): EXT(draw_frame((0,0),w,h,thickness_fframe);) fi - if (sw_fframe=2)or(sw_fframe=3): EXT(draw_frame(p0,w0,h0,thickness_fframe);) fi - if sw_fframe=4: EXT(drawdot(0,0); drawdot(w,0); drawdot(w,h); drawdot(0,h);) fi + if (sw_fframe=1)or(sw_fframe=3): ext(draw_frame((0,0),w,h,thickness_fframe);) fi + if (sw_fframe=2)or(sw_fframe=3): ext(draw_frame(p0,w0,h0,thickness_fframe);) fi + if sw_fframe=4: ext(drawdot(0,0); drawdot(w,0); drawdot(w,h); drawdot(0,h);) fi for i=1 upto cntM: addto currentpicture also mol_stru[i] shifted posM[0][i]; mol_stru[i]:=nullpicture; - if sw_mframe=1: EXT(draw_frame(p[i],w[i],h[i],thickness_mframe)) fi + if sw_mframe=1: ext(draw_frame(p[i],w[i],h[i],thickness_mframe)) fi endfor if f_ext=1: addto currentpicture also mol_stru[0]; mol_stru[0]:=nullpicture; fi endchar; @@ -257,7 +276,7 @@ enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def set_def_MC= save /,//,/*,*/,**,*/*,~,~~,^,^^,`,'`,<,>,>>,:>,&,:,=,\,\\,*\,\*,*\*,@,$,{,},#, - |,||,|<,>|,|<=,|:,:|,_,d,w,z,inside_def_MC; + |,||,|<,>|,|<=,|=,=|,|:,:|,_,d,w,z,inside_def_MC; inside_def_MC:=1; _:=Me; d:=db; w:=wf; z:=zf; tertiarydef a=b == change_bond(a,b) enddef; @@ -275,7 +294,9 @@ def set_def_MC= def \\ == \~dm enddef; def *\ == \~wf enddef; def \* == \~zf enddef; def *\* == \~wv enddef; def |: == (_push,0) enddef; def :| == (_pop,0) enddef; def |< == (_push,1) enddef; def >| == (_pop,1) enddef; - def |<=primary n == ``n,(_push,1) enddef; + def |<=primary n == ``n,(_push,0) enddef; + def |=primary n == (_push,0),``n enddef; + def =| == (_pop,0) enddef; def | == (_push,2) enddef; def || == (_pop,2) enddef; def /secondary n == (_postA,n) enddef; def //secondary n == (_postB,n) enddef; def */secondary n == (_postC,n) enddef; def /*secondary n == (_postD,n) enddef; @@ -333,13 +354,13 @@ vardef '''(text TXT)= sub_int %------- Retern value ------- enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -def FR(expr a,b) = +def fuse_ring(expr a,b) = PA(_jp_bond,a) PA(_rot_ang,180) PA(_get_len,a) PA(_push,0) PA(_chg_len,_ring_len) for i==1 upto b-2:: PA(_mk_bond,360 DIV b) endfor PA(_pop,0) if a>=1:: PA(_cyc_eB,0) elseif a>=-999:: PA(_cyc_eB,a-b+2) else:: PA(_cyc_eB,a) fi enddef; %------------------------------------------------------------------------------------------------- -def FFR(expr a,b,c) = +def fuse_ring_bonds(expr a,b,c) = PA(_jp_bond,xpart(a)) PA(_rot_ang,180) PA(_push,0) if b==6:: PA(_chg_len,0) for i==1 upto c-1:: PA(_mk_bond,60) endfor elseif b==5:: if c==2:: PA(_chg_len,1.25) PA(_mk_bond,80) @@ -348,7 +369,7 @@ def FFR(expr a,b,c) = PA(_pop,0) if ypart(a)<=0:: PA(_cyc_eB,ypart(a)-c+1) else:: PA(_cyc_eB,ypart(a)) fi enddef; %------------------------------------------------------------------------------------------------- -def FRR(expr a,b,c) = +def fuse_ring_rate(expr a,b,c) = PA(_jp_bond,a) PA(_rot_ang,180) PA(_push,0) PA(_chg_len,c DIV 10) if b==5:: PA(_mk_bond,72-((c-9) MUL 1.5)) PA(_mk_bond,72+(c-9)) PA(_mk_bond,72+(c-9)) elseif b==6:: PA(_mk_bond,60-(c-8)) for i==1 upto 3:: PA(_mk_bond,60+((c-8) DIV 2)) endfor @@ -365,16 +386,16 @@ vardef change_bond(expr a,b) = if known b:: if numeric b:: if (b>=si)and(b<=bd_):: if b==dl:: PP(a,_dl) else:: PX(a)(_set_line,b) fi elseif (b>=?3)and(b<=?20):: - if a>=sub_int_start:: for i==1 upto cntD[a]:: FR(parD[a][i],b-?3+3) endfor - else:: FR(a,b-?3+3) + if a>=sub_int_start:: for i==1 upto cntD[a]:: fuse_ring(parD[a][i],b-?3+3) endfor + else:: fuse_ring(a,b-?3+3) fi - elseif b==Ph1:: FR(a,6) PA(_dl,-2) PA(_dl,-4) - elseif b==Ph2:: FR(a,6) PA(_dl,-1) PA(_dl,-3) PA(_dl,-5) + elseif b==Ph1:: fuse_ring(a,6) PA(_dl,-2) PA(_dl,-4) + elseif b==Ph2:: fuse_ring(a,6) PA(_dl,-1) PA(_dl,-3) PA(_dl,-5) elseif b==_jump_at:: PA(_jp_bond,a) elseif b==_connect_at:: PA(_cyc_sB,a) elseif comD[b][1]==_fuse:: - if comD[b][2]<=6:: FFR(a,parD[b][1],comD[b][2]) - elseif (comD[b][2]>=11)and(comD[b][2]<=15):: FRR(a,parD[b][1],comD[b][2]) + if comD[b][2]<=6:: fuse_ring_bonds(a,parD[b][1],comD[b][2]) + elseif (comD[b][2]>=11)and(comD[b][2]<=15):: fuse_ring_rate(a,parD[b][1],comD[b][2]) fi fi elseif color b:: color_list[incr cntC]:=b; PX(a)(_set_colorB,cntC) @@ -443,10 +464,12 @@ def ext_setup= labeloffset:=3bp; save em; em=defaultscale*defaultsize; - if (defaultfont="draw")or(f_MP=0)or(sw_label_emu=1): + if (f_MP=0)or(sw_label_emu=1): save label,dotlabel; - def label = label_emu enddef; + def label = label_emu enddef; def dotlabel = dotlabel_emu enddef; + else: + defaultfont:="uhvr8r"; fi if (sw_arrow=0)or(f_MP=0): save drawarrow,drawdblarrow; @@ -455,24 +478,7 @@ def ext_setup= fi enddef; %-------------------------------------------------------------------------------------------------- -def EXT(text TXT)= - begingroup - save w,h,wd,ht,n,p,am,aw; - pair p[]; - ext_setup; - w:=xpart(fsize); - h:=ypart(fsize); - w0:=w-2margin_lr; - h0:=h-2margin_tb; - p0:=(margin_lr,margin_tb); - aw:=atom_wd; - n:=cntM; - for i=1 upto n: p[i]:=posM[1][i]; w[i]:=wdM[i]; h[i]:=htM[i]; endfor - TXT addto mol_stru[0] also currentpicture; clearit; f_ext:=1; - endgroup; -enddef; -%-------------------------------------------------------------------------------------------------- -def ext(text TXT)= +def add_mol(text TXT)= begingroup save w,h,n,l,p,am,aw,A,B; numeric A[]dir,B[]dir; @@ -489,6 +495,23 @@ def ext(text TXT)= endgroup; enddef; %-------------------------------------------------------------------------------------------------- +def ext_font(text TXT)= + begingroup + save w,h,wd,ht,n,p,am,aw; + pair p[]; + ext_setup; + w:=xpart(fsize); + h:=ypart(fsize); + w0:=w-2margin_lr; + h0:=h-2margin_tb; + p0:=(margin_lr,margin_tb); + aw:=atom_wd; + n:=cntM; + for i=1 upto n: p[i]:=posM[1][i]; w[i]:=wdM[i]; h[i]:=htM[i]; endfor + TXT addto mol_stru[0] also currentpicture; clearit; f_ext:=1; + endgroup; +enddef; +%-------------------------------------------------------------------------------------------------- vardef label_emu@#(expr STR,POS) = %% modified 'thelabel@#(expr s,z)' of plain.mp save oft,fx,fy,wds,sC,bA; pair oft,oft.lft,oft.rt,oft.top,oft.bot,oft.ulft,oft.llft,oft.urt,oft.lrt; @@ -706,7 +729,7 @@ def MC(text TXT)= mol_stru[cntM]:=currentpicture; clearit; endgroup; - if ((sw_aux_out=1)or(sw_rep_out=1)or(sw_mol_out>=1))and(f_MP=1): proc_calc_out; fi + if ((sw_aux_out=1)or(sw_rep_out=1)or(sw_mol_out>=1)or(sw_calc=1))and(f_MP=1): proc_calc; fi %----------------------------------------------------------------------------------------------- %%%% message "count of usr ="& decimal(sub_usr) &" "& decimal(sub_usr-sub_usr_start); %%%% message "count of int ="& decimal(sub_int) &" "& decimal(sub_int-sub_int_start); @@ -1164,7 +1187,7 @@ OCOMe:=OCO!:='(O,!,//O,!); NMeMe:=NMe!:='(N!,!); NHCOMe:=NHCO!:='(NH,!,//O,!); NHiPr:=NHMe!:='(NH,!,iPr); NHtBu:='(NH,!,tBu); NHMe:=NH!:='(NH,!); NHEt:=NH!2:='(NH,!x2); !NH!:='(!,NH,!); !CO!:='(!,//O,!); !OH:='(!,OH); !SH:='(!,SH); !NH2:='(!,NH2); !OMe:=!O!:='(!,OMe); !COOH:='(!,COOH); !CH3:='(!,CH3); !CN:='(!,CN); !iPr:=!Me!:='(!,iPr); !tBu:='(!,tBu); !Ph:='(!,Ph); -!CHO:='(!,CHO); !NO2:='(!,NO2); +!CHO:='(!,CHO); !NO2:='(!,NO2); !Cl:='(!,Cl); !F:='(!,F); !?3:='(!,?3); !?4:='(!,?4); !?5:='(!,?5); !?6:='(!,?6); CF2:='(/F,60,F); CCl2:='(/Cl,60,Cl); CBr2:='(/Br,60,Br); CF3:='(/F,/F^60,60,F); CCl3:='(/Cl,/Cl^60,60,Cl); CBr3:='(/Br,/Br^60,60,Br); %================================================================================================== @@ -1383,22 +1406,13 @@ STb("SH")("S","H"); STb("CHO")("C","H","O"); STb("N{O_2_}")("N","O","O"); STb("N{H_2_}")("N","H","H"); STb("S{O_3_}")("S","O","O","O"); STb("COOH")("C","O","O","H"); STb("C{H_3_}")("C","H","H","H"); STb("C{F_3_}")("C","F","F","F"); %================================================================================================== -def proc_calc_out= +def proc_calc= begingroup save warning_cnt,MWp,knownA,bondC,tmp_wtp,bond_cnt,cnt_hide_H; numeric sumA[],bondC[],hideH[]; - string sumA,s_tag,s_var; - inf_NO:=inf_EN:=inf_JN:=inf_FM:=inf_CAS:=inf_USE:=inf_EXA:=inf_EXB:=inf_MW:=""; - cal_MW:=cal_MW_str:=cal_FM:=""; cnt_hide_H:=warning_cnt:=MW_num:=MI_num:=MWp:=0; + string sumA; + cnt_hide_H:=warning_cnt:=num_MW:=num_MI:=MWp:=0; %------------------------------------------------------------------------------------------ - for j=1 upto inf_num: - nA:=0; for i=0 upto length(info[j]): if pic_c(i,info[j])=":": nA:=i; fi exitif nA>0; endfor - if nA>0: - s_tag:=substring (0,nA) of info[j]; - s_var:=substring (nA+1,length(info[j])) of info[j]; - if known scantokens("inf_"&s_tag): scantokens("inf_"&s_tag):=s_var; fi - fi - endfor for i=1 upto tbl_cnt: sumA[i]:=0; endfor for i=1 upto cntA: knownA:=bond_cnt:=0; @@ -1442,14 +1456,14 @@ def proc_calc_out= nA:=tbl_atom_wt[i]/100*sumA[i]; MWp:=MWp+nA; if (MWp<40)and(nA<40): - MW_num:= MW_num+tbl_atom_wt[i]*sumA[i]; - MI_num:= MI_num+tbl_atom_mi[i]*sumA[i]; + num_MW:= num_MW+tbl_atom_wt[i]*sumA[i]; + num_MI:= num_MI+tbl_atom_mi[i]*sumA[i]; fi cal_FM:=cal_FM&stripP(tbl_atom_str[i]) if sumA[i]>=2: &decimal(sumA[i]) fi; fi endfor - cal_MI:=substring (0,10) of decimal(MI_num); - cal_MW:=substring (0,8) of decimal(MW_num); + cal_MI:=substring (0,10) of decimal(num_MI); + cal_MW:=substring (0,8) of decimal(num_MW); if sw_aux_out=1: proc_auxfile_out; fi if sw_rep_out=1: proc_report_out; fi if sw_mol_out>=1: proc_mol_out; fi @@ -1529,7 +1543,7 @@ def proc_report_out= fixed_r(12)(cal_MW_str)&"["&fixed_r(12)(cal_MI_str)&"]"; printf "------------------------------------------------------------------"; printf " Weight Calc: " &cal_MW_str &" / Input: " - if inf_MW<>"": &inf_MW &" / weight gap= " &decimal(MW_num-scantokens(inf_MW)) fi; + if inf_MW<>"": &inf_MW &" / weight gap= " &decimal(num_MW-scantokens(inf_MW)) fi; printf " Fomula Calc: "&cal_FM&" / Input: " if inf_FM<>"": &inf_FM&" / "& iif(inf_FM=cal_FM,"MACTCH","NOT MACTCH") fi; printf "=================================================================="; -- cgit v1.2.3