diff options
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG | 7 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/README | 2 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_exa_soc.mf | 8 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_example.pdf | bin | 241812 -> 242077 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf | 22 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.pdf | bin | 476539 -> 475962 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_manual.tex | 43 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.pdf | bin | 123162 -> 123160 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex | 3 | ||||
| -rw-r--r-- | Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf | 23 |
10 files changed, 66 insertions, 42 deletions
diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG index 611d4ab2851..0191b91b22c 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG +++ b/Master/texmf-dist/doc/metapost/mcf2graph/CHANGELOG @@ -1,6 +1,11 @@ ******************************************************************************* - Changelog of mcf2graph software package by Akira Yamaji 2016-08-06 + Changelog of mcf2graph software package by Akira Yamaji 2016-08-21 ******************************************************************************* +[ver. 3.97 / 2016-08-21] + -change bond type name 'ov' to 'si_' + -add bond type 'wf_','wb_','bd_' + -update MCF syntax manual + [ver. 3.96 / 2016-08-06] -large scaled rings can fuse 5,6,7,8 membered ring scaled 11/10,12/10,13/10,14/10,15/10 diff --git a/Master/texmf-dist/doc/metapost/mcf2graph/README b/Master/texmf-dist/doc/metapost/mcf2graph/README index 9a1a8a58a9a..1711f2d0217 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/README +++ b/Master/texmf-dist/doc/metapost/mcf2graph/README @@ -1,7 +1,7 @@ ******************************************************************************** mcf2graph : Convert Molecular Coding Format to graphics with METAFONT/METAPOST Author : Akira Yamaji - version : 3.96 2016-08-06 + version : 3.97 2016-08-21 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 e0833ba7e6e..fbe8c08ee82 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 2016.08.06 +% Molecular Coding Format for mcf_example.tex by Akira Yamaji 2016.08.21 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph.mf; +input mcf2graph.mf; %%% it must be version 3.97 or later %------------------------------------------------------------------------- font_wd#:=33mm#; font_ht#:=24mm#; @@ -238,7 +238,7 @@ endfont %************************************************************************** beginfont("EN:Tetrodotoxine") MCf({,``1,<60,-90,60,-30`1.15,150,60,,#3*,-135,60,-30`1.15,150,, - #10\,O,60`1.33,60,~ov,#8*,-15~ov,O,,},#9*,45,-60,OH,1^120://NH, + #10\,O,60`1.33,60,~si_,#8*,-15~si_,O,,},#9*,45,-60,OH,1^120://NH, @(5~zf^-15,7,9^-75,12,13~zf)/OH,@(2,6^180)NH) endfont %*************************************************************************** @@ -370,7 +370,7 @@ endfont %************************************************************************** beginfont("EN:Morphine") MCf(<30,Ph,2=?6,-4=?6,(1,12)=?5[2],-1:O,-1=zb, - 7*,60~wf`0.75,70~ov`1.3,45,N,/Me,&9~wb, + 7*,60~wf`0.75,70~si_`1.3,45,N,/Me,&9~wb, 15=dl,6:/OH,8^180:*/H,12:/*OH) endfont %************************************************************************** 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 be83fbebaf0..9cdc045a25a 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_man_soc.mf b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_man_soc.mf index 8dcf33c778e..07a530f60c8 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 2016.08.06 +% Molecular Coding Format file for mcf_manual.tex by Akira.Yamaji 2016.08.21 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -input mcf2graph.mf; +input mcf2graph.mf; %% it must be version 3.97 or later %------------------------------------------------------------------------ font_wd#:=60mm#;% font width font_ht#:=40mm#;% font height @@ -55,14 +55,17 @@ beginfont("EN:Connect atom") endfont %*********************************************************************** beginfont("EN:ring") + max_bond_width:=0.25; sw_numberB:=1; sw_start_vector:=1; MCf(?6) endfont %*********************************************************************** beginfont("EN:rotate 1") + max_bond_width:=0.25; + sw_numberB:=1; sw_start_vector:=1; - MCf(<30,!4,<30,?6) + MCf(``1,0~vf,0~vf,<90,0~vf,<-90,0~vf) endfont %*********************************************************************** beginfont("EN:change bond 1") @@ -72,22 +75,23 @@ endfont %*********************************************************************** beginfont("EN:change bond 2") ratio_chain_ring:=1; - MCf(<30,!~wf,!~wb,!~zf,!~zb) + MCf(<30,!~wf,!~wb,!~zf,!~zb,!~vf) endfont %*********************************************************************** beginfont("EN:change bond 3") ratio_chain_ring:=1; - MCf(<30,!4,1=vf,2=vb,3=dt,4=wv) + MCf(<30,!5,1=vb,2=dt,3=wv,4=bd,5=bz) endfont %*********************************************************************** beginfont("EN:change bond 4") ratio_chain_ring:=1; - MCf(<30,!3,!`2,!,@(3~bd`2^-30,5~ov^85`3,3~bz`3^-70)/Me) + MCf(<30,!7,$(2,4,6)dr) endfont %*********************************************************************** -beginfont("EN:change bond 4") +beginfont("EN:over line") ratio_chain_ring:=1; - MCf(<30,!7,$(2,4,6)dr) + max_bond_width:=0.25; + MCf(<-30,!8`.4,!`.2,60`.6,90`3,@(2~si_,4~wf_,6~wb_,8~bd_)/Me`1) endfont %*********************************************************************** beginfont("EN:change bond length1") @@ -597,7 +601,7 @@ endfont %*************************************************************************** beginfont("EN:Atoropin","CAS:51-55-8","FM:C17H23NO3","MW:289.37") MCf(<-30,O,!,//O,!,!,Ph, - #1\~zb^-120,|,?7`1.1,6*\^190`1.25,N,/Me,&3~wb,#3\~wv,!,OH) + #1\~zb^-120,|,?7,6*\^190`1.12,N,/Me,&3~wb,#3\~wv,!,OH) endfont %*************************************************************************** beginfont("EN:Validamycin") 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 9eb75f91201..e6e758e1d5d 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 fbcf34b1d9e..7a2bf1d9fc7 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 2016.08.06 +% Molecular Coding Format manual by Akira Yamaji 2016.08.21 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \documentclass[a4paper]{article} \usepackage{graphicx} @@ -96,7 +96,7 @@ beginfont("NO:1","EN:Ampicillin") > begin font(information) MCf(<45,?4,2:N,2=?5,-1:S, > begin MCF (1) @(3^45,4^-45)/*H,1://O^15,5:/*COOH^-18, > @(6^35,6^-35)/Me, > - 4\^75,NH,!,//O,!,/*NH,!,Ph) > end MCF + 4\^75,NH,!,//O,!,/*NH,!,Ph) > end MCF endfont > end font %------------------------------------------------------------------------ beginfont("NO:2","EN:Cholesterol") > begin font(information) @@ -267,7 +267,8 @@ n* : Jump to An \begin{verbatim} <angle : rotate current angle - <30,!4,<30,?6 + ``1, + 0~vf,0~vf,<90,0~vf,<-90,0~vf \end{verbatim} \end{minipage} \MCFstructure @@ -289,57 +290,61 @@ tm : triple \vspace{\gpman}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][\htman]{90mm} -\MCFtitle{Change bond type (1)} +\MCFtitle{Change bond type (2)} \begin{verbatim} a~type : ~~type,a wf : wedge forward wb : wedge backward zf : wedge dotted zb : wedge dotted backward +vf : vector forward - <30,!~wf,!~wb,!~zf,!~zb + <30,!~wf,!~wb,!~zf,!~zb,!~vf,!~vb \end{verbatim} \end{minipage} \MCFstructure \vspace{\gpman}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][\htman]{90mm} -\MCFtitle{Change bond type (2)} +\MCFtitle{Change bond type (3)} \begin{verbatim} Bn=bond type : change bond type at Bn -vf : vector forward vb : vector backward dt : dotted wv : wave +bd : broad +bz : broad dotted - <30,!4,1=vf,2=vb,3=dt,4=wv + <30,!5,1=vb,2=dt,3=wv,4=bd,5=bz \end{verbatim} \end{minipage} \MCFstructure \vspace{\gpman}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][\htman]{90mm} -\MCFtitle{Change bond type (3)} +\MCFtitle{Change bond type (4)} \begin{verbatim} -bd : broad single -bz : broad dotted -ov : over line +$(2,4,6)dr : 2=dr,4=dr,6=dr + +<30,!7,$(2,4,6)dr -<30,!3,!`2,!, - @(3~bd`2^-30,5~ov`3^85,3~bz`3^-70)/Me +** <30,!7,2=dr,4=dr,6=dr -** 3~bd^-45`2 : ~~bd,^^-45,'`2,3 \end{verbatim} \end{minipage} \MCFstructure \vspace{\gpman}\\ %----------------------------------------------------------------------------- \begin{minipage}[t][\htman]{90mm} -\MCFtitle{Change bond type (4)} +\MCFtitle{Over line} \begin{verbatim} -$(2,4,6)dr : 2=dr,4=dr,6=dr +si_ : single over line +wf_ : wedge forward over line +wb_ : wedge backward over line +bd_ : broad over line -<30,!7,$(2,4,6)dr +<-30,!8`.4,!`.2,60`.6,90`3, +@(2~si_,4~wf_,6~wb_,8~bd_)/Me`1 \end{verbatim} \end{minipage} @@ -1411,7 +1416,7 @@ mcf_man_soc;91;1;Ampicillin \begin{verbatim} <-30,O,!,//O,!,!,Ph, #1\~zb^-120, - |,?7`1.1,6*\^190`1.25,N,/Me,&3~wb, + |,?7,6*\^190`1.02,N,/Me,&3~wb, #3\~wv,!,OH \end{verbatim} \end{minipage} 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 0e60edde594..cb68fe31e7d 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 9d0f1b99042..207ec7cfd83 100644 --- a/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex +++ b/Master/texmf-dist/doc/metapost/mcf2graph/mcf_mplib_exa.tex @@ -1,6 +1,7 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2016.8.06 +% Example of MCF typest with LuaLaTeX(luamplib) by A.Yamaji 2016.8.21 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%% mcf2graph.mf it must be version 3.97 or later \documentclass{article} %------------------------------------------------------------------------------ \usepackage{luamplib}% diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf index a778a1da880..b674e468a9c 100644 --- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf +++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% mcf2graph ver 3.96 Copyright (c) 2013-2016 Akira Yamaji +% mcf2graph ver 3.97 Copyright (c) 2013-2016 Akira Yamaji % % Permission is hereby granted, free of charge, to any person obtaining a copy of this software % and associated documentation files (the "Software"), to deal in the Software without restriction, @@ -90,7 +90,7 @@ def_com(-4000)(_term,_jp_atom,_jp_atom_abs,_jp_bond,_cyc,_cyc_sB,_cyc_eB,_set_li _dl,_N,_O,_S,_H,_tmp_line,_chg_len,_get_len,_ring_len,_tmp_len,_rot_ang,_set_ang,_adj_ang,_chg_env, _tmp_env,_set_colorA,_set_colorB,_postA,_postB,_postC,_postD,_postE,_postF,_set_psA,_stack_reset, _set_clr,_set_adr,_mk_bond,_set_atom,_arg_ang,_chg_atom,_tmp_rot,_fuse,_push,_pop,_size_a); -def_com(1)(si,dl,dr,dm,tm,wf,wb,bd,bz,zf,zb,ov,dt,no,ar,vf,vb,wv,nl); +def_com(1)(si,dl,dr,dm,tm,wf,wb,bd,bz,zf,zb,dt,no,ar,vf,vb,wv,nl,si_,wf_,wb_,bd_); %------------------------------------------------------------------------------------------------- def parameter_list= sw_checklist,sw_numberA,sw_numberB,sw_mol_frame,sw_auxout,sw_solid,sw_expand,sw_MOLout, @@ -279,7 +279,7 @@ def PB(expr a,b)= cntBS:=cntBS+1; comMC[ab_num][cntBS]:=a; parMC[ab_num][cntBS]: def $$(text t)(expr e) = begingroup save cntBS; cntBS:=0; ab_num:=ab_num+1; if known e:: if numeric e:: - if (e>=si)and(e<=nl):: if e==dl:: for list==t:: PB(_dl,list) endfor + if (e>=si)and(e<=bd_):: if e==dl:: for list==t:: PB(_dl,list) endfor else:: for list==t:: PB(_set_adr,list) PB(_set_line,e) endfor fi elseif (e>=?3)and(e<=?20):: for list==t:: !?(list)(e-?3+3) endfor elseif e==Ph1:: !?(t)(6) PB(_dl,-2) PB(_dl,-4) @@ -382,8 +382,8 @@ def MCd(expr RW,RH)(expr FW,FH)(text s)= else: for i=1 upto 4: proc_skeleton; scaling; resize(RW,RH); size_setup; endfor fi fi font_setup; if sw_subst_off=1: cntA:=cntA_skeleton; cntB:=cntB_skeleton; fi - for i=1 upto cntB: if lineB[i]<>ov: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor - for i=1 upto cntB: if lineB[i]=ov: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor + for i=1 upto cntB: if lineB[i]<si_ : draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor + for i=1 upto cntB: if lineB[i]>=si_: draw_bond(i,sB[i],eB[i],angB[i],lineB[i]); fi endfor for i=1 upto cntA: if (sw_numberA>=1)and(i>=numberA_start)and(i<=numberA_end): if sw_numberA=2: nA:=i-numberA_start+1; @@ -605,9 +605,18 @@ if (nC>0)and(LN<>0): elseif LN=zb:wz_put(Le,sfB(Ls,ww,am),sfB(Ls,ww,ap),nB); elseif LN=dt:for i=0 step .75zebra_gap/length(Le-Ls) until 1: drawdot i[Ls,Le]; endfor elseif LN=wv:draw_wv; - elseif LN=ov:erase draw 0.15[Ls,Le]--0.85[Ls,Le] wpcs gap; draw pA Cp(nB); elseif LN=vf:draw pA Cp(nB);draw sfB(Le,gap,ANG-150)--Le--sfB(Le,gap,ANG+150) Cp(nB); - elseif LN=vb:draw pA Cp(nB);draw sfB(Ls,gap,ANG-30)--Ls--sfB(Ls,gap,ANG+30) Cp(nB); fi + elseif LN=vb:draw pA Cp(nB);draw sfB(Ls,gap,ANG-30)--Ls--sfB(Ls,gap,ANG+30) Cp(nB); + elseif LN=si_:erase draw 0.15[Ls,Le]--0.85[Ls,Le] wpcs .75gap; draw pA Cp(nB); + elseif LN=wf_:erase fill sfB(0.15[Ls,Le],.5ww,ap)--sfB(0.15[Ls,Le],.5ww,am)-- + sfB(0.85[Ls,Le],1.25ww,am)--sfB(0.85[Ls,Le],1.25ww,ap)--cycle; + fill Ls--sfB(Le,ww,am)--sfB(Le,ww,ap)--cycle; + elseif LN=wb_:erase fill sfB(0.15[Ls,Le],1.25ww,ap)--sfB(0.15[Ls,Le],1.25ww,am)-- + sfB(0.85[Ls,Le],.5ww,am)--sfB(0.85[Ls,Le],.5ww,ap)--cycle; + fill sfB(Ls,ww,am)--Le--sfB(Ls,ww,ap)--cycle; + elseif LN=bd_:erase draw 0.15[Ls,Le]--0.85[Ls,Le] wpcs 1.5gap; + draw pA withpen penrazor rotated ap scaled gap Cp(nB); + fi if (sw_numberB>=1)and(n>=numberB_start)and(n<=numberB_end): if sw_numberB=2: nB:=n-numberB_start+1; elseif sw_numberB=3: if numberB_end<cntB: nB:=numberB_end-n+1; else: nB:=cntB-n+1; fi |