diff options
author | Karl Berry <karl@freefriends.org> | 2020-11-03 22:17:49 +0000 |
---|---|---|
committer | Karl Berry <karl@freefriends.org> | 2020-11-03 22:17:49 +0000 |
commit | f843c3726969f1ad1dfd8851fa7784d1b43cdcda (patch) | |
tree | b37c8a00f19546fa70299ffda2a30f3f48566c3e | |
parent | 7ca2811db642b89ee352d71791418c7113877b78 (diff) |
mcf2graph (3nov20)
git-svn-id: svn://tug.org/texlive/trunk@56846 c570f23f-e606-0410-a88d-b1316a301751
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG | 6 | ||||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/README | 4 | ||||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf | 55 | ||||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf | bin | 306332 -> 306745 bytes | |||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex | 3 | ||||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf | 39 | ||||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf | bin | 575278 -> 597534 bytes | |||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | 146 | ||||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf | bin | 201949 -> 201981 bytes | |||
-rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex | 16 | ||||
-rw-r--r-- | Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf | 69 |
11 files changed, 230 insertions, 108 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG index b3bcfd022ec..a162e00951a 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG +++ b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG @@ -1,6 +1,10 @@ ******************************************************************************* - Changelog of mcf2graph software package by Akira Yamaji 2020-08-30 + Changelog of mcf2graph software package by Akira Yamaji 2020-11-03 ******************************************************************************* +[ver. 4.53 / 2020-11-03] + -improve inline definition + -update MCF manual(add index),example + [ver. 4.52 / 2020-08-30] -improve aux file output,input -update MCF manual,example diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README index 7f830cef14d..1946281e8df 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/README +++ b/Master/texmf-dist/doc/metapost/mcf2graph/README @@ -1,7 +1,7 @@ ******************************************************************************** mcf2graph : Convert Molecular Coding Format to graphics with METAFONT/METAPOST Author : Akira Yamaji - version : 4.52 2020-08-30 + version : 4.53 2020-11-03 E-mail : mcf2graph@gmail.com Located at : http://www.ctan.org/pkg/mcf2graph ******************************************************************************** @@ -21,7 +21,7 @@ ( 4) mcf_setup.sty Style file for aux file input ( 5) mcf_manual.tex MCF syntax manual(LaTeX file) ( 6) mcf_man_soc.mf Molecular difinition file for mcf_manual.tex - ( 7) mcf_manual.pdf PDF of (4) (used pdftex(LaTeX)) + ( 7) mcf_manual.pdf PDF of (4) (used pdftex(LaTeX),makeindex) ( 8) mcf_example.tex LaTeX example, Make file 'mcf_exa_soc-info.aux' before typeset >mpost -s ahlength=1 mcf_exa_soc.mf diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf index 8cbd78defec..dae7e38efab 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf @@ -1,13 +1,13 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2020.08.30 +% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2020.11.03 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph.mf; %%% it must be version 4.52 or later +input mcf2graph.mf; %%% it must be version 4.53 or later %------------------------------------------------------------------------- fsize:=(33mm,24mm); max_blength:=4.5mm; %------------------------------------------------------------------------- %%%%sw_aux_out:=1; -%%%%sw_fframe:=1; +%%%%sw_fframe:=4; %%%%sw_aframe:=1; %%%%sw_mframe:=1; %%%%sw_expand:=1; @@ -28,11 +28,12 @@ tag1:="F"; tag2:="C"; tag3:="fm"; tag4:="mw"; tag5:="EN"; tag6:="MW"; %%%% for i=nA step nA until h: draw(0,i)--(w,i); endfor ); %*************************************************************************** beginfont("EN:Imidacloprid","MW:255.662") - MC(<30,Ph,1:N,6:/Cl,3:\,!,|,?5,2=dl,1:N,3:N,2:\,NH,!,NO2) + MC(<30,Ph,1:N,6:/Cl,3:\,!,|,?5,2=dl,1:N,3:N,2:/'(NH,!,NO2)) endfont %*************************************************************************** beginfont("EN:Thiamethoxam","MW:291.71") - MC(<30,?6,{4,6}:N,2:O,6:/_,5:\\,N,!,NO2,4:\,!,|,?5,{1,3}=dl,3:N,5:S,4:/Cl) + MC(<30,?6,{4,6}:N,2:O,6:/_,5://'(N,!,NO2), + 4:\,!,|,?5,{1,3}=dl,3:N,5:S,4:/Cl) endfont %*************************************************************************** beginfont("EN:Pyridaphenthion","MW:340.334") @@ -40,17 +41,17 @@ beginfont("EN:Pyridaphenthion","MW:340.334") endfont %*************************************************************************** beginfont("EN:Permethrin","MW:391.288") - MC(<-30,?3,2^-35:*/_,2^35:/*_,1:\,!!,/Cl,!,Cl, + MC(<-30,?3,2^-35:*/_,2^35:/*_,1:/'(!!,/Cl,!,Cl), 3:\,//O,!,O,!2,|,Ph,3:\,O,-60,Ph) endfont %*************************************************************************** beginfont("EN:Isoprothiolane","MW:290.392") - MC(<-30,!,/_,!,O,!,//O,|,!2,//O,!,O,!,/_,!,2:\\,|,?5,{2,5}:S) + MC(<-30,!,/_,!,O,!,//O,!,//'(?5,2:S,5:S),!,//O,!,O,!,/_,!) endfont %*************************************************************************** beginfont("EN:Oxine-Copper","MW:351.852") - MC(Ph,4:N,5=Ph,-4:\,O,-60,<90,Cu,-90,O,60,|,Ph,5=Ph,10:N, - ||,4:@,12~vf:#,23:@,12~vf:#) + MC(Ph,4:N,5=Ph,-4:\,O,-60,<90,Cu,-90,O,60,|,Ph,5=Ph,10:N,||, + 4:@,12~vf:#,23:@,12~vf:#) endfont %*************************************************************************** beginfont("EN:Tetraconazole","MW:372.145") @@ -65,7 +66,7 @@ beginfont("EN:Endosulfan","MW:406.904"); endfont; %*************************************************************************** beginfont("EN:Oxadiargyl","MW:341.19") - MC(<30,Ph,{1,3}:/Cl,4:\,|,?5,2=d,{1,2}:N,4:O,5://O,-3:/tBu,$6:\,O,!2,!!!) + MC(<30,Ph,{1,3}:/Cl,6:/'(O,!2,!!!),4:\,|,?5,2=d,{1,2}:N,4:O,5://O,-3:/tBu) endfont %*************************************************************************** beginfont("EN:Oxaziclomefone","MW:376.277") @@ -146,21 +147,21 @@ endfont beginfont("EN:Cefquinome","MW:627.6903") MC(<45,?4,-3=?6,-4=dl,2:N,8:S, 3^45:/*H,1://O^15,5:/*COOH, - 4:*\^15,NH,!,//O,!2,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2,-6:\\,N,-60,O,!, + 4:*\^15,NH,!,//O,!,//'(N,!,O,!),!,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2, 6:\,!,Ph,-2=?6,-10:N) endfont %*************************************************************************** beginfont("EN:Ceftiofur","MW:523.5626") MC(<45,?4,-3=?6,-4=dl,2:N,8:S, 3^45:/*H,1://O^15,5:/*COOH, - 4:*\^15,NH,!,//O,!2,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2,-6:\\,N,-60,O,!, + 4:*\^15,NH,!,//O,!,//'(N,!,O,!),!,?5,{-2,-5}=dl,-3:S,-1:N,-2:/NH2, 6:\,!,S,!,//O,!,?5,{-1,-3}=dl,-4:O) endfont %*************************************************************************** beginfont("EN:Cefuroxime","MW:424.3852") MC(<45,?4,-3=?6,-4=dl,2:N,8:S, 3^45:/*H,1://O^15,5:/*COOH, - 4:*\^15,NH,!,//O,!2,?5,{-1,-3}=dl,-4:O,-6:\\,N,-60,O,!, + 4:*\^15,NH,!,//O,!,//'(N,!,O,!),!,?5,{-1,-3}=dl,-4:O, 6:\,!,O,!,//O,!,NH2) endfont %*************************************************************************** @@ -176,8 +177,7 @@ beginfont("EN:Gentamycin","MW:477.596") MC(<-30,?6, 1:\*,O,0~zb,?6,-5:O,5:\*,O,0~zb,?6,-5:O, {2,4}:*/NH2,20:/*NH2,6:*/OH, - 11:*/OH^-35,11:/*_^35,12:*/NH!,13:/*OH, - 17:\,*/_,!,NH,!) + 11:*/OH^-35,11:/*_^35,12:*/NH!,13:/*OH,17:/'(*/_,!NH!)) endfont %*************************************************************************** beginfont("EN:Kanamycin","MW:484.499") @@ -206,8 +206,8 @@ endfont beginfont("EN:Neospiramycin","MW:698.9") MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|, {12,14}=dl,2:O,1:/*_,5:/*OH,3://O,10:/*_,6:/*O!>vt, - -6:\*,O,!~wb,?6`.7,-5:O,-3:/*NMe!,-4:*/_, - 7:\*,O,0~wb,?6`.7,-5:O,-2:*/NMe!,-1:/*OH,-4:*/_,-3:/*OH, + -6:\*,O,!~wb,?6`.7,-5:O,-3:/*N!_,-4:*/_, + 7:\*,O,0~wb,?6`.7,-5:O,-2:*/N!_,-1:/*OH,-4:*/_,-3:/*OH, 8:\*,!,!!,O) endfont %*************************************************************************** @@ -223,8 +223,8 @@ endfont beginfont("EN:Spiramycin","MW:843.1") MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|, {12,14}=dl,2:O,1:/*_,5:/*OH,3://O,10:/*_,6:/*O!>vt, - -6:\*,O,!~wb,?6`.7,-5:O,-3:/*NMe!,-4:*/_, - 7:\*,O,0~wb,?6`.7,-5:O,-2:*/NMe!,-1:/*OH,-4:*/_, + -6:\*,O,!~wb,?6`.7,-5:O,-3:/*N!_,-4:*/_, + 7:\*,O,0~wb,?6`.7,-5:O,-2:*/N!_,-1:/*OH,-4:*/_, -3:\*`1,O,60~wb`1.5,?6`.7,-5:O,{-2^35,-3}:*/OH,{-2^-35,-4}:/*_, 8:\*,!,!!,O) endfont @@ -233,7 +233,7 @@ beginfont("EN:Tylocin","MW:916.10") MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|, {12,14}=dl,2:O,1:/*!,5:/*OH,3://O,10:/*_,6:/*_,-6://O,-3:/_, -1:*\,-60,O,0~wb,?6`.7,-5:O,-3:/*OH,-4:*/_,{-1,-2}:/*O!, - 7:\*,O,0~wb,?6`.7,-5:O,-2:*/NMe!,-1:/*OH,-4:*/_, + 7:\*,O,0~wb,?6`.7,-5:O,-2:*/N!_,-1:/*OH,-4:*/_, -3:\*`1,O,60~wb`1.5,?6`.7,-5:O,{-2^35,-3}:*/OH,{-2^-35,-4}:/*_, 8:\*,!,!!,O) endfont @@ -242,31 +242,31 @@ beginfont("EN:Tilmicosin","MW:869.133") MC(<-90,|=1,60,60,-60,60,60,-60,60,60,-60,60,60,60,-60,60,-60,1:#,=|, {12,14}=dl,2:O,1:/*!,5:/*OH,{3,11}://O,{6,10}:/*_,14:/_, -1:*\,-60,O,0~zb,?6`.7,-5:O,{-1,-2}:*/O!,-3:*/OH,-4:/*_, - 7:\*,O,0,?6`.7,-5:O,-2:*/NMe!,{-1,-3}:/*OH,-4:*/_, + 7:\*,O,0,?6`.7,-5:O,-2:*/N!_,{-1,-3}:/*OH,-4:*/_, 8:\*,!2,?6`.7,-6:N,{-2,-4}:*/_) endfont %*************************************************************************** beginfont("EN:Chlortracyclin","MW:478.88") MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_^-35,2:/Cl, - {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2 + {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2 ) endfont %*************************************************************************** beginfont("EN:Oxytetracyclin","MW:460.434") MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_^-35,11:*/OH, - {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2 + {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2 ) endfont %*************************************************************************** beginfont("EN:Tetracyclin","MW:444.435") MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_^-35, - {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2 + {5,7~zf^35,13~wf^60,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2 ) endfont %*************************************************************************** beginfont("EN:Doxycyclin","MW:444.43") MC(<30,Ph,{-4,-3,-3}=?6,{16,19}=dl,{10,18}://O,7:*/_, - {5,13~wf^60,11~wf,14,16}:/OH,15:*/NMe!,17:\,//O,!,NH2 + {5,13~wf^60,11~wf,14,16}:/OH,15:*/N!_,17:\,//O,!,NH2 ) endfont %*************************************************************************** @@ -430,7 +430,7 @@ MC(<30,|=1,<-120,60,60,60,-60,60,60,-60,60,60,60,-60,60,60,=|,1:#, 14:O,13:/*!,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_, {6^35,11,12^-35}:*/OH, $3:\*,O,30,|,?6`.7,2:O,{3,5^35}:/_,4:/OH,5^-35:/O!, - $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMe!) + $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/N!_) endfont; %************************************************************************** beginfont("EN:Paclitaxel","MW:853.918") @@ -446,8 +446,7 @@ beginfont("EN:Mevastatin","MW:390.52") endfont %*************************************************************************** beginfont("EN:Sesamine","MW:354.35") - MC(<54,?5,1=?5,{4,7}:O,{1^-54,2^54}:*/H, - $5:*\^-12,Ph,|,-3=?5,{-1,-3}:O,$8:*\^-12,Ph,|,-3=?5,{-1,-3}:O) + MC(<54,?5,1=?5,{4,7}:O,{1^-54,2^54}:*/H,{5,8}:*/'(Ph,4=?5,7:O,9:O)^-12) endfont %************************************************************************** beginfont("EN:Morphine","MW:285.343") diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf Binary files differindex b412a69a436..423db59f667 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex index 784d2d61a2e..fcda26a9b84 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.tex @@ -1,10 +1,11 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2020.08.30 +% Example of MCF typeset by LaTeX mcf_examples.tex by A.Yamaji 2020.09.22 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage{graphicx} %--------------------- \usepackage{mcf_setup} +%%%%\pdfpkresolution=1200 %--------------------- \pagestyle{empty} \topmargin=-20mm diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf index ea8912bda76..cd570b7e8a3 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf @@ -1,7 +1,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2020.08.30 +% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2020.11.03 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph.mf; %% it must be version 4.52 or later +input mcf2graph.mf; %% it must be version 4.53 or later %------------------------------------------------------------------------ sw_mframe:=0; sw_expand:=0; @@ -11,7 +11,7 @@ sw_expand:=0; %*********************************************************************** fsize:=(40mm,25mm); blength:=6mm; -%*********************************************************************** +%*************************************************************************** beginfont("EN:Glycine") MC(<30,NH2,!2,COOH) endfont @@ -25,35 +25,35 @@ beginfont("EN:L-Valine") endfont %*********************************************************************** beginfont("EN:L-Leucine") - MC(<30,NH2,!~wb,!,COOH,2:\,!,/_,!) + MC(<30,NH2,!~wb,/!iPr,!,COOH) endfont %*********************************************************************** beginfont("EN:L-Isoleucine") - MC(<30,NH2,!~wb,!,COOH,2:\,/*_,!2) + MC(<30,NH2,!~wb,/'(/*_,!2),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Serine") - MC(<30,NH2,!~wb,!,COOH,2:/!OH) + MC(<30,NH2,!~wb,/!OH,!,COOH) endfont %*********************************************************************** beginfont("EN:L-Threonine") - MC(<30,NH2,!~wb,!,COOH,2:\,/_,!~wf,OH) + MC(<30,NH2,!~wb,/'(/_,!~wf,OH),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Cysteine") - MC(<30,NH2,!~wb,!,COOH,2:/!SH) + MC(<30,NH2,!~wb,/!SH,!,COOH) endfont %*********************************************************************** beginfont("EN:L-Methionine") - MC(<30,NH2,!~wb,!,COOH,2:\,!2,SMe) + MC(<30,NH2,!~wb,/'(!2,SMe),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Phenylalanine") - MC(<30,NH2,!~wb,!,COOH,2:/!Ph) + MC(<30,NH2,!~wb,/!Ph,!,COOH) endfont %*********************************************************************** beginfont("EN:L-Tyrosine") - MC(<30,NH2,!~wb,!,COOH,2:\,!,Ph,-3:/OH) + MC(<30,NH2,!~wb,/'(!Ph,-3:/OH),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Triptophan") @@ -69,7 +69,7 @@ beginfont("EN:L-Glutamine") endfont %*********************************************************************** beginfont("EN:L-Asparagine") - MC(<30,NH2,!~wb,!,COOH,2:\,!,//O,!,NH2) + MC(<30,NH2,!~wb,/'(!,//O,!,NH2),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Aspartic acid") @@ -77,11 +77,11 @@ beginfont("EN:L-Aspartic acid") endfont %*********************************************************************** beginfont("EN:L-Glutamic acid") - MC(<30,NH2,!~wb,!,COOH,2:\,!2,COOH) + MC(<30,NH2,!~wb,/'(!2,COOH),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Lysine") - MC(<30,NH2,!~wb,!,COOH,2:\,!4,NH2) + MC(<30,NH2,!~wb,/'(!4,NH2),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Arginine") @@ -97,11 +97,11 @@ beginfont("EN:L-DOPA") endfont %*********************************************************************** beginfont("EN:Ornithine") - MC(<30,NH2,!~wb,!,COOH,2:\,!3,NH2) + MC(<30,NH2,!~wb,/'(!3,NH2),!,COOH) endfont %*********************************************************************** beginfont("EN:Citrulline") - MC(<30,NH2,!~wb,!,COOH,2:\,!3,NH,!,//O,!,NH2) + MC(<30,NH2,!~wb,/'(!3,NH,!,//O,!,NH2),!,COOH) endfont %*********************************************************************** beginfont("EN:GABA") @@ -117,7 +117,7 @@ beginfont("EN:4-amino benzoic acid") endfont %*********************************************************************** beginfont("EN:L-Carboxyl glutamic acid") - MC(<30,NH2,!~wb,!,COOH,2:\,!,/COOH,!,COOH) + MC(<30,NH2,!~wb,/'(!,/COOH,!,COOH),!,COOH) endfont %*********************************************************************** beginfont("EN:L-Hydroxy Prorine") @@ -1108,9 +1108,8 @@ endfont beginfont("EN:Colchicine","MW:385.41") fsize:=(60mm,25mm); MC( - <30,Ph,{1,2,6}:/O!,|,-4=?7, - |,-5=?7,{-1,-4,-6}=dl,-2://O,-3:/O!, - $9:\,NH,!,//O,! + <30,Ph,{1,2,6}:/O!,-4=?7,-5=?7,{-1,-4,-6}=dl,-2://O,-3:/O!, + 9:\,NH,!,//O,! ) endfont %*************************************************************************** diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf Binary files differindex 233e70eecd7..a3582e5ba83 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex index 4664a2eea00..165b0c721f5 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Molecular Coding Format manual by Akira Yamaji 2020.08.30 +% Molecular Coding Format manual by Akira Yamaji 2020.11.03 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} %%%%\documentclass[a4paper,twoside]{article} @@ -8,6 +8,8 @@ %%%%\usepackage{epstopdf} %%%%\usepackage[dvipdfmx]{graphicx} \usepackage[pdftex]{hyperref} +\usepackage{makeidx} +\makeindex %%%%\usepackage[dvipdfmx]{hyperref} %--------------------- \usepackage{mcf_setup} @@ -112,9 +114,10 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Chain use !,!n} +\index{"!}% \begin{verbatim} - ! : take value 60 or -60 depend on - current angle and enviroment + ! : take value 60 or -60 depend on + current angle and environment !6 : !,!,!,!,!,! <-30,!,!,!,!,!,! @@ -123,6 +126,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Jump to atom} +\index{"@}% \begin{verbatim} n:@ : Jump to An ** An: atom number(-999<=n<=4095) @@ -132,6 +136,7 @@ exact mass, molecular formula. \MCFgraph %------------------------------------ \subsubsection{Branch bond} +\index{\textbackslash}% \begin{verbatim} 3:\ : 3:@,0 @@ -140,6 +145,10 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Branch modified bond} +\index{*\textbackslash}% +\index{\textbackslash*}% +\index{\textbackslash\textbackslash}% +\index{*\textbackslash*}% \begin{verbatim} 2:\ : 2:@,0 4:*\ : 4:@,0~wf @@ -152,6 +161,9 @@ exact mass, molecular formula. \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- +\index{\textasciicircum}% ^ +\index{\textasciitilde}% ~ +\index{`}% \begin{verbatim} <30,!6, 2:\~dr,!, : 2:@,0~dr,! @@ -161,6 +173,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Connect atom} +\index{\#}% \begin{verbatim} n:# : Connect to An n1@#n2 : n1:@,n2:# @@ -170,6 +183,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Ring} +\index{?}% \begin{verbatim} ?n : n membered ring(3<=n<=20) ?6 : <-120,60,60,60,60,60,1:# @@ -178,6 +192,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Rotate current angle} +\index{\textgreater}% \begin{verbatim} <angle : rotate current angle @@ -187,6 +202,14 @@ exact mass, molecular formula. %----------------------------------------------------------------------------- \subsection{Change bond type} \subsubsection{Double,triple} +\index{\textasciitilde}% +\index{\textasciitilde\textasciitilde}% +\index{"!"!}% +\index{"!"!"!}% +\index{dm}% +\index{dl}% +\index{db}% +\index{tm}% \begin{verbatim} a~type : ~~type,a dm : double middle @@ -206,6 +229,10 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Wedge} +\index{wf}% +\index{wb}% +\index{zf}% +\index{zb}% \begin{verbatim} wf : wedge forward / wb : wedge backward zf : wedge dotted @@ -220,6 +247,8 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Vector} +\index{vf}% +\index{vb}% \begin{verbatim} vf:vector forward / vb:vector backward @@ -232,6 +261,10 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Dotted,wave} +\index{dt}% +\index{wv}% +\index{bd}% +\index{bz}% \begin{verbatim} Bn=bond type : change bond type at Bn dt : dotted / wv : wave @@ -246,6 +279,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Change multiple bond type} +\index{vf}% \begin{verbatim} {2,4,6}=dr : 2=dr,4=dr,6=dr @@ -254,6 +288,10 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Over line} +\index{si\_}% +\index{wf\_}% +\index{wb\_}% +\index{bd\_}% \begin{verbatim} si_ : single over line wf_ : wedge forward over line @@ -267,6 +305,7 @@ exact mass, molecular formula. %----------------------------------------------------------------------------- \subsection{Change bond length} \subsubsection{Chain length} +\index{`}% \begin{verbatim} (!,!n)`length : change length of !,!n @@ -276,6 +315,7 @@ exact mass, molecular formula. \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- +\index{``}% \begin{verbatim} ``length : change all bond length after @@ -301,6 +341,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Addressed atom} +\index{:}% \begin{verbatim} 2:O : change A2 C to O {3,4}:N : change A3,A4 C to N @@ -310,6 +351,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Brock address} +\index{\textbar}% | \begin{verbatim} | : divide brock @@ -318,6 +360,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Reset brock address} +\index{\textbar\textbar}% || \begin{verbatim} || : reset brock adress @@ -326,6 +369,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Absolute address} +\index{\$}% $ \begin{verbatim} $2:N : change A$2 C to N ** $n : (1<=n<=3095) @@ -451,6 +495,11 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Insert modified group} +\index{//}% +\index{*/}% +\index{/*}% +\index{*/*}% +\index{**}% \begin{verbatim} // : double (double middle) */ : wedge forward @@ -466,11 +515,15 @@ exact mass, molecular formula. // /* */ */* ** \end{verbatim} %----------------------------------------------------------------------------- +\index{\textasciicircum}% ^ +\index{\textasciitilde}% ~ +\index{`}% +\index{\textless}% \begin{verbatim} ~ : change type ^ : change angle ` : change length - > : change enviroment + > : change environment <-30,``1,!, /_`2^30,!2,/!2>lr,!2,/!2>rl,!) @@ -504,9 +557,11 @@ exact mass, molecular formula. %----------------------------------------------------------------------------- \subsection{Chain environment} \subsubsection{Horizontal,vertical} +\index{hz}% +\index{vt}% \begin{verbatim} - >hz : horizontal enviroment (default) - >vt : vertical enviroment + >hz : horizontal environment (default) + >vt : vertical environment ?4, {3^-90,3^-30,3^90}:/'(!3,"{hz}")>hz, @@ -515,9 +570,11 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Left-right,right-left} +\index{lr}% +\index{rl}% \begin{verbatim} - >lr : left-right enviroment - >rl : right-left enviroment + >lr : left-right environment + >rl : right-left environment <-30,!6, {3^-30,3,3^30}:/'(!3,"{lr}")>lr, @@ -526,6 +583,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Fixed rotate angle} +\index{\textgreater}% \begin{verbatim} >45 : rotate 45 @@ -544,10 +602,10 @@ exact mass, molecular formula. %----------------------------------------------------------------------------- \subsection{Miscellaneous} %----------------------------------------------------------------------------- -\subsubsection{Change atom and add group} +\subsubsection{} \begin{verbatim} NH,SO,SOO : - inset hetero atom and group + insert hetero atom and group simultaneously <-30,!2,NH,!,SO,!,SOO,! @@ -556,6 +614,8 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Make block} +\index{\textbar\textless \textgreater\textbar}% |< +\index{\textbar= =\textbar}% |= \begin{verbatim} |< : start brock >| : end brock @@ -591,6 +651,7 @@ exact mass, molecular formula. \section{Option parameter} %------------------------------------------------------------------------------ \subsection{Angle parameter} +\index{mangle}% \begin{verbatim} mangle=0 ** default @@ -603,6 +664,7 @@ exact mass, molecular formula. \subsection{Size/Ratio parameter} %----------------------------------------------------------------------------- \subsubsection{Bond length} +\index{blength}% \begin{verbatim} (fit to font size) blength=0 ** default @@ -624,6 +686,7 @@ exact mass, molecular formula. \MCFgraph %------------------------------------------------------------------------------ \subsubsection{Molecular size} +\index{msize}% \begin{verbatim} msize=(1,1) ** default \end{verbatim} @@ -641,6 +704,7 @@ exact mass, molecular formula. \MCFgraph %------------------------------------------------------------------------------ \subsubsection{Molecular position} +\index{mposition}% \begin{verbatim} mposition=(0.5,0.5) ** default \end{verbatim} @@ -659,6 +723,7 @@ exact mass, molecular formula. \subsection{Size parameter} %----------------------------------------------------------------------------- \subsubsection{Font size} +\index{fsize}% \begin{verbatim} fsize=(font width,font height) ** default: (30mm,20mm) @@ -668,6 +733,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Font margin} +\index{fmargin}% \begin{verbatim} fmargin=(margin left rigth,top bottom) ** default: (0.4mm,0.4mm) @@ -677,6 +743,7 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Offset thickness of bond} +\index{offset\_thickness}% \begin{verbatim} default: offset_thickness=0.2pt \end{verbatim} @@ -686,7 +753,8 @@ exact mass, molecular formula. 0pt 0.2pt 0.5pt \end{verbatim} %----------------------------------------------------------------------------- -\subsubsection{Offset of doublebond gap} +\subsubsection{Offset of double bond gap} +\index{offset\_bond\_gap}% \begin{verbatim} default: offset_bond_gap=0.3pt \end{verbatim} @@ -697,6 +765,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Offset of atom width} +\index{offset\_atom}% \begin{verbatim} default: offset_atom=0.8pt \end{verbatim} @@ -707,6 +776,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Offset of wedge width} +\index{offset\_wedge}% \begin{verbatim} default: offset_wedge=0.4pt \end{verbatim} @@ -717,6 +787,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Max bond length} +\index{max\_blength}% \begin{verbatim} default: max_blength=10mm \end{verbatim} @@ -729,6 +800,7 @@ exact mass, molecular formula. \subsection{Ratio parameter} %----------------------------------------------------------------------------- \subsubsection{Thickness/bond length} +\index{ratio\_thickness\_bond}% \begin{verbatim} default: ratio_thickness_bond=0.015 \end{verbatim} @@ -739,6 +811,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Char/bond thickness} +\index{ratio\_char\_bond}% \begin{verbatim} default: ratio_char_bond=1.5 \end{verbatim} @@ -748,7 +821,8 @@ exact mass, molecular formula. 1.0 1.5 2.0 \end{verbatim} %----------------------------------------------------------------------------- -\subsubsection{Bondgap/bond length} +\subsubsection{Bond gap/bond length} +\index{ratio\_bondgap\_bond}% \begin{verbatim} default: ratio_bondgap_bond= 0.15 \end{verbatim} @@ -759,6 +833,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Atom/bond length} +\index{ratio\_atom\_bond}% \begin{verbatim} default: ratio_atom_bond= 0.36 \end{verbatim} @@ -769,6 +844,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Wedge/bond length} +\index{ratio\_wedge\_bond}% \begin{verbatim} default: ratio_wedge_bond=0.12 \end{verbatim} @@ -779,6 +855,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Font atom gap/atom length} +\index{ratio\_atomgap\_atom}% \begin{verbatim} default: ratio_atomgap_atom= 0.050 \end{verbatim} @@ -789,6 +866,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Chain/ring length} +\index{ratio\_chain\_ring}% \begin{verbatim} default: ratio_chain_ring= 0.66 \end{verbatim} @@ -799,6 +877,7 @@ exact mass, molecular formula. \end{verbatim} %----------------------------------------------------------------------------- \subsubsection{Zebra gap/bond length} +\index{ratio\_zebragap\_bond}% \begin{verbatim} default: ratio_zebragap_bond=0.12 \end{verbatim} @@ -813,6 +892,9 @@ exact mass, molecular formula. \subsection{Drawing mode} %----------------------------------------------------------------------------- \subsubsection{Numbering atom} +\index{numberA}% +\index{numberA\_start}% +\index{numberA\_end}% \begin{verbatim} numberA_start:=3; numberA_end:=8; default: sw_numberA=0 : @@ -826,6 +908,9 @@ exact mass, molecular formula. \end{picture} %----------------------------------------------------------------------------- \subsubsection{Numbering bond} +\index{numberB}% +\index{numberB\_start}% +\index{numberB\_end}% \begin{verbatim} numberB_start:=3; numberB_end:=8; default: sw_numberB=0 : @@ -839,6 +924,7 @@ exact mass, molecular formula. \end{picture} %----------------------------------------------------------------------------- \subsubsection{Trimming mode} +\index{sw\_trimming}% \begin{verbatim} sw_trimming:=0; ** default msize:=(1,0.7); @@ -854,21 +940,24 @@ exact mass, molecular formula. \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Expand mode} +\index{sw\_expand}% \begin{verbatim} MCat(0, .5)(<30,Ph,4:/COOH,3:/NH2) sw_expand:=1; MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) ** default: sw_expand=0 \end{verbatim} -\MCFgraph\\ +\MCFgraph %----------------------------------------------------------------------------- \subsubsection{Group off mode} +\index{sw\_group\_off}% \begin{verbatim} ** default: sw_group_off=0 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Single bond mode} +\index{sw\_single}% \begin{verbatim} ** default: sw_single=0 \end{verbatim} @@ -877,6 +966,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) \subsection{Frame} %----------------------------------------------------------------------------- \subsubsection{Font frame} +\index{sw\_fframe}% \begin{verbatim} (Draw font frame) fmargin:=(5mm,2mm); @@ -900,12 +990,14 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Molecular frame} +\index{sw\_mframe}% \begin{verbatim} sw_mframe=1 ** default:sw_mframe=0 \end{verbatim} \MCFgraph %----------------------------------------------------------------------------- \subsubsection{Atom frame} +\index{sw\_aframe}% \begin{verbatim} sw_aframe=1 ** default: sw_aframe=0 MC(<30,COOH,!,COOH) @@ -951,6 +1043,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) \section{Function} %----------------------------------------------------------------------------- \subsection{Function MC()} +\index{MC()}% \begin{verbatim} (Draw molecule) @@ -969,6 +1062,7 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) \MCFgraph %----------------------------------------------------------------------------- \subsection{Function MCat()} +\index{MCat()}% \begin{verbatim} (Draw molecule at mposition) @@ -1007,6 +1101,17 @@ MCat(1, .5)(<30,Ph,4:/COOH,3:/NH2) %=============================================================================== \newpage \subsection{Function add()} +\index{add()}% +\index{plus}% +\index{minus}% +\index{lonepair}% +\index{lonepairdiam}% +\index{lonepairdiam}% +\index{circlediam}% +\index{circlepen}% +\index{/*}% +\index{**}% +\index{\textgreater\textgreater}% \begin{verbatim} (Add graphic to molecule) @@ -1114,6 +1219,7 @@ endfont %----------------------------------------------------------------------------- \newpage \subsection{Function ext()} +\index{ext()}% \begin{verbatim} (Extra graphic to font) @@ -1191,6 +1297,7 @@ endfont \end{verbatim} \MCFgraph\MCFgraph\MCFgraph\MCFgraph \subsubsection{Global ext() setting} +\index{ext\_clear}% \begin{verbatim} ext_clear: reset global ext() @@ -1240,10 +1347,10 @@ endfont beginfont("EN:Colchicine","MW:385.41") fsize:=(60mm,25mm); MC( - <30,Ph,{1,2,6}:/O!,|,-4=?7, - |,-5=?7,{-1,-4,-6}=dl, + <30,Ph,{1,2,6}:/O!,-4=?7, + -5=?7,{-1,-4,-6}=dl, -2://O,-3:/O!, - $9:\,NH,!,//O,! + 9:\,NH,!,//O,! ) endfont \end{verbatim} @@ -1312,6 +1419,7 @@ endfont \onecolumn \section{Example to use mcf2graph} \subsection{Molecular definition file} +\index{sw\_aux\_out}% \begin{verbatim} %------------------------------------------------------------------------- input mcf2graph.mf; % input macro @@ -1386,6 +1494,7 @@ beginfont("EN:beta-Carotene") .... endfont tag1:="F"; tag2:="C"; tag3:="mw"; tag4:="fm"; tag5:="EN"; \end{verbatim} \paragraph{(Output)} +\index{aux\_delimiter}% \begin{verbatim} (sw_aux_out=1) F:mcf_man_soc;C:1;mw:349.40462;fm:C16H19N3O4S;EN:Ampicillin @@ -1427,6 +1536,7 @@ h : font height \noindent% \subsection{Report output} \paragraph{(Insert option parameter setting)} +\index{sw\_rep\_out}% \begin{verbatim} sw_rep_out:=1; ** default : sw_rep_out=0 @@ -1489,6 +1599,7 @@ h : font height \noindent% \subsection{MOL file output} \paragraph{(Insert option parameter setting)} +\index{sw\_mol\_out}% \begin{verbatim} sw_mol_out:=1; % MOL(V2000) sw_mol_out:=2; % MOL(V3000) @@ -1602,6 +1713,7 @@ endfont; \newpage \subsection{LaTeX file example} %############################################################################ +\index{mcf\_setup.sty}% \begin{verbatim} %-------------------------------------------------------------------- \documentclass[a4paper]{article} @@ -1634,4 +1746,6 @@ endfont; \INFO{F:mcf_man_soc,C:139,NO:1,mw:349.40462,fm:C16H19N3O4S,EN:Ampicillin}% \INFO{F:mcf_man_soc,C:140,NO:2,mw:386.6532,fm:C27H46O,EN:Cholesterol}% %------------------------------------------------------------------------ +\printindex +%------------------------------------------------------------------------ \end{document} diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf Binary files differindex 314b6cbe23f..ed6e3e605b8 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex index d35a55eed20..17d23cd4cb0 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex @@ -1,7 +1,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2020.08.30 +% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2020.11.03 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%%% mcf2graph.mf it must be version 4.52 or later +%%% mcf2graph.mf it must be version 4.53 or later \documentclass{article} %------------------------------------------------------------------------------ \usepackage{luamplib}% @@ -174,7 +174,7 @@ beginfont("NO:5","EN:Erythromycin","MW:733.93"); 14:O,13:/*Et,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_, {6^35,11,12^-35}:*/OH, $3:\*,O,30,|,?6`.7,2:O,{3,5^35}:/_,4:/OH,5^-35:/O!, - $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMeMe + $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/N!_ ) endfont; \end{verbatim} @@ -187,7 +187,7 @@ beginfont("NO:5","EN:Erythromycin","MW:733.93"); 14:O,13:/*Et,{1,9}://O,{2,10}:*/_,{4,6^-35,8,12^35}:/*_, {6^35,11,12^-35}:*/OH, $3:\*,O,30,|,?6`.7,2:O,{3,5^35}:/_,4:/OH,5^-35:/O!, - $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/NMeMe + $5:\*^30`1.7,O,!,|,?6`.7,6:O,5:/_,2:/OH,3:/N!_ ) ext( defaultscale:=0.8; @@ -206,8 +206,8 @@ beginfont("EN:Paclitaxel","MW:853.918") MC( ?6,5=d,3:@,|=1,36,45,45,45,45,=|,$5:#,-4=?6,-4=?4,||,-1=wb,-3=wf,-1:O, {4^35,4^-35,6}:/_,{3^-60,15}:*/OH,8:/*H^-60,9:*/_^60,10://O, - $1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph, - $7:\*,O,-45,//O,60,Ph,$11:*\,O,-60,//O,60,$12:\*^-15,O,60,//O,-60 + 1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph, + 7:\*,O,-45,//O,60,Ph,11:*\,O,-60,//O,60,12:\*^-15,O,60,//O,-60 ) endfont \end{verbatim} @@ -218,8 +218,8 @@ beginfont("EN:Paclitaxel","MW:853.918") MC( ?6,5=d,3:@,|=1,36,45,45,45,45,=|,$5:#,-4=?6,-4=?4,||,-1=wb,-3=wf,-1:O, {4^35,4^-35,6}:/_,{3^-60,15}:*/OH,8:/*H^-60,9:*/_^60,10://O, - $1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph, - $7:\*,O,-45,//O,60,Ph,$11:*\,O,-60,//O,60,$12:\*^-15,O,60,//O,-60 + 1:\,O,!,//O,!,*/OH,!,/Ph,60~wf,NH,-60,//O,60,Ph, + 7:\*,O,-45,//O,60,Ph,11:*\,O,-60,//O,60,12:\*^-15,O,60,//O,-60 ) ext( defaultscale:=0.8; diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf index e28af21d625..9314283dea8 100644 --- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf +++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% mcf2graph ver 4.52 Copyright (c) 2013-2020 Akira Yamaji +% mcf2graph ver 4.53 Copyright (c) 2013-2020 Akira Yamaji % % Permission is hereby granted, free of charge, to any person obtaining a copy of this software % and associated documentation files (the "Software"), to deal in the Software without restriction, @@ -37,6 +37,9 @@ % Set to use plain.mp (label,arrow,atom) : mpost -s labeloffset=2 FILENAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% tracingstats:=1; +message "---------------------------------------------"; +message "This is mcf2graph ver 4.53 2020.11"; +message "---------------------------------------------"; %------------------------------------------------------------------------------------------------- newinternal com,par,nA,nB,nC,nD,nE,nF,nP; numeric save_num[],comD[][],parD[][],adrD[][],cntD[],tbl_atom[],tbl_group[][],f_char[], @@ -125,8 +128,6 @@ else: f_MP:=0; fi clearit; %-------------------------------------------------------------------------------------------------- -message "---------------------------------------------"; -message "This is mcf2graph ver 4.52 2020.08"; if f_MP=1: if bboxmargin=0: message "output no image file"; elseif bboxmargin=1: message "output first font only"; @@ -149,8 +150,8 @@ if f_MP=1: message "outputtemplate="&outputtemplate; message "atomfont="&atomfont; message "defaultfont="&defaultfont; + message "---------------------------------------------"; fi -message "---------------------------------------------"; %-------------------------------------------------------------------------------------------------- let DIV= /; let MUL= *; let LT= <; let GT= >; let AND= &; let :: = : ; let == = =; let ef=elseif; %-------------------------------------------------------------------------------------------------- @@ -160,15 +161,14 @@ def ext(text TXT)= sw_ext_all:=1; def EXT_ALL = TXT enddef; enddef; def ext_clear= sw_ext_all:=0; def EXT_ALL = enddef; enddef; %-------------------------------------------------------------------------------------------------- ?3:=?20:=Ph:=Ph1:=Ph2:=hz:=0; vt:=1; -ratio_chain_ring:= 0.66; ratio_atom_bond:=0.36; -ratio_thickness_bond:=0.015; ratio_thickness_char:=0.1; -ratio_char_bond:=1.5; ratio_bondgap_bond:=0.15; ratio_zebragap_bond:=0.12; -ratio_zebra_black:=0.4; ratio_wedge_bond:=0.12; ratio_atomgap_atom:=0.040; +ratio_chain_ring:=0.66; ratio_atom_bond:=0.36; ratio_thickness_bond:=0.015; +ratio_thickness_char:=0.1; ratio_char_bond:=1.5; ratio_bondgap_bond:=0.15; +ratio_zebragap_bond:=0.12; ratio_zebra_black:=0.4; ratio_wedge_bond:=0.12; +ratio_atomgap_atom:=0.040; offset_thickness:=0.2bp; offset_bond_gap:=0.3bp; offset_zebra_gap:=0.1bp; -offset_atom:=0.8pt; offset_wedge:=0.4bp; max_labelsize:=20mm; +offset_atom:=0.8pt; offset_wedge:=0.4bp; thickness_fframe:=0.2bp; thickness_mframe:=0.2bp; thickness_aframe:=0.1bp; -max_blength:=10mm; blength:=0; mangle:=0; -dottedline_gap:=1.5bp; +max_blength:=10mm; blength:=mangle:=0; max_labelsize:=20mm; dottedline_gap:=1.5bp; %-------------------------------------------------------------------------------------------------- fsize:=(30mm,20mm); fmargin:=(0.4mm,0.4mm); msize:=(1,1); mposition:=(0.5,0.5); %================================================================================================== @@ -190,7 +190,7 @@ def_com(-4090)(_com,_jp_atom,_jp_absA,_jp_bond,_cyc,_cyc_sB,_cyc_eB,_set_line,_d _chg_len,_get_len,_ring_len,_tmp_len,_rot_ang,_adj_ang,_chg_env,_tmp_env,_set_colorA,_set_colorB, _group_si,_set_adr,_mk_bond,_set_atom,_arg_ang,_chg_atom,_tmp_rot,_fuse,_size_atom,_numeric, _jump_at,_connect_at,_set_and,_chg_charge,_nop,_mark,_moff,_term,_len_s,_len_e,_len_ss,_len_ee, - _group_s,_group_e,si,dl,dr,db,dm,tm,wf,wb,bd,bz,zf,zb,dt,wv,nl,vf,vb,nb,si_,wf_,wb_,bd_); + _group_s,_group_e,_rest,si,dl,dr,db,dm,tm,wf,wb,bd,bz,zf,zb,dt,wv,nl,vf,vb,nb,si_,wf_,wb_,bd_); %-------------------------------------------------------------------------------------------------- def parameter_list= sw_rep_out,sw_numberA,sw_numberB,sw_mframe,sw_aux_out,sw_expand,sw_mol_out,sw_calc,sw_single, @@ -313,7 +313,7 @@ def endfont= enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def set_def_MC= - save /,//,/*,*/,**,*/*,~,^,`,``,<,>,&,:,=,\,\\,*\,\*,*\*,@,#,@#,$, + save /,//,/*,*/,**,*/*,~,^,',`,``,<,>,&,:,=,\,\\,*\,\*,*\*,@,#,@#,$, {,},|,||,|||,|=,=|,|<,>|,|:,:|,_,d,w,z,inside_def_MC; inside_def_MC:=1; _:=Me; d:=db; w:=wf; z:=zf; @@ -332,13 +332,14 @@ def set_def_MC= def \ == @,0 enddef; def \\ == \~dm enddef; def *\ == \~wf enddef; def \* == \~zf enddef; def *\* == \~wv enddef; def | == (_com,_mark) enddef; def || == (_com,_moff) enddef; def ||| == (_com,_term) enddef; - def |< == (_com,_len_s) enddef; def >| == (_com,_len_e) enddef; + def |< == (_com,_len_s) enddef; def >| == (_com,_len_e) enddef; def |: == (_com,_len_ss) enddef; def :| == (_com,_len_ee) enddef; def |=primary n == |<,(_chg_len,n) enddef; def =| == >| enddef; def /secondary n == if known n:: (_group_si,n) else:: _nop fi enddef; def //secondary n == /n~dm enddef; def */secondary n == /n~wf enddef; def /*secondary n == /n~zf enddef; def */*secondary n == /n~wv enddef; def **secondary n == /n~nb enddef; + vardef '(text TXT)== read_mcf(incr parts_usr)(|,TXT,(_com,_rest)); parts_usr enddef; enddef; %================================================================================================= vardef '(text TXT)= read_mcf(incr parts_usr)(TXT); parts_usr enddef; @@ -743,8 +744,8 @@ enddef; %------------------------------------------------------------------------------------------------- def MC(text TXT)= begingroup - save markA,markB,f_bra,envT,envB,lenT,lineT,strAT,cnt_group,bondL,temp_lenE,temp_lenF, - temp_cntB,f_end,f_term,rotT,f_at,f_lineT,f_rotT,f_lenT,f_envT,angT, + save markA,markB,saveA,saveB,f_bra,envT,envB,lenT,lineT,strAT,cnt_group,bondL,temp_lenE, + temp_lenF,temp_cntB,f_end,f_term,rotT,f_at,f_lineT,f_rotT,f_lenT,f_envT,angT, maxX,maxY,sA,sC,sD,pA,pB,factor,m_wd,m_ht,crR,CP,CPe,CPx,defaultsize,defaultscale; %----------------------------------------------------------------------------------------------- def CP= com_par enddef; @@ -972,12 +973,13 @@ enddef; def proc_bond_atom(expr a)(expr n)= f_bra:=f_end:=f_term:=rotT:=f_lineT:=f_rotT:=f_lenT:=f_envT:=envT:=envB:=strAT:=f_at:=0; bondL:=crR; lenT:=crR; sB[0]:=0; eB[0]:=1; lineT:=si; - andAT:=markA:=markB:=0; + andAT:=markA:=markB:=saveA:=saveB:=0; %----------------------------------------------------------------------------------------------- for i=n upto cntD[a]: com:=comD[a][i]; par:=parD[a][i]; if com=_mk_bond: if (par=0)and(rotT<>0): rotT:=0; fi add_atom; ef com=_set_adr: adrT:=par; - ef com=_com: if par=_mark: markA:=cntA; markB:=cntB; + ef com=_com: if par=_mark: saveA:=markA; saveB:=markB; markA:=cntA; markB:=saveB:=cntB; + ef par=_rest: markA:=saveA; markB:=saveB; ef par=_moff: markA:=markB:=0; ef par=_term: termA; ef par=_len_s: temp_lenE:=bondL; ef par=_len_e: bondL:=temp_lenE; @@ -1097,10 +1099,10 @@ def add_bond(expr ROT)= fi cntB:=cntB+1; posBs:=posBe; enddef; -%================================================================================================== +%================================================================================================= vardef getA(expr n)= if n>=0: markA+n ef n>=-999: cntA+n+1 else: n+4095 fi enddef; vardef getB(expr n)= if n>=0: markB+n ef n>=-999: cntB+n+1 else: n+4095 fi enddef; -%-------------------------------------------------------------------------------------------------- +%------------------------------------------------------------------------------------------------- def termA= if f_term=0: if f_bra=0: @@ -1171,17 +1173,17 @@ def draw_atom(expr NUM)= endfor endgroup enddef; -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def draw_bond(expr NUM)= begingroup save ww,ap,am,ang,col,len,Ls,Le,nL,nS,nE,pA,zA,zL,wpcs; pair pA,Ls,Le; path zA,zL; def wpcs expr n= withpen pencircle scaled n enddef; - %------------------------------------------------------------------------------------------------ + %----------------------------------------------------------------------------------------------- nL:=lineB[NUM]; ang:=angB[NUM]; nS:=sB[NUM]; nE:=eB[NUM]; col:=colorB[NUM]; zL:=posA[nS]--posA[nE]; ww:=wedge_wd; ap:=ang+90; am:=ang-90; - %------------------------------------------------------------------------------------------------ + %----------------------------------------------------------------------------------------------- if (numS[nS]=0)and(numS[nE]=0)or(sw_numberA=1)or(sw_numberB=1): Ls:=posA[nS]; Le:=posA[nE]; pA:=(.1,.9); ef numS[nS]=0: Le:=zL intersectionpoint frame_str(nE); Ls:=posA[nS]; pA:=(.15,1); @@ -1189,7 +1191,7 @@ def draw_bond(expr NUM)= else: Ls:=zL intersectionpoint frame_str(nS); Le:=zL intersectionpoint frame_str(nE); pA:=(0,1); fi zA:=Ls--Le; len:=length(Le-Ls); - %------------------------------------------------------------------------------------------------ + %----------------------------------------------------------------------------------------------- pickup pencircle scaled bond_pen_wd; if (nL=si)or(sw_single=1): draw zA Cp(col); ef nL=dl: draw zA Cp(col); draw sfB(subpath pA of zA,bondgap,ap) Cp(col); @@ -1259,7 +1261,7 @@ Me:='(); Et:='(!); Pr:='(!,!); Bu:='(!,!,!); for i=4,5,6: for j=2 upto i-2: ?[i][j]:='((_fuse,i),(j,0)); endfor endfor for i=5,6,7,8: for j=11 upto 15: ?[i][j]:='((_fuse,i),(j,0)); endfor endfor %================================================================================================= -H :='("H");C:='("C");N:='("N");O:='("O");S:='("S");P:='("P");F:='("F");I:='("I");K:='("K"); +H :='("H");C:='("C");N:='("N");O:='("O");S:='("S");P:='("P");F:='("F");I:='("I"); K:='("K"); Si:='("{Si}");Al:='("{Al}");Mg:='("{Mg}");Zn:='("{Zn}");As:='("{As}");Co:='("{Co}");Cu:='("{Cu}"); Ag:='("{Ag}");Au:='("{Au}");Sn:='("{Sn}");Cl:='("{Cl}");Br:='("{Br}");Li:='("{Li}");Cr:='("{Cr}"); Na:='("{Na}");Ca:='("{Ca}");Hg:='("{Hg}");Ni:='("{Ni}");Ti:='("{Ti}");U:='("U"); @@ -1269,29 +1271,32 @@ O[1]:= '("{O^+^}"); O[-1]:='("{O^-^}"); N[1]:='("{N^+^}"); N[-1]:='("{N^-^} S[1]:= '("{S^+^}"); S[-1]:='("{S^-^}"); P[1]:='("{P^+^}"); P[-1]:='("{P^-^}"); Li[1]:='("{Li^+^}"); Na[1]:='("{Na^+^}"); Cl[-1]:='("{Cl^-^}"); Br[-1]:='("{Br^-^}"); %------------------------------------------------------------------------------------------------- -R:='("R"); R1:='("{R^1^}"); R2:='("{R^2^}"); R3:='("{R^3^}"); R4:='("R^4^"); R5:='("{R^5^}"); +R:='("R"); R1:='("{R^1^}"); R2:='("{R^2^}"); R3:='("{R^3^}"); R4:='("R^4^"); R5:='("{R^5^}"); R6:='("R6"); R7:='("{R^7^}"); R8:='("{R^8^}"); R9:='("{R^9^}"); R10:='("R^10^"); R11:='("{R^11^}"); %------------------------------------------------------------------------------------------------- CHO:='("CHO"); OH:='("OH"); COOH:='("COOH"); CH2:='("C{H_2_}"); CH3:='("C{H_3_}"); CN:='("CN"); NH2:='("N{H_2_}"); NO2:='("N{O_2_}"); SH:='("SH"); SO3:='("S{O_3_}"); NH:='(N,/H~nl); %------------------------------------------------------------------------------------------------- -NMe:=N!:='(N,/_); iPr:=Me!:='(/_,60); tBu:='(/_,/_^60,60); SO:='(S,//O); SOO :='(S,//O^-35,//O^35); +NMe:=N!:='(N,/_); iPr:=Me!:='(/_,60); tBu:='(/_,/_^60,60); SO:='(S,//O); SOO:='(S,//O^-35,//O^35); OMe:=O!:='(O,!); OEt:=O!2:='(O,!,!); OPr:=O!3:='(O,!,!,!); OiPr:=OMe!:='(O,!,iPr); SMe:=S!:='(S,!); SEt:=S!2:='(S,!,!); SPr:=S!3:='(S,!,!,!); SiPr:=SMe!:='(S,!,iPr); %------------------------------------------------------------------------------------------------- COO:='(//O,!,O); COOMe:=COO!:='(COO,!); COOEt:=COO!2:='(COO,!,!); COOiPr:=COOMe!:='(COO,!,iPr); COOPr:=COO!3:='(COO,!,!,!); COOtBu:='(COO,!,tBu); COMe:=CO!:='(//O,!); COEt:=CO!2:='(//O,!,!); COPr:=CO!3:='(//O,!,!,!); -OCOMe:=OCO!:='(O,!,//O,!); NMeMe:=NMe!:='(N!,!); NMeEt:=NMe!2:='(N!,!,!); NMePr:=NMe!3:='(N!,!,!,!); -NHCOMe:=NHCO!:='(NH,!,//O,!); NHiPr:=NHMe!:='(NH,!,iPr); NHtBu:='(NH,!,tBu); NHMe:=NH!:='(NH,!); -NHEt:=NH!2:='(NH,!,!); NHPr:=NH!3:='(NH,!,!,!); +OCOMe:=OCO!:='(O,!,//O,!); NMeMe:=NMe!:=N!_:='(N!,!); NMeEt:=NMe!2:=N!2_:='(N!,!,!); +NMePr:=NMe!3:='(N!,!,!,!); +NHCOMe:=NHCO!:='(NH,!,//O,!); NHiPr:=NHMe!:='(NH,!,iPr); NHtBu:='(NH,!,tBu); +NHMe:=NH!:='(NH,!); NHEt:=NH!2:='(NH,!,!); NHPr:=NH!3:='(NH,!,!,!); %------------------------------------------------------------------------------------------------- !OH:='(!,OH); !SH:='(!,SH); !NH2:='(!,NH2); !COMe:=!CO!:='(!,//O,!); !COEt:=!CO!2:='(!,CO!2); !COPr:=!CO!3:='(!,CO!3); !OMe:=!O!:='(!,O!); !OEt:=!O!2:='(!,O!2); !OPr:=!O!3:='(!,O!3); !OiPr:=!OMe!:='(!,OMe!); !SMe:=!S!:='(!,S!); !SEt:=!S!2:='(!,S!2); !SPr:=!S!3:='(!,S!3); !SiPr:=!SMe!:='(!,SMe!); -!NHMe:=!NH!:='(!,NH!); !NHEt:=!NH!2:='(!,NH!2); !NHPr:=!NH!3:='(!,NH!3); !NHiPr:=!NHMe!:='(!,NHMe!); -!COOH:='(!,COOH); !COOMe:=!COO!:='(!,COO!); !COOEt:=!COO!2:='(!,COO!2); !COOPr:=!COO!3:='(!,COO!3); +!NHMe:=!NH!:='(!,NH!); !NHEt:=!NH!2:='(!,NH!2); !NHPr:=!NH!3:='(!,NH!3); +!NHiPr:=!NHMe!:='(!,NHMe!); +!COOH:='(!,COOH); !COOMe:=!COO!:='(!,COO!); !COOEt:=!COO!2:='(!,COO!2); +!COOPr:=!COO!3:='(!,COO!3); !COOtBu:='(!,COOtBu); !OCOMe:=!OCO!:='(!,OCO!); !NMeMe:=!NMe!:='(!,NMe!); !NMeEt:=!NMe!2:='(!,NMe!2); !NMePr:=!NMe!3:='(!,NMe!3); !CH3:='(!,CH3); !CN:='(!,CN); !iPr:=!Me!:='(!,iPr); !tBu:='(!,tBu); |