%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % mcf2graph ver 5.12 Copyright (c) 2013-2024 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, % including without limitation the rights to use, copy, modify, merge, publish, distribute, % sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is % furnished to do so, subject to the following conditions: % % The above copyright notice and this permission notice shall be included in all copies % or substantial portions of the Software. % % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,EXPRESS OR IMPLIED, % INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,FITNESS FOR A PARTICULAR PURPOSE % AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, % DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. %------------------------------------------------------------------------------------------------- % mcf2graph is MetaPost macro package convert Molecular Coding Format(MCF) to graphic file % sgv/eps/png/mdl molfile %------------------------------------------------------------------------------------------------- % This package is located at : http://www.ctan.org/pkg/mcf2graph % Suggestion or request mail to : mcf2graph@gmail.com %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% message "* This is mcf2graph ver 5.12 2024.02.25"; tracingstats:=1; prologues:=3; warningcheck:=0; %------------------------------------------------------------------------------------------------- newinternal string EN_; numeric save_num[],pcode_com[][],pcode_par[][],pcode_cnt[],tbl_atom[],tbl_group[][],tbl_atom_wt[], tbl_atom_mi[],tbl_char_wd[],tbl_char_ht[],at_char[],mc_indent[],op_indent[],ex_indent[], ad_indent[],unit_lines[],info[],tbl_asc[],lenw[]; string row[][],save_str[],tbl_atom_str[],str_tbl[],arg_s[],mc[],ex[],ad[],op[],tag[],rw[], lib_tag[][],lib_val[][],mc,ex,ad,op,aux_delimiter,default_library,EN,FM,MW,MI,CAT,JN,CAS, USE,EXA,EXB,file_input,file_output,default_temp_file,mpfont,atomfont,tempc,temps,blanks, sC,sI,sS,sT,sV,forbiddens; pair save_pair[],msize,mposition,fsize,fmargin,save_mposition,?,?wf,?zf,?w,?z,?O,?NH; %------------------------------------------------------------------------------------------------- fig_num:=str_cnt:=tbl_cnt:=mangle:=sw_frame:=sw_trimming:=sw_ext_all:=sw_abbreviate:=sw_expand:=0; sw_comment:=sw_output:=sw_numbering:=tag_cnt:=rw_cnt:=pcode_all:=0; numbering_start:=1; numbering_end:=4095; %------------------------------------------------------------------------------------------------- aux_delimiter:=";"; blanks:= " "; forbiddens:=" &()[]{}^=;!'+,`~"; for s="No","EN","JN","MW","MI","FM","CAT","CAS","USE","EXA","EXB": tag[incr tag_cnt]:=s; endfor MW_n:=0; Fig:=1; Mcode:=2; Calc:=4; Info:=8; Table:=16; Report:=32; MOL2k:=64; MOL3k:=128; Atom:=8; Bond:=16; Group:=32; Mol:=64; Outside:=1; Inside:=2; Bothside:=Outside+Inside; %------------------------------------------------------------------------------------------------- PRS:=ASCII("(");PRE:=ASCII(")");BRS:=ASCII("{");BRE:=ASCII("}");BKS:=ASCII("[");BKE:=ASCII("]"); CMA:=ASCII(",");EQU:=ASCII("=");AST:=ASCII("*");SLS:=ASCII("/");GTN:=ASCII("<");LTN:=ASCII(">"); AMP:=ASCII("&");HSH:=ASCII("#");HAT:=ASCII("^");TLD:=ASCII("~");BQT:=ASCII("`");CLN:=ASCII(":"); AMK:=ASCII("@");QUT:=ASCII("'");BAR:=ASCII("|");PLS:=ASCII("+");MIS:=ASCII("-");BLK:=ASCII(" "); BSL:=ASCII("\");QES:=ASCII("?"); %------------------------------------------------------------------------------------------------- for s="??!","!?!","!!!","!?","?!","??","*/*","/*","*/","//","**","##","||","\\": rw[incr rw_cnt]:=s; lenw[rw_cnt]:=length(s); endfor %------------------------------------------------------------------------------------------------- let DIV= /; let MUL= *; let LT= <; let GT= >; let AND= &; let :: = : ; let == = =; let ef=elseif; let ISP=intersectionpoint; def ]]]=] ] ] enddef; let +++ = ++; let +- = +; %------------------------------------------------------------------------------------------------- def ext(text t)= sw_ext_all:=1; def EXT_ALL = t enddef; enddef; def ext_clear= sw_ext_all:=0; def EXT_ALL = enddef; enddef; def wpcs expr n= withpen pencircle scaled n enddef; def ppcs expr n= pickup pencircle scaled n enddef; def sbp(expr m,n)expr p=subpath(m*length(p),n*length(p)) of p enddef; def printf expr s= write s to file_output enddef; def warning(expr s)= message "% "&decimal(fig_num)&fdr(3)(incr warning_cnt)&")"&s; enddef; %------------------------------------------------------------------------------------------------- vardef frac primary n= n-floor n enddef; vardef iif(expr a,b,c)=if a: b else: c fi enddef; vardef subc(expr i,s)= substring(i-1,i) of s enddef; vardef sfrt(expr a,b,c)= a shifted ((b,0) rotated c) enddef; vardef fsr(expr n)(expr s)= (substring(0,n-length(s)) of blanks)&s enddef; vardef fsl(expr n)(expr s)= s&(substring(0,n-length(s)) of blanks) enddef; vardef fdr(expr n)(expr s)= if length(decimal(s))>n: substring (0,n) of decimal(s) else: fsr(n)(decimal(s)) fi enddef; vardef fdl(expr n)(expr s)= fsl(n)(decimal(s)) enddef; %================================================================================================= default_library:="main_lib.mcf"; default_temp_file:="temp.mcf"; mpfont:="uhvr8r"; atomfont:="draw"; defaultfont:=mpfont; %--default ahangle=45--------------------------------------------------------------------- if ahangle=1: outputformat:="png"; hppp:=vppp:=0.12; % png format(600dpi) ef ahangle=11: outputformat:="png"; hppp:=vppp:=0.06; % png format(1200dpi) ef ahangle=2: outputformat:="eps"; % eps format(.eps) ef ahangle=3: outputformat:="eps"; % eps format(.mps) ef ahangle=45: outputformat:="svg"; % svg format *default fi %--default ahlength=4--------------------------------------------------------------------- if ahlength=3: sw_output:=Fig; sw_expand:=1; % output figure(expanded) ef ahlength=4: sw_output:=Fig; % output figure *default ef ahlength=5: sw_output:=MOL2k; sw_expand:=1; % output MOL(V2000) ef ahlength=6: sw_output:=MOL3k; sw_expand:=1; % output MOL(V3000) ef ahlength=7: sw_output:=Report; % output report fi %-- default bboxmargin=2------------------------------------------------------------------ if bboxmargin=3: ext(defaultfont:=mpfont; defaultscale:=.3; label.rt(EN,(0,0));) ef bboxmargin=4: sw_output:=Fig+Calc; ext(defaultfont:=mpfont; defaultscale:=.3; label.rt(EN&" / "&MW&" / "&decimal(MW_n-scantokens(MW)),(0,0));) fi %--default outputtemplate:="%j-%3c."&"svg"------------------------------------------------ if outputformat="svg": outputtemplate:="s%3c-%{EN_}.svg"; ef outputformat="png": outputtemplate:="p%3c-%{EN_}.png"; ef (outputformat="eps")and(ahangle=3): outputtemplate:="%j-%3c.mps"; else: outputtemplate:="%j-%3c."&outputformat; fi %----------------------------------------------------------------------------------------- message "* jobname="&jobname; message "* numbersystem="&numbersystem; message "* outputformat="&outputformat; message "* outputtemplate="&outputtemplate; if ahlength=5: message "* output MOL file(V2000)"; message "* "&jobname&"-nnn-"&"EN"&".mol"; ef ahlength=6: message "* output MOL file(V3000)"; message "* "&jobname&"-nnn-"&"EN"&".mol"; ef ahlength=7: message "* output report file"; message "* file name="&jobname&"-report.txt"; fi clearit; %------------------------------------------------------------------------------------------------- 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_hashgap_bond:=0.12; ratio_hash_black:=0.4; ratio_wedge_bond:=0.12; ratio_atomgap_atom:=0.04; offset_thickness:=0.2; offset_bond_gap:=0.3; offset_hash_gap:=0.1; offset_atom:=0.8; offset_wedge:=0.4; thickness_frame:=0.2; max_blength:=10mm; blength:=mangle:=0; max_labelsize:=20mm; dottedline_gap:=1.5; fsize:=(30mm,20mm); fmargin:=(0.4mm,0.4mm); msize:=(1,1); mposition:=(0.5,0.5); ahangle:=45; ahlength:=4; defaultsize:=8; defaultscale:=1; labeloffset:=3; ext_defaultline:=0.5; lonepairdiam:=lonepairspace:=circlediam:=circlepen:=bboxmargin:=0; mc_length:=100; outputformatoptions:=""; %================================================================================================= pcode_emb_start:=1001; % 1001 => 1900 for embedded pcode (max 900) pcode_emi_start:=1901; % 1901 => 2000 for embedded internal pcode (max 100) pcode_usr_start:=2001; % 2001 => 3000 for user pcode (max 1000) pcode_int_start:=3000; % 3001 => 4000 for internal pcode (max 1000) %------------------------------------------------------------------------------------------------- def def_com(expr n)(text tx)= nA:=n; forsuffixes list=tx:: list:=nA; nA:=nA+1; endfor enddef; def_com(-4090)(_com,_jp_atom,_jp_absA,_jp_bond,_cyc,_cyc_sB,_cyc_eB,_set_line,_tmp_line,_chg_len, _get_len,_ring_len,_tmp_len,_rot_ang,_adj_ang,_chg_env,_tmp_env,_set_colorA,_set_colorB, _group_si,_group_dm,_group_wf,_group_zf,_set_adr,_mk_bond,_set_atom,_arrange_ang,_chg_atom, _tmp_rot,_fuse,_size_atom,_numeric,_jump_at,_set_add,_chg_add,_nop,_mark,_moff,_term,_len_s, _len_e,_len_ss,_len_ee,_group_s,_group_e,_rest,_charge,_from,_until, si,dl,dl_,dr,dr_,db,dm,dm_,tm,wf,wb,bd,bz,zf,zb,dt,wv,nl,vf,vb,nb,wf_r,wb_r,bd_r,arc_lb,arc_br, arc_lbr,arc_ltr,si_,wf_,wb_,zf_,zb_,wv_,bd_); %------------------------------------------------------------------------------------------------- def parameter_list= sw_numbering,sw_expand,sw_output,sw_ext_all,sw_frame,sw_trimming,sw_abbreviate,ratio_atom_bond, ratio_thickness_bond,ratio_char_bond,ratio_chain_ring,ratio_bondgap_bond,ratio_hash_black, ratio_hashgap_bond,ratio_thickness_char,ratio_wedge_bond,ratio_atomgap_atom,lonepairdiam, lonepairspace,offset_atom,offset_wedge,max_blength,offset_hash_gap,offset_bond_gap, thickness_frame,offset_thickness,numbering_start,numbering_end,defaultsize,defaultscale, labeloffset,mangle,blength,fsize,fmargin,msize,mposition,defaultfont,atomfont,dottedline_gap enddef; %------------------------------------------------------------------------------------------------- def init_par(text t)= nA:=nB:=nC:=0; for list=t: if numeric list: save_num[incr nA]:=list; ef pair list: save_pair[incr nB]:=list; ef string list: save_str[incr nC]:=list; fi endfor enddef; %------------------------------------------------------------------------------------------------- def store_par(text t)= nA:=nB:=nC:=0; for list=t: if numeric list: if save_num[incr nA]<>list: save_num[nA]:=list; fi ef pair list: if save_pair[incr nB]<>list: save_pair[nB]:=list; fi ef string list: if save_str[incr nC]<>list: save_str[nC]:=list; fi fi endfor enddef; %------------------------------------------------------------------------------------------------- def restore_par(text t)= nA:=nB:=nC:=0; forsuffixes list=t: if numeric list: if list<>save_num[incr nA]: list:=save_num[nA]; fi ef pair list: if list<>save_pair[incr nB]: list:=save_pair[nB]; fi ef string list: if list<>save_str[incr nC]: list:=save_str[nC]; fi fi endfor enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def beginfigm= begingroup save ','',`,``,//,@,#,#@,##,\,\\,\*,|=,|<,**,++,_,f_ext,blen,ext,add,ang_br,fw_n,bw_n, info_cnt,bond_cntA,firstc,warning_cnt,hideH,hideH_cnt,cntM,cntA,cntB, minX,minY,maxX,maxY,posA,posM,lineB,sB,eB,angB,angA,lenB,angX,numS,sumA,bond_num,wdM,htM, chargeA,addA,add_rot,mol_pic,color_list,filter_s,no,mw,mi,fm; numeric hideH[],lineB[],sB[],eB[],angB[],angA[],lenB[],angX[],strA[],sumA[],bond_num[], wdM[],htM[],chargeA[],addA[],add_rot[]; pair posA[],posM[][]; string mi,no,fm,mw,firstc,filter_s; picture mol_pic[]; color color_list[]; %----------------------------------------------------------------------------------------------- store_par(parameter_list); no:=mc:=ex:=ad:=op:=temps:=mw:=mi:=fm:=filter_s:=""; EN:=JN:=MW:=FM:=MI:=CAS:=CAT:=EXA:=EXB:=USE:="-"; f_ext:=cntM:=mc_row:=ex_row:=ad_row:=op_row:=info_cnt:=err_cnt:=0; let ext=ext_to_fig; let add=add_to_molecule; let ++=add_to_molecule; let **=ext_to_fig; def ' = define_parts enddef; def '' = readm enddef; def \ = drawm enddef; def \\ = putm enddef; def \* = checkm enddef; def $ = getm enddef; def @ expr p = mposition:=p; enddef; def # expr p = fsize:=p; enddef; def #@ expr p = fmargin:=p; enddef; def `(expr s) = define_group_string(s)() enddef; def `` = define_group_string enddef; def ## expr p = msize:=p; enddef; def |=(expr n) = blength:=n; enddef; def |<(expr n) = max_blength:=n; enddef; def _ expr s = EN:=s; enddef; pcode_num:=pcode_usr_start; pcode_int:=pcode_int_start; fig_num:=fig_num+1; mol_pic[0]:=nullpicture; enddef; %------------------------------------------------------------------------------------------------- def endfigm= %-------------------------------------------------------------------------------------------- if cntM>=1: %-------------------------------------------------------------------------------------------- if scan_bit(sw_output,Fig): if EN<>"-": EN_:=forbidden_to_underbar(EN); fi beginfig(fig_num) %------------------------------------------------------------------------------------------ if sw_ext_all=1: ext_to_fig(EXT_ALL); fi if sw_trimming>=1: nA:=nC:=4095; nB:=nD:=-4095; for i=1 upto cntM: if xpart(posM[1][i])nB: nB:=xpart(posM[2][i]); fi if ypart(posM[1][i])nD: nD:=ypart(posM[2][i]); fi endfor fig_wd:=nB-nA+2xpart(fmargin); fig_ht:=nD-nC+2ypart(fmargin); fsize:=(fig_wd,fig_ht); for i=1 upto cntM: posM[0][i]:=posM[0][i]+fmargin-(nA,nC); posM[1][i]:=posM[1][i]+fmargin-(nA,nC); endfor fi %---------------------------------------------------------------------------------------- if scan_bit(sw_frame,Outside): draw_frame((0,0),fsize,thickness_frame); else: draw_corner(fsize,0.004); fi if scan_bit(sw_frame,Inside): draw_frame(fmargin,fsize-2fmargin,thickness_frame); fi for i=1 upto cntM: addto currentpicture also mol_pic[i] shifted posM[0][i]; mol_pic[i]:=nullpicture; if scan_bit(sw_frame,Mol): ext(draw_frame(p[i],(w[i],h[i]),thickness_frame)) fi endfor if f_ext=1: addto currentpicture also mol_pic[0]; mol_pic[0]:=nullpicture; fi %----------------------------------------------------------------------------------------- endfig; clearit; fi %--------------------------------------------------------------------------------------------- if scan_bit(sw_output,Report): proc_report_out; fi if scan_bit(sw_output,MOL2k): proc_mol_out(2000); fi if scan_bit(sw_output,MOL3k): proc_mol_out(3000); fi %--------------------------------------------------------------------------------------------- ef scan_bit(sw_output,Fig): EN_:="no_figure"; beginfig(fig_num) defaultscale:=.6; draw_frame((0,0),fsize,thickness_frame) label("no figure",0.5fsize); endfig; clearit; fi %--------------------------------------------------------------------------------------------- if err_cnt=0: if scan_bit(sw_output,Mcode): proc_mc_out; message "["&decimal(fig_num)&"]:"&EN; fi if scan_bit(sw_output,Report): proc_report_out; message "["&decimal(fig_num)&"]:"&EN; fi if scan_bit(sw_output,MOL2k): proc_mol_out(2000); message "["&decimal(fig_num)&"]:"&EN; fi if scan_bit(sw_output,MOL3k): proc_mol_out(3000); message "["&decimal(fig_num)&"]:"&EN; fi fi %--------------------------------------------------------------------------------------------- restore_par(parameter_list); endgroup; enddef; %================================================================================================= def readm(text s)= save fw_n,bw_n; for list=s: fw_n:=scan_char(" ",list,1,1)-1; bw_n:=scan_char(" ",list,-1,1); mc_indent[incr mc_row]:=fw_n; mc[mc_row]:=substring(fw_n,bw_n) of list; mc:=mc&mc[mc_row]; endfor enddef; %================================================================================================= def getm(expr a)=if string a: read_unit(get_adr("EN",a)) ef numeric a: read_unit(a) fi enddef; %------------------------------------------------------------------------------------------------- def read_unit(expr n)= save nF; nF:=0; if (n>=1)and(n<=ucount): for i=1 upto info[n]: for j=1 upto tag_cnt: if lib_tag[n][i]=tag[j]: scantokens(tag[j]):=lib_val[n][i]; fi endfor endfor for i=1 upto unit_lines[n]: temps:=row[n][i]; firstc:=subc(1,temps); exitif firstc=";"; if firstc=":": nF:=1; ef firstc="=": nF:=2; ef firstc="*": nF:=3; ef firstc="+": nF:=4; ef firstc="%": else: fw_n:=scan_char(" ",temps,1,1)-1; temps:=substring(fw_n,length(temps)) of temps; if nF=1: mc_indent[incr mc_row]:=fw_n; mc[mc_row]:=temps; mc:=mc&temps; ef nF=2: op_indent[incr op_row]:=fw_n; op[op_row]:=temps; op:=op&temps; ef nF=3: ex_indent[incr ex_row]:=fw_n; ex[ex_row]:=temps; ex:=ex&temps; ef nF=4: ad_indent[incr ad_row]:=fw_n; ad[ad_row]:=temps; ad:=ad&temps; fi fi endfor fi enddef; %================================================================================================= vardef get_adr(expr t,v)= save adr_n; adr_n:=0; for n=1 upto ucount: for i=1 upto info[n]: for j=1 upto tag_cnt: if (lib_tag[n][i]=t)and(lib_val[n][i]=v): adr_n:=n; fi endfor exitif adr_n>=1; endfor endfor message if adr_n>1: "* found [" else: "* not found [" fi &v&"]"&"("&decimal(adr_n)&")"; adr_n enddef; %------------------------------------------------------------------------------------------------- def putm= if op_row>=1: scantokens(op) fi if mc_row>=1: if checkm(mc)=0: drawm(scantokens(mc)) fi fi if ad_row>=1: add(scantokens(ad)) fi if ex_row>=1: ext(scantokens(ex)) fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% vardef define_parts(text t)= pcode_num:=pcode_num+-1; read_mcf(pcode_num)(t); pcode_num enddef; vardef abs_adress primary n = if n LT 0:: (n+-360)-4095 else:: n-4095 fi enddef; primarydef a from_until b = (_from,a),(_until,b) enddef; primarydef a op_plus b = define_parts(a,b) enddef; tertiarydef a bond__bond b = (a,b) enddef; tertiarydef a bond___bond b = (a+-2000,b) enddef; tertiarydef a bond____bond b = (a+-2000,b+-2000) enddef; tertiarydef a op_equ b = if (known a)and(known b):: change_bond(a,b) else:: _nop fi enddef; tertiarydef a op_col b = if (known a)and(known b):: change_atom(a,b) else:: _nop fi enddef; tertiarydef a op_hat b = if known b:: (_tmp_rot,b),a else:: _nop,a fi enddef; tertiarydef a op_til b = if known b:: (_tmp_line,b),a else:: _nop,a fi enddef; tertiarydef a op_lth b = if known b:: (_tmp_env,b),a else:: _nop,a fi enddef; tertiarydef a op_bqu b = if known b:: (_tmp_len,b),a else:: _nop,a fi enddef; def rot_angle primary n = (_rot_ang,n) enddef; def cyc_atom primary n = (_cyc,n) enddef; def jump_atom_abs primary a = if numeric a:: (_jp_atom,$a) ef pair a:: (_jp_atom,$1),<$0,angle(a)~0`length(a),<$0 fi enddef; def jump_atom primary a = if numeric a:: (_jp_atom,a) ef pair a:: <$0,angle(a)~0`length(a),<$0 fi enddef; def chg_length primary n = (_com,_len_s),(_chg_len,n) enddef; def group_si secondary n = if known n:: (_group_si,n) else:: _nop fi enddef; def group_dm secondary n = if known n:: (_group_dm,n) else:: _nop fi enddef; def group_wf secondary n = if known n:: (_group_wf,n) else:: _nop fi enddef; def group_zf secondary n = if known n:: (_group_zf,n) else:: _nop fi enddef; def group_wv secondary n = /n~wv enddef; def group_nb secondary n = /n~nb enddef; %================================================================================================= def read_mcf(expr n)(text t)= begingroup if unknown inside_mc:: save /,//,/*,*/,**,*/*,~,^,`,<,>,:,=,+,\,\\,*\,\*,*\*,@,@$,$,&,&$,#,##,{,},|,||,_, --,---,----,CP,CA,CC,DL,FR,inside_mc; inside_mc:=1; | :=mark_adress; || :=reset_adress; ##:=reset_length; _:=NO_ATOM; \:=0; \\:=zero_dm; *\:=zero_wf; \*:=zero_zf; *\*:=zero_wv; let = ==op_equ; let : ==op_col; let ^ ==op_hat; let ~ ==op_til; let > ==op_lth; let `==op_bqu; let -- == bond__bond; let --- == bond___bond; let ---- == bond____bond; let + ==op_plus; let } ==); let @$ ==jump_atom_abs; let < ==rot_angle; let @ ==jump_atom; let & ==cyc_atom; let # ==chg_length; let / ==group_si; let // ==group_dm; let */ ==group_wf; let /* ==group_zf; let */*==group_wv; let **==group_nb; let CP == pcode_add; let CA == pcode_add_adr; let FR == fuse_ring_bonds; def DL(expr p)==CA(_set_line,dl,p) enddef; def CB(expr p)==CP(_mk_bond,p) enddef; def CC(expr p)==CP(_com,p) enddef; def $==abs_adress enddef; def &$==&.$ enddef; def {==read_number( enddef; fi %---------------------------------------------------------------------------------------------- pcode_cnt[n]:=0; for list==t:: if known list:: if pair list:: pcode_cnt[n]:= pcode_cnt[n]+-1; pcode_com[n][pcode_cnt[n]]:=xpart(list); pcode_par[n][pcode_cnt[n]]:=ypart(list); ef numeric list:: if list==_nop:: message "unknown command in "AND decimal(n); ef list>=pcode_emb_start:: expand_pcode(n,list); else:: pcode_cnt[n]:=pcode_cnt[n]+-1; pcode_com[n][pcode_cnt[n]]:=_mk_bond; pcode_par[n][pcode_cnt[n]]:=list; fi fi else:: message "unknown command in "AND decimal(n); fi endfor endgroup enddef; %------------------------------------------------------------------------------------------------- def expand_pcode(expr n,a)= if n==0:: for i==1 upto pcode_cnt[a]:: if pcode_com[a][i]>=pcode_emb_start:: expand_pcode(n,pcode_com[a][i]); else:: pcode_cnt[n]:=pcode_cnt[n]+-1; pcode_com[n][pcode_cnt[n]]:=pcode_com[a][i]; pcode_par[n][pcode_cnt[n]]:=pcode_par[a][i]; fi endfor else:: pcode_cnt[n]:=pcode_cnt[n]+-1; pcode_com[n][pcode_cnt[n]]:=a; fi enddef; %------------------------------------------------------------------------------------------------- vardef read_number(text t)= save :,'; let : == from_until; def ' == +-2000 enddef; pcode_int:=pcode_int+-1; nA:=0; for list==t:: if known list:: if numeric list:: if list==_nop:: message "unknown command in "AND decimal(pcode_int); else:: nA:=nA+-1; pcode_com[pcode_int][nA]:=_numeric; pcode_par[pcode_int][nA]:=list; fi ef pair list:: if xpart(list)==_from:: nB:=ypart(list); ef xpart(list)==_until:: nC:=ypart(list); for i==nB upto nC:: nA:=nA+-1; pcode_com[pcode_int][nA]:=_numeric; pcode_par[pcode_int][nA]:=i; endfor else:: nA:=nA+-1; pcode_com[pcode_int][nA]:=xpart(list); pcode_par[pcode_int][nA]:=ypart(list); fi fi else:: message "unknown command in "AND decimal(pcode_int); fi endfor pcode_cnt[pcode_int]:=nA; pcode_int enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def fuse_ring(expr a,b) = CP(_jp_bond,a) CP(_rot_ang,180) CP(_get_len,a) CC(_len_s) CP(_chg_len,_ring_len) for i==1 upto b-2:: CB(360 DIV b) endfor CC(_len_e) if a<=0:: CP(_cyc_eB,a-b+-2) else:: CP(_cyc_eB,a) fi enddef; %------------------------------------------------------------------------------------------------- def fuse_ring_bonds(expr s,e,b,c) = CP(_jp_bond,s) CP(_rot_ang,180) CC(_len_s) if b==6:: CP(_chg_len,1) for i==1 upto c-1:: CB(60) endfor ef b==5:: if c==2:: CP(_chg_len,1.25) CB(80) ef c==3:: CP(_chg_len,1.1) CB(78) CB(72) fi ef b==4:: CP(_chg_len,1.225) CB(105) fi CC(_len_e) if e<=0:: CP(_cyc_eB,e-c+-1) else:: CP(_cyc_eB,e) fi enddef; %------------------------------------------------------------------------------------------------- def fuse_ring_size(expr a,b,c) = CP(_jp_bond,a) CP(_rot_ang,180) CC(_len_s) CP(_chg_len,c DIV 10) if b==5:: CB(72-((c-9) MUL 1.5)) CB(72+-(c-9)) CB(72+-(c-9)) ef b==6:: CB(60-(c-8)) for i==1 upto 3:: CB(60+-((c-8) DIV 2)) endfor ef b==7:: CB(360 DIV 7-(c-8)) for i==1 upto 4:: CB(360 DIV 7+-((c-8) DIV 2.5)) endfor ef b==8:: CB(45-(c-8)) for i==1 upto 5:: CB(45+-((c-8) DIV 3)) endfor fi CC(_len_e) if a<=0:: CP(_cyc_eB,a-b+-2) else:: CP(_cyc_eB,a) fi enddef; %================================================================================================= vardef change_bond(expr a,b) = if known b:: pcode_int:=pcode_int+-1; nC:=0; if numeric b:: if (b>=si)and(b<=bd_):: if a>=pcode_int_start:: for i==1 upto pcode_cnt[a]:: if pcode_com[a][i]==_numeric:: if pcode_par[a][i]<=1800:: CA(_set_line,b,pcode_par[a][i]) ef b==dl:: CA(_set_line,dr,pcode_par[a][i]-2000) ef b==dr:: CA(_set_line,dl,pcode_par[a][i]-2000) else:: CA(_set_line,b,pcode_par[a][i]-2000) fi fi endfor else:: CP(_set_adr,a) CP(_set_line,b) fi elseif (b>=?3)and(b<=?8[15]):: if numeric a:: if a>=pcode_int_start:: for i==1 upto pcode_cnt[a]:: if pcode_com[a][i]==_numeric:: if b==Ph1:: fuse_ring(pcode_par[a][i],6) DL(-2) DL(-4) ef b==Ph2:: fuse_ring(pcode_par[a][i],6) DL(-1) DL(-3) DL(-5) ef (b>=?5[11])and(b<=?8[15]):: fuse_ring_size(a,pcode_com[b][1],pcode_par[b][1]) else:: fuse_ring(pcode_par[a][i],b-?3+-3) fi else:: if b==?6:: if (pcode_com[a][i]<=1800)and(pcode_par[a][i]<=1800):: FR(pcode_com[a][i],pcode_par[a][i],6,4) ef pcode_par[a][i]<=1800:: FR(pcode_com[a][i]-2000,pcode_par[a][i],6,3) else:: FR(pcode_com[a][i]-2000,pcode_par[a][i]-2000,6,2) fi ef b==?5:: if (pcode_com[a][i]<=1800)and(pcode_par[a][i]<=1800):: FR(pcode_com[a][i],pcode_par[a][i],5,3) ef pcode_par[a][i]<=1800:: FR(pcode_com[a][i]-2000,pcode_par[a][i],5,2) fi ef b==?4:: FR(pcode_com[a][i],pcode_par[a][i],4,2) ef b==Ph1:: FR(pcode_com[a][i],pcode_par[a][i],6,4) DL(-1) DL(-3) ef b==Ph2:: FR(pcode_com[a][i],pcode_par[a][i],6,4) DL(-2) DL(-4) fi fi endfor else:: if b==Ph1:: fuse_ring(a,6) DL(-2) DL(-4) ef b==Ph2:: fuse_ring(a,6) DL(-1) DL(-3) DL(-5) ef (b>=?5[11])and(b<=?8[15]):: fuse_ring_size(a,pcode_com[b][1],pcode_par[b][1]) else:: fuse_ring(a,b-?3+-3) fi fi ef pair a:: if b==?6:: if (xpart a<=1800)and(ypart a<=1800):: FR(xpart a,ypart a,6,4) ef ypart a<=1800:: FR((xpart a)-2000,ypart a,6,3) else:: FR((xpart a)-2000,(ypart a)-2000,6,2) fi ef b==?5:: if (xpart a<=1800)and(ypart a<=1800):: FR(xpart a,ypart a,5,3) ef ypart a<=1800:: FR((xpart a)-2000,ypart a,5,2) fi ef b==?4:: FR(xpart a,ypart a,4,2) fi fi fi elseif color b:: cntC:=cntC+-1; color_list[cntC]:=b; CA(_set_colorB,cntC,a) fi pcode_cnt[pcode_int]:=nC; pcode_int fi enddef; %------------------------------------------------------------------------------------------------- vardef change_atom(expr a,b)= if known b:: pcode_int:=pcode_int+-1; nC:=0; if numeric b:: if (b GT pcode_emb_start)and(b<=pcode_atm_end):: CA(_chg_atom,b,a) ef b==NH:: CA(_chg_atom,N,a) if sw_expand==0:: CP(_tmp_line,nl) fi CC(_group_s) CA(_group_si,H,a) CC(_group_e) ef b==N?:: CA(_chg_atom,N,a) CC(_group_s) CA(_group_si,_,a) CC(_group_e) ef b==N?2:: CA(_chg_atom,N,a) CC(_group_s) CA(_group_si,!,a) CC(_group_e) ef b==??:: CP(_tmp_rot, 35) CC(_group_s) CA(_group_si,_,a) CC(_group_e) CP(_tmp_rot,-35) CC(_group_s) CA(_group_si,_,a) CC(_group_e) ef b==n_:: CC(_group_s) CP(_set_add,MIS) CP(_chg_add,a) CC(_group_e) ef b==p_:: CC(_group_s) CP(_set_add,PLS) CP(_chg_add,a) CC(_group_e) fi ef pair b:: CC(_group_s) if a>=pcode_emb_start:: for i==1 upto pcode_cnt[a]:: if pcode_com[a][i]==_numeric:: if pcode_par[a][i]<=1800:: CA(xpart(b),ypart(b),pcode_par[a][i]) ef xpart(b)==_group_wf:: CA(_group_zf,ypart(b),pcode_par[a][i]-2000) ef xpart(b)==_group_zf:: CA(_group_wf,ypart(b),pcode_par[a][i]-2000) else:: CA(xpart(b),ypart(b),pcode_par[a][i]) fi else:: CP(pcode_com[a][i],pcode_par[a][i]) fi endfor else:: CA(xpart(b),ypart(b),a) fi CC(_group_e) ef color b:: cntC:=cntC+-1; color_list[cntC]:=b; CA(_set_colorA,cntC,a) fi pcode_cnt[pcode_int]:=nC; pcode_int fi enddef; %------------------------------------------------------------------------------------------------- def pcode_add(expr c,p)= nC:=nC+-1; pcode_com[pcode_int][nC]:=c; pcode_par[pcode_int][nC]:=p; enddef; def pcode_add_adr(expr c,p,a)= if a>=pcode_emb_start:: for i==1 upto pcode_cnt[a]:: if pcode_com[a][i]==_numeric:: pcode_add(_set_adr,pcode_par[a][i]) pcode_add(c,p) else:: pcode_add(pcode_com[a][i],pcode_par[a][i]) fi endfor else:: pcode_add(_set_adr,a) pcode_add(c,p) fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def ext_setup= pickup pencircle scaled ext_defaultline; dotlabeldiam:=3; labeloffset:=3; em:=defaultscale*defaultsize; defaultfont:=mpfont; let # = scaled; let << = rotated; let => = shifted; __ = (1,0); An:=cntA; Bn:=cntB; primarydef a /* b = point b of a enddef; enddef; %------------------------------------------------------------------------------------------------- def add_to_molecule(text t)= begingroup save w,h,n,l,p,am,aw,A,B,An,Bn,plus,minus,lonepair,__,#,=>,<<,/*; numeric A[]dir,B[]up,A[]ang,B[]ang; pair __,p[],A[],B[]s,B[]e,B[]m,A[]up,A[]left,A[]right,A[]down,B[]up,B[]left,B[]right,B[]down; path B[]; def plus = circled_plus_add enddef; def minus = circled_minus_add enddef; def lonepair = lone_pair_add enddef; ext_setup; w:=mol_wd; h:=mol_ht; l:=blen; aw:=atom_wd; p0:=(minX,minY); lonepairdiam:=0.3aw; lonepairspace:=.7aw; circlediam:=.6aw; circlepen:=.2; for i=1 upto cntA: A[i]:=posA[i]; A[i]ang:=angX[i]; A[i]up:=dir(angX[i]); A[i]left:=dir(angX[i]+90); A[i]right:=dir(angX[i]-90); A[i]down:=dir(angX[i]+180); endfor for i=1 upto cntB: B[i]s:=posA[sB[i]]; B[i]e:=posA[eB[i]]; B[i]m:=0.5[B[i]s,B[i]e]; B[i]:=B[i]s--B[i]e; B[i]ang:=angB[i]; B[i]up:=dir(angB[i]); B[i]down:=dir(angB[i]+180); B[i]left:=dir(angB[i]+90); B[i]right:=dir(angB[i]-90); endfor t addto mol_pic[cntM] also currentpicture; clearit; endgroup; enddef; %------------------------------------------------------------------------------------------------- def ext_to_fig(text t)= begingroup save w,h,An,Bn,wd,ht,n,p,am,aw,__,#,<<,=>,/*; pair __,p[]; ext_setup; w:=xpart(fsize); h:=ypart(fsize); w0:=w-2xpart(fmargin); h0:=h-2ypart(fmargin); p0:=fmargin; aw:=atom_wd; n:=cntM; for i=1 upto n: p[i]:=posM[1][i]; w[i]:=wdM[i]; h[i]:=htM[i]; endfor t addto mol_pic[0] also currentpicture; clearit; f_ext:=1; endgroup; enddef; %------------------------------------------------------------------------------------------------- vardef circled_plus_add= nA:=circlediam; nB:=circlepen; image(draw fullcircle scaled nA wpcs nB; draw (-.5nA,0)--(.5nA,0) wpcs nB; draw (0,-.5nA)--(0,.5nA) wpcs nB;) enddef; %------------------------------------------------------------------------------------------------- vardef circled_minus_add= nA:=circlediam; nB:=circlepen; image(draw fullcircle scaled nA wpcs nB; draw (-.5nA,0)--(.5nA,0) wpcs nB;) enddef; %------------------------------------------------------------------------------------------------- vardef lone_pair_add expr n= image(draw (0,0) wpcs lonepairdiam; draw ((0,lonepairspace) rotated n) wpcs lonepairdiam;) enddef; %================================================================================================= def drawm(text t)= begingroup save f_bra,temp_strA,temp_lenE,temp_lenF,temp_cntB,f_term,f_at,f_lineT,f_rotT,angL,lenL,cpos, tpos,f_lenT,f_envT,factor,m_wd,m_ht,raise_pos,slen,sdir,char_wd,char_ht,tcol,f_col,knownA, group_num,markA,markB,saveA,saveB,bondL,lenT,lineT,angT,rotT,envT,envB,rate_cr,posBs,posBe, group_par,group_cnt,group_com,colorA,colorB,aW,aH,fW,fH,hW,hW,hH,qH,fP,hP,ww,aw,ap,am, Ls,Le,pA,zA,zL; numeric group_com[][],group_par[][],group_cnt[],colorA[],colorB[]; pair cpos,tpos,raise_pos,posBs,posBe,pA,Ls,Le; path frameA[],zA,zL; %----------------------------------------------------------------------------------------------- if sw_expand=1: rate_cr:=1; else: rate_cr:=-ratio_chain_ring; fi cntA:=cntB:=cntC:=group_num:=0; str_tbl[0]:="C"; str_cnt:=2000; %----------------------------------------------------------------------------------------------- fig_wd:=xpart(fsize); fig_ht:=ypart(fsize); %=============================================================================================== read_mcf(0)(t,(_com,_term)); proc_bond_atom(0)(1); if (group_num>0)and(not scan_bit(sw_abbreviate,Group)): expand_group(1); fi %-scaling--------------------------------------------------------------------------------------- if blength>1: blen:=blength; proc_size_setup; proc_skeleton(0); proc_scaling; elseif blength>0: blen:=fig_wd*blength; proc_size_setup; proc_skeleton(0); proc_scaling; else: blen:=3mm; proc_size_setup; if xpart(msize)<1: m_wd:=fig_wd*xpart(msize); else: m_wd:=fig_wd; fi if ypart(msize)<1: m_ht:=fig_ht*ypart(msize); else: m_ht:=fig_ht; fi for i=1 upto 6: proc_skeleton(0); proc_scaling; if (mol_ht/mol_wd)>(m_ht/m_wd): if ypart(msize)>1: factor:=ypart(msize)/mol_ht; else: factor:=((fig_ht-2ypart(fmargin))*ypart(msize))/mol_ht; fi else: if xpart(msize)>1: factor:=xpart(msize)/mol_wd; else: factor:=((fig_wd-2xpart(fmargin))*xpart(msize))/mol_wd; fi fi exitif (factor>=1-eps)and(factor<=1+eps); blen:=blen*factor; proc_size_setup; endfor if blen>max_blength: blen:=max_blength; proc_size_setup; proc_skeleton(0); proc_scaling; fi fi %----------------------------------------------------------------------------------------------- for i=1 upto cntA: if addA[i]<>0: tempc:=char(addA[i]); if tempc="+": chargeA[i]:=1; ef tempc="-": chargeA[i]:=-1; else: chargeA[i]:=0; fi else: chargeA[i]:=0; fi endfor %=============================================================================================== if scan_bit(sw_output,Fig): %-draw atom----------------------------------------------------------------------------------- if sw_numbering=0: for i=1 upto cntA: if strA[i]<>0: draw_atom(i); fi endfor fi %-draw add to atom---------------------------------------------------------------------------- if (not scan_bit(sw_numbering,Atom))and(not scan_bit(sw_numbering,Bond)): for i=1 upto cntA: if addA[i]<>0: draw_char(char(addA[i]),sfrt(posA[i],atom_wd,angX[i]+add_rot[i])); fi endfor fi %-draw bond----------------------------------------------------------------------------------- for i=1 upto cntB: if lineB[i]=si_: draw_bond(i); fi endfor %-atom numbering------------------------------------------------------------------------------ if scan_bit(sw_numbering,Atom): for i=1 upto cntA: if (i>=numbering_start)and(i<=numbering_end): defaultscale:=.18blen/defaultsize; nH:=1.2defaultsize*defaultscale; if i<=9: nW:=nH; ef i<=99: nW:=1.3nH; else: nW:=1.9nH; fi erase fill unitsquare xscaled nW yscaled nH shifted (posA[i]-(nW/2,nH/2)); draw unitsquare xscaled nW yscaled nH shifted (posA[i]-(nW/2,nH/2)) wpcs 0.1; label(decimal(i),posA[i]); fi endfor fi %-bond numbering------------------------------------------------------------------------------ if scan_bit(sw_numbering,Bond): for i=1 upto cntB: if (i>=numbering_start)and(i<=numbering_end): defaultscale:=.18blen/defaultsize; nH:=1.2defaultsize*defaultscale; if i<=9: nW:=nH; ef i<=99: nW:=1.3nH; else: nW:=1.9nH; fi nH:=defaultsize*defaultscale; tpos:=.5[posA[sB[i]],posA[eB[i]]]; erase fill unitsquare xscaled nW yscaled nH shifted (tpos-(nW/2,nH/2)); draw unitsquare xscaled nW yscaled nH shifted (tpos-(nW/2,nH/2)) wpcs 0.1; label(decimal(i),tpos); fi endfor fi %--------------------------------------------------------------------------------------------- if xpart(mposition)>1: nX:=xpart(mposition)-minX; else: nX:=xpart(fmargin)-minX+(fig_wd-mol_wd-2xpart(fmargin))*xpart(mposition); fi if ypart(mposition)>1: nY:=ypart(mposition)-minY; else: nY:=ypart(fmargin)-minY+(fig_ht-mol_ht-2ypart(fmargin))*ypart(mposition); fi posM[0][incr cntM]:=(nX,nY); posM1[cntM]:=(minX+nX,minY+nY); posM2[cntM]:=(maxX+nX,maxY+nY); wdM[cntM]:=mol_wd; htM[cntM]:=mol_ht; mol_pic[cntM]:=currentpicture; clearit; fi if sw_output>=Calc: proc_calc(0); fi endgroup; enddef; %------------------------------------------------------------------------------------------------- def expand_group(expr n)= save_group_num:=group_num; save_pcode_cnt:=pcode_cnt[0]; for i=n upto group_num: for j=1 upto group_cnt[i]: if group_com[i][j]>=pcode_emb_start: expand_pcode(0,group_com[i][j]); else: pcode_com[0][incr pcode_cnt[0]]:=group_com[i][j]; pcode_par[0][pcode_cnt[0]]:=group_par[i][j]; fi endfor endfor proc_bond_atom(0)(save_pcode_cnt+1); if group_num>save_group_num: expand_group(save_group_num+1); fi enddef; %================================================================================================= def draw_frame(expr o,p,n)= draw ((0,0)--(xpart p,0)--p--(0,ypart p)--cycle) shifted o withpen pensquare scaled n; enddef; %------------------------------------------------------------------------------------------------- def draw_corner(expr p,n)= draw (0,0) wpcs n; draw(xpart p,0) wpcs n; draw p wpcs n; draw(0,ypart p) wpcs n; enddef; %------------------------------------------------------------------------------------------------- def proc_size_setup= atom_wd:= blen*ratio_atom_bond+offset_atom; wedge_wd:= blen*ratio_wedge_bond+offset_wedge; hash_gap:= blen*ratio_hashgap_bond+offset_hash_gap; bondgap:= blen*ratio_bondgap_bond+offset_bond_gap; bond_pen_wd:= blen*ratio_thickness_bond+offset_thickness; enddef; %------------------------------------------------------------------------------------------------- def proc_scaling= minX:=minY:=4095; maxX:=maxY:=-4095; for i=1 upto cntA: nX:=xpart(posA[i]); nY:=ypart(posA[i]); if strA[i]<>0: nU:=nD:=nP:=nL:=nR:=0; for j=1 upto length(str_tbl[strA[i]]): tempc:=subc(j,str_tbl[strA[i]]); if tempc="^": nU:=.5atom_wd; ef tempc="_": nD:=.5atom_wd; ef (tempc<>"{")and(tempc<>"}"): nP:=nP+atom_wd*tbl_char_wd[ASCII(tempc)]; fi endfor if (angX[i]<=90)or(angX[i]>=270): nR:=nP; else: nL:=nP; fi if (nX-nL+.5atom_wd)maxX: maxX:=nX+nR-.5atom_wd; fi if (nY-nD-.5atom_wd)maxY: maxY:=nY+nU+.5atom_wd; fi else: if nXmaxX: maxX:=nX; fi if nYmaxY: maxY:=nY; fi fi endfor mol_wd:=maxX-minX; mol_ht:=maxY-minY; enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def proc_bond_atom(expr a)(expr n)= f_bra:=f_term:=rotT:=f_lineT:=f_rotT:=f_lenT:=f_envT:=envT:=envB:=temp_strA:=f_at:=0; bondL:=rate_cr; lenT:=rate_cr; sB[0]:=0; eB[0]:=1; lineT:=si; addAT:=markA:=markB:=saveA:=saveB:=0; %----------------------------------------------------------------------------------------------- for i=n upto pcode_cnt[a]: nC:=pcode_com[a][i]; nP:=pcode_par[a][i]; if nC=_mk_bond: if (nP=0)and(rotT<>0): rotT:=0; fi add_atom(0); ef nC=_set_adr: adrT:=nP; ef nC=_com: if nP=_mark: saveA:=markA; saveB:=markB; markA:=cntA; markB:=cntB; ef nP=_rest: markA:=saveA; markB:=saveB; ef nP=_moff: markA:=markB:=0; ef nP=_term: termA; ef nP=_len_s: temp_lenE:=bondL; ef nP=_len_e: bondL:=temp_lenE; ef nP=_len_ss: temp_lenF:=bondL; ef nP=_len_ee: bondL:=temp_lenF; ef nP=_group_s: f_at:=1; if lineT<>si: f_lineT:=1; fi if rotT<>0: f_rotT:=1; fi if lenT<>rate_cr: f_lenT:=1; fi if envT<>hz: f_envT:=1; fi ef nP=_group_e: f_at:=0; f_lineT:=f_rotT:=f_lenT:=f_envT:=rotT:=envT:=0; lineT:=si; lenT:=rate_cr; fi ef nC=_set_atom: temp_strA:=nP; ef nC=_group_si: add_group; ef nC=_group_dm: lineT:=dm; add_group; ef nC=_group_wf: lineT:=wf; add_group; ef nC=_group_zf: lineT:=zf; add_group; ef nC=_jp_bond: termA; nA:=getB(nP); check_adrB(nA); sB[cntB+1]:=sB[nA]; f_bra:=1; ef nC=_jp_atom: termA; nA:=getA(nP); check_adrA(nA); sB[cntB+1]:=nA; f_bra:=1; ef nC=_jp_absA: sB[cntB+1]:=nP; f_bra:=1; temp_cntB:=cntB; ef nC=_chg_atom: strA[getA(adrT)]:=pcode_par[nP][1]; ef nC=_chg_len: if nP=_ring_len: bondL:=ringL; else: bondL:=nP; fi ef nC=_get_len: if nP=_tmp_len: if bondL=rate_cr: bondL:=lenT; fi ef nP=_ring_len: if lenT<>rate_cr: bondL:=lenT; else: if bondL<0: bondL:=1; fi fi else: ringL:=lenB[getB(nP)]; fi ef nC=_tmp_len: lenT:=nP; ef nC=_set_line: lineB[getB(adrT)]:=nP; ef nC=_tmp_line: lineT:=nP; ef nC=_tmp_rot: rotT:=nP; ef nC=_cyc: check_adrA(getA(nP)); add_atom(getA(nP)); ef nC=_cyc_eB: add_atom(eB[getB(nP)]); ef nC=_cyc_sB: add_atom(sB[getB(nP)]); ef nC=_chg_env: envB:=nP; ef nC=_tmp_env: envT:=nP; ef nC=_set_colorA: colorA[getA(adrT)]:=nP; ef nC=_set_colorB: colorB[getB(adrT)]:=nP; ef nC=_set_add: addAT:=nP; ef nC=_chg_add: addA[getA(nP)]:=addAT; addAT:=0; if rotT<>0: add_rot[getA(nP)]:=rotT; fi else: fi endfor enddef; %------------------------------------------------------------------------------------------------- def add_group= if f_at=1: nE:=getA(adrT); check_adrA(nE); else: nE:=cntA+1; fi group_cnt[incr group_num]:=0; store_group(_jp_absA,nE) store_group(_com,_mark) store_group(_com,_len_s) if lineT<>nb: store_group(_tmp_line,lineT) fi if rotT<>0: store_group(_rot_ang,rotT) fi if lenT<>rate_cr: store_group(_chg_len,lenT) ef bondL<>rate_cr: if bondL>=0: store_group(_chg_len,-bondL) else: store_group(_chg_len,bondL) fi fi if envT<>hz: store_group(_chg_env,envT) fi if lineT=nl: store_group(_chg_len,_size_atom) store_group(_adj_ang,0) fi if lineT<>nb: store_group(_mk_bond,0) fi if nP<>NO_ATOM: for i=1 upto pcode_cnt[nP]: store_group(pcode_com[nP][i],pcode_par[nP][i]) endfor fi store_group(_com,_len_e) store_group(_chg_env,hz) store_group(_com,_term) store_group(_com,_rest) if f_lineT=0: lineT:=si; fi if f_lenT=0: lenT:=rate_cr; fi if f_rotT=0: rotT:=0; fi if f_envT=0: envT:=hz; fi enddef; %------------------------------------------------------------------------------------------------- def store_group(expr a,b)= group_com[group_num][incr group_cnt[group_num]]:=a; group_par[group_num][group_cnt[group_num]]:=b; enddef; %------------------------------------------------------------------------------------------------- def add_atom(expr n)= lineB[incr cntB]:=lineT; lineT:=si; if lenT=rate_cr: lenB[cntB]:=bondL; else: lenB[cntB]:=lenT; lenT:=rate_cr; fi if f_bra=0: strA[incr cntA]:=temp_strA; sB[cntB]:=cntA; addA[cntA]:=addAT; addAT:=temp_strA:=add_rot[cntA]:=0; if rotT<>0: add_rot[cntA]:=rotT; rotT:=0; fi else: f_bra:=0; fi if n=0: eB[cntB]:=cntA+1; f_term:=0; else: eB[cntB]:=n; f_term:=1; fi enddef; %------------------------------------------------------------------------------------------------- def check_adrA(expr n)= if (n>iif(f_term=0,cntA+1,cntA))or(n<=0): errmessage("cntA=[ "&decimal(n)&" ]"); fi enddef; def check_adrB(expr n)= if (n>cntB)or(n<=0): errmessage("cntB=[ "&decimal(n)&" ]"); fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def proc_skeleton(expr n)= markA:=markB:=cntA:=cntB:=f_bra:=rotT:=f_term:=0; envT:=envB:=f_lineT:=f_rotT:=f_lenT:=f_envT:=0; lineT:=si; angT:=mangle; angA[0]:=angB[0]:=angX[0]:=0; posA[0]:=posBs:=posBe:=(0,0); %----------------------------------------------------------------------------------------------- for i=1 upto pcode_cnt[n]: nC:=pcode_com[n][i]; nP:=pcode_par[n][i]; if nC=_mk_bond: if (nP=0)and(rotT<>0):nP:=rotT; rotT:=0; fi add_bond(nP,1); ef nC=_com: if nP=_mark: saveA:=markA; saveB:=markB; markA:=cntA; markB:=cntB; ef nP=_rest: markA:=saveA; markB:=saveB; ef nP=_moff: markA:=markB:=0; ef nP=_term: termB; ef nP=_group_e: lineT:=si; lenT:=rate_cr; rotT:=envT:=0; fi ef nC=_jp_bond: termB; nA:=getB(nP); posBs:=posA[sB[nA]]; angT:=angB[nA]; f_bra:=1; rotT:=0; ef nC=_jp_atom: termB; adrT:=getA(nP); posBs:=posA[adrT]; angT:=angX[adrT]; f_bra:=1; rotT:=0; ef nC=_jp_absA: adrT:=nP; posBs:=posA[adrT]; angT:=angX[adrT]; f_bra:=1; rotT:=0; temp_cntB:=cntB; ef nC=_adj_ang: angT:=adjust_ang(angT); ef nC=_rot_ang: if nP>-3700: angT:=(angT+nP) mod 360; else: angT:=(nP+4095) mod 360; fi ef nC=_tmp_rot: rotT:=nP; ef nC=_chg_env: envB:=nP; ef nC=_tmp_env: envT:=nP; ef nC=_cyc: add_bond(angle(posA[getA(nP)]-posBs)-angT,0); ef nC=_cyc_sB: add_bond(angle(posA[sB[getB(nP)]]-posBs)-angT,0); ef nC=_cyc_eB: add_bond(angle(posA[eB[getB(nP)]]-posBs)-angT,0); else: fi endfor enddef; %------------------------------------------------------------------------------------------------- def add_bond(expr n,f)= if n=_arrange_ang: nA:=arrange_ang(angT mod 360); else: nA:=n; fi if f_bra=0: adrT:=incr cntA; posA[cntA]:=posBs; angA[cntA]:=angT; angX[cntA]:=(angT+nA/2+iif(nA>=0,-90,90)) mod 360; else: f_bra:=0; fi cntB:=cntB+1; if nA>-3700: angB[cntB]:=angT:=(angT+nA) mod 360; else: angB[cntB]:=angT:=nA+4095; fi if f=1: if lenB[cntB]=_size_atom: posBe:=sfrt(posBs,atom_wd,angT); else: nA:=lenB[cntB]; if nA<0: nB:=glu_atom(adrT)+glu_atom(cntA+1); nA:=abs(nA); else: nB:=0; fi posBe:=sfrt(posBs,nA*blen+nB,angT); fi posA[cntA+1]:=posBe; f_term:=0; else: f_term:=1; fi posBs:=posBe; enddef; %------------------------------------------------------------------------------------------------- vardef arrange_ang(expr n)= if cntB=0: angT:=(angT-180) mod 360; 180 else: if envB>=pcode_emb_start: pcode_par[envB][cntB-temp_cntB] else: if envB=hz: if n=0: 60 ef n<=90: -60 ef n<=180: 60 ef n<270: -60 else: 60 fi ef envB=vt: if n=0: -60 ef n<90: 60 ef n<=180: -60 ef n<=270: 60 else: -60 fi ef abs(envB)<=180: envB fi fi fi enddef; %------------------------------------------------------------------------------------------------- vardef adjust_ang(expr n)= if (n<40)or(n>320): 0 ef n<140: 90 ef n<220: 180 else: 270 fi 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: strA[incr cntA]:=temp_strA; addA[cntA]:=addAT; add_rot[cntA]:=rotT; addAT:=temp_strA:=rotT:=0; else: f_bra:=0; fi f_term:=1; fi enddef; %------------------------------------------------------------------------------------------------- def termB= if f_term=0: if f_bra=0: angX[incr cntA]:=angT; else:f_bra:=0; fi f_term:=1; fi enddef; %------------------------------------------------------------------------------------------------- vardef glu_atom(expr n)= if strA[n]<>0: nE:=angT mod 90; nF:=0.5atom_wd; (iif(nE<45,sind nE,cosd nE)*nF)+++nF else: 0 fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def draw_atom(expr n)= if atomfont<>"draw": defaultfont:=atomfont; defaultsize:=atom_wd; fi temps:=str_tbl[strA[n]]; slen:=length(temps); nC:=nS:=0; raise_pos:=(0,0); tpos:=posA[n]; if (angX[n]<=90)or(angX[n]>=270): sdir:=1; else: sdir:=-1; fi for i=1 upto slen: if nC=0: tempc:=subc(i,temps); if (sdir=-1)and(tempc="{"): nD:=i; nC:=0; for j=nD upto slen: nC:=nC+1; exitif subc(j+1,temps)="}"; endfor fi else: nC:=nC-1; tempc:=subc(nD+nC,temps); fi if tempc="_": raise_pos:=iif(raise_pos=(0,0),(0,-.5atom_wd),(0,0)); ef tempc="^": raise_pos:=iif(raise_pos=(0,0),(0, .5atom_wd),(0,0)); ef (tempc<>"{")and(tempc<>"}"): nS:=nS+1; char_wd:=atom_wd*tbl_char_wd[ASCII(tempc)]; char_ht:=atom_wd; if nS=1: if (sdir=-1)and(char_wd0: drawoptions(withcolor color_list[tcol]); f_col:=1; fi fi if atomfont="draw": draw_char(tempc,tpos+raise_pos); else: label(tempc,tpos+raise_pos); fi if f_col=1: drawoptions(); fi tpos:=tpos+(.5char_wd*sdir,0); fi endfor nA:=0.56atom_wd; nB:=0.06atom_wd; if sdir=1: frameA[n]:=posA[n]-(nA,nA)--tpos+(nB,-nA)--tpos+(nB,nA)--posA[n]+(-nA,nA)--cycle; else: frameA[n]:=tpos-(nB,nA)--posA[n]+(nA,-nA)--posA[n]+(nA,nA)--tpos+(-nB,nA)--cycle; fi if scan_bit(sw_frame,Atom): draw frameA[n] wpcs thickness_frame; fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def draw_bond(expr n)= nL:=lineB[n]; angL:=angB[n]; nS:=sB[n]; nE:=eB[n]; f_col:=0; tcol:=colorB[n]; zL:=posA[nS]--posA[nE]; ww:=wedge_wd; ap:=angL+90; am:=angL-90; aw:=atom_wd; %----------------------------------------------------------------------------------------------- if (strA[nS]=0)and(strA[nE]=0)or(sw_numbering>=1): Ls:=posA[nS]; Le:=posA[nE]; pA:=(.1,.9); ef strA[nS]=0: Ls:=posA[nS]; Le:=zL ISP frameA[nE]; pA:=(.15,1); ef strA[nE]=0: Ls:=zL ISP frameA[nS]; Le:=posA[nE]; pA:=(0,.85); else: Ls:=zL ISP frameA[nS]; Le:=zL ISP frameA[nE]; pA:=(0,1); fi zA:=Ls--Le; lenL:=length(Le-Ls); %----------------------------------------------------------------------------------------------- if known tcol: if tcol<>0: drawoptions(withcolor color_list[tcol]); f_col:=1;fi fi pickup pencircle scaled bond_pen_wd; if (nL=si)or(scan_bit(sw_abbreviate,Bond)): draw zA; ef nL=dl: draw zA; draw sfrt(subpath pA of zA,bondgap,ap); ef nL=dr: draw zA; draw sfrt(subpath pA of zA,bondgap,am); ef nL=dm: draw sfrt(zA,bondgap/1.75,ap); draw sfrt(zA,bondgap/1.75,am); ef nL=db: nA:=iif(((angL-angX[nS]) mod 360)<=180,ap,am); draw zA; draw sfrt(subpath pA of zA,bondgap,nA); ef nL=tm: draw zA; draw sfrt(zA,bondgap,ap); draw sfrt(zA,bondgap,am); ef nL=wf: fill Ls--sfrt(Le,ww,am)--sfrt(Le,ww,ap)--cycle; ef nL=wb: fill sfrt(Ls,ww,am)--Le--sfrt(Ls,ww,ap)--cycle; ef nL=bd: draw zA withpen penrazor rotated ap scaled bondgap; ef nL=bz: bz_put(sfrt(Ls,ww,ap),sfrt(Le,ww,ap),sfrt(Ls,ww,am),sfrt(Le,ww,am)); ef nL=zf: wz_put(Ls,sfrt(Le,ww,ap),sfrt(Le,ww,am)); ef nL=zb: wz_put(Le,sfrt(Ls,ww,am),sfrt(Ls,ww,ap)); ef nL=dt: for i=0 step .75hash_gap/lenL until 1: drawdot i[Ls,Le]; endfor ef nL=wv: nA:=.4bondgap; nB:=round(lenL/nA); draw Ls for i=1 upto nB: ..controls(point (i-.5)/nB of sfrt(zA,nA,iif(odd i,ap,am))) ..point i/nB of zA endfor ef nL=wf_r: filldraw Ls--sfrt(Le,.35ww,am)--sfrt(Le,.35ww,ap)--cycle wpcs .05ww; ef nL=wb_r: filldraw sfrt(Ls,.35ww,am)--Le--sfrt(Ls,.35ww,ap)--cycle wpcs .05ww; ef nL=bd_r: draw zA wpcs .65bondgap; ef nL=vf: draw zA;draw sfrt(Le,bondgap,angL-150)--Le--sfrt(Le,bondgap,angL+150); ef nL=vb: draw zA;draw sfrt(Ls,bondgap,angL-30)--Ls--sfrt(Ls,bondgap,angL+30); ef nL=si_: erase draw subpath (.15,.85) of zA wpcs 0.8bondgap; draw zA; ef nL=dl_: erase draw subpath (.15,.85) of sfrt(subpath pA of zA,.5bondgap,ap) wpcs 1.8bondgap; draw zA; draw sfrt(subpath pA of zA,bondgap,ap); ef nL=dr_: erase draw subpath (.15,.85) of sfrt(subpath pA of zA,.5bondgap,am) wpcs 1.8bondgap; draw zA; draw sfrt(subpath pA of zA,bondgap,am); ef nL=dm_: erase draw subpath(0.15,0.85) of zA wpcs 1.8 bondgap; draw sfrt(zA,bondgap/1.75,ap); draw sfrt(zA,bondgap/1.75,am); ef nL=wf_: erase draw subpath (0.15,0.85) of (Ls--sfrt(Le,ww,am)) wpcs 0.8bondgap; erase draw subpath (0.15,0.85) of (Ls--sfrt(Le,ww,ap)) wpcs 0.8bondgap; fill Ls--sfrt(Le,ww,am)--sfrt(Le,ww,ap)--cycle; ef nL=wb_: erase draw subpath (0.15,0.85) of (sfrt(Ls,ww,am)--Le) wpcs 0.8bondgap; erase draw subpath (0.15,0.85) of (sfrt(Ls,ww,ap)--Le) wpcs 0.8bondgap; fill sfrt(Ls,ww,am)--Le--sfrt(Ls,ww,ap)--cycle; ef nL=zf_: erase draw subpath (0.15,0.85) of (Ls--sfrt(Le,ww,am)) wpcs 0.8bondgap; erase draw subpath (0.15,0.85) of zA wpcs 0.8bondgap; erase draw subpath (0.15,0.85) of (Ls--sfrt(Le,ww,ap)) wpcs 0.8bondgap; wz_put(Ls,sfrt(Le,ww,ap),sfrt(Le,ww,am)); ef nL=zb_: erase draw subpath (0.15,0.85) of (sfrt(Ls,ww,am)--Le) wpcs 0.8bondgap; erase draw subpath (0.15,0.85) of zA wpcs 0.8bondgap; erase draw subpath (0.15,0.85) of (sfrt(Ls,ww,ap)--Le) wpcs 0.8bondgap; wz_put(Le,sfrt(Ls,ww,am),sfrt(Ls,ww,ap)); ef nL=bd_: erase draw subpath(0.15,0.85) of zA wpcs 1.6bondgap; draw zA withpen penrazor rotated ap scaled bondgap; ef nL=nb: %-- bond type for glycan ---------------------------------------------------------------------- ef nL=arc_lb: draw Ls--Ls-(0,aw)..posA[nE]+(-1.2aw,0)..posA[nE]-(.6aw,0); ef nL=arc_br: draw posA[nS]+(.6aw,0)..posA[nS]+(1.2aw,0)..Le-(0,aw)--Le; ef nL=arc_lbr: draw posA[nS]+(0,iif(strA[nS]=0,0,-.6aw))--posA[nS]+(0,-.8aw) ..0.5[posA[nS],posA[nE]]+(0,-1.7aw)..posA[nE]+(0,-.8aw) --posA[nE]+(0,iif(strA[nE]=0,0,-.6aw)); ef nL=arc_ltr: draw posA[nS]+(0,iif(strA[nS]=0,0,0.6aw))--posA[nS]+(0,.8aw) ..0.5[posA[nS],posA[nE]]+(0,1.7aw)..posA[nE]+(0,.8aw) --posA[nE]+(0,iif(strA[nE]=0,0,.6aw)); %---------------------------------------------------------------------------------------------- fi if f_col=1: drawoptions(); fi enddef; %------------------------------------------------------------------------------------------------ def wz_put(expr a,b,c)= nB:=round(lenL/hash_gap); for i=1 upto nB: nA:=i/nB; if i=1: nD:=0; else: nD:=(i-ratio_hash_black)/nB; fi fill nD[a,b]--nD[a,c]--nA[a,c]--nA[a,b]--cycle; endfor enddef; %------------------------------------------------------------------------------------------------ def bz_put(expr a,b,c,d)= nB:=round(lenL/hash_gap); for i=0 upto nB-1: nA:=i/nB; nD:=nA+ratio_hash_black/nB; fill nA[b,a]--nA[d,c]--nD[d,c]--nD[b,a]--cycle; endfor enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def char_size_set(expr w,h)(expr s)= for j=1 upto length(s): nN:=ASCII(subc(j,s)); tbl_char_wd[nN]:=w; tbl_char_ht[nN]:=h; endfor enddef; %------------------------------------------------------------------------------------------------- char_size_set( 1, 1)("CGHMNOQW"); char_size_set( 0.9, 1)("ABDFIJKPRSTUVXY"); char_size_set( 0.8, 1)("ELZ"); char_size_set( 0.7, 1)("0123456789nhtfg"); char_size_set( 0.7, 0.7)("-+"); char_size_set(0.45,0.95)("l"); char_size_set(0.75, 0.8)("opq"); char_size_set( 0.8, 0.8)("e"); char_size_set( 0.9, 0.8)("wm"); char_size_set( 0.7, 0.8)("abdcksuvrxyz"); char_size_set(0.35, 0.9)("i"); char_size_set( 0.5, 0.9)("j"); %------------------------------------------------------------------------------------------------- def dw expr p = draw p shifted cpos enddef; def dwv expr p = draw p withpen penrazor scaled fP shifted cpos enddef; def dwvs(expr n) expr p = draw p withpen penrazor scaled (fP*n) shifted cpos enddef; def dwh expr p = draw p withpen penrazor rotated 90 scaled fP shifted cpos enddef; def cdw expr p = cutdraw p shifted cpos enddef; %------------------------------------------------------------------------------------------------- def Z_a=( 0,hP) enddef; def Z_b=(hP, 0) enddef; def Z_c=(hP,hP) enddef; def Z_d=(aW,hP) enddef; def Z_e=(fW, 0) enddef; def Z_f=(hW,aH) enddef; def Z_g=(hW, 0) enddef; def Z_h=( 0,hH) enddef; def Z_i=(hW,fW) enddef; def Z_j=( 0,qH) enddef; def Z_k=(aW,qH) enddef; def Z_l=(.75aW,0) enddef; def Z_m=(hP,hH) enddef; def Z_n=(fW,fH) enddef; def Z_o=(fW,hH) enddef; def Z_p=(hW,aW) enddef; def Z_q=( 0,fH) enddef; def Z_r=(hP,fH) enddef; def Z_s=(hW,fH) enddef; def Z_t=(fW,aH) enddef; def Z_u=(aW,fH) enddef; def Z_v=(aW,hH) enddef; def Z_w=(hP,aH) enddef; def Z_x=(hW,hP) enddef; def Z_y=(hW,hH) enddef; def Z_z=(fW,hP) enddef; %------------------------------------------------------------------------------------------------- def circ_O = Z_o..(.8aW,fH-qP)..tension 1.5..(.2aW,fH-qP)..Z_m.. (.2aW,1.5hP)..tension 1.5..(.8aW,1.5hP)..cycle enddef; def circ_Oh = (hP,qH)..Z_x..(fW,qH)..Z_y..cycle enddef; def circ_Oa = (hP,0.35aH)..Z_x..(fW,0.35aH)..(hW,.7aH)..cycle enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def draw_char(expr s,p)= aW:=atom_wd*tbl_char_wd[ASCII(s)]*(1-2ratio_atomgap_atom); aH:=atom_wd*tbl_char_ht[ASCII(s)]*(1-2ratio_atomgap_atom); cpos:=p-(aW/2,atom_wd/2*(1-2ratio_atomgap_atom)); fP:=bond_pen_wd*ratio_char_bond; hP:=fP/2; qP:=fP/4; fW:=aW-hP; hW:=aW/2; fH:=aH-hP; hH:=aH/2; qH:=aH/4; %----------------------------------------------------------------------------------------------- pickup pencircle scaled fP; if s="C": cdw sbp(.05,.95)circ_O; ef s="H": dwv Z_b--Z_w; dw Z_m--Z_o; dwv Z_e--Z_t; ef s="O": dw circ_O; ef s="N": dwv Z_b--Z_w; dwv Z_e--Z_t; dwvs(1.4)(1.4hP,aH)--(aW-1.4hP,0); ef s="S": cdw sbp(.05,.45)circ_O; cdw sbp(.55,.95)circ_O; dw (fW,.3aH){up}..{up}(hP,.7aH); ef s="F": dwh Z_q--Z_u; dwh (0,.45aH)--(fW,.45aH); dw Z_b--Z_r; ef s="P": dwv Z_b--Z_w; dw Z_r--(.65aW,fH){right}..(fW,.7aH)..{left}(.65aW,.44aH)..(hP,.44aH); ef s="I": dwv Z_x--Z_s; dwh (hW-fP,hP)--(hW+fP,hP); dwh (hW-fP,fH)--(hW+fP,fH); ef s="l": dwv Z_g--Z_f; dwh Z_s--Z_r; dwh Z_x--Z_z; ef s="2": cdw (hP,1.3hP)..(.4fW,.35fH)..(fW,.65aH)..Z_s..(hP,.65aH); dwh Z_d--Z_a; ef s="3": cdw sbp(0,.75)circ_Oh; cdw sbp(.25,.98)circ_Oh shifted (0,hH-hP); dwh (.3aW,hH)--Z_y; ef s="4": dwh Z_j--Z_k; dwv Z_l--(0.75aW,aH)--(1.2hP,qH+hP); dwv (.75aW+qP,aH)--(1.7hP,qH+hP); ef s="-": dwh Z_m--Z_o; ef s="+": dwv Z_x--Z_s; dwh Z_m--Z_o; ef s="A": dwvs(1.14)Z_b--Z_f--Z_e; dw .33[Z_b,Z_f]--.33[Z_e,Z_f]; ef s="B": dw Z_r--Z_s{right}..(.9fH,.75aH)..{left}Z_y--Z_m--Z_y{right}..(.9fH,qH).. {left}Z_x--Z_c; dwv Z_b--Z_w; ef s="D": dw Z_r--Z_s..Z_o..Z_x--Z_c; dwv Z_b--Z_w; ef s="E": pickup pensquare scaled fP; dw Z_z--Z_c--Z_r--Z_n; dw Z_m--Z_o; ef s="G": cdw sbp(.06,.97)circ_O; dwh bot Z_y-- bot Z_v; ef s="J": cdw Z_m..(hP,.4aH){down}..{right}Z_x{right}..{up}(fW,.4aH)..Z_t; ef s="K": cdw Z_b--Z_w; cdw .35[.45[Z_b,Z_w],Z_u]--Z_e; cdw .35[Z_b,Z_w]--Z_u; ef s="L": dwh Z_d--Z_a; dwv Z_b--Z_w; ef s="M": dwv Z_b--Z_w; dwvs(1.14)Z_w--Z_x--Z_t; dwv Z_t--Z_e; ef s="Q": dw circ_O; dw (.6aW,.4aH)--Z_e; ef s="R": dwv Z_b--Z_w; dw Z_r--(.65aW,fH){right}..(fW,.7aH)..{left}(.65aW,.44aH)..(hP,.44aH); cdw Z_e{up}..{left}(hW,.44aH); ef s="T": dwh Z_q--Z_u; dwv .5[Z_q,Z_u]--Z_g; ef s="U": cdw Z_w..Z_m{down}..{right}Z_x{right}..{up}Z_o..Z_t; ef s="V": dwvs(1.2)Z_w--Z_g--Z_t; ef s="W": dwvs(1.08)Z_w--(aW/4,0)--Z_f--Z_l--Z_t; ef s="X": dwvs(1.4)Z_w..Z_e; dwvs(1.4) Z_b..Z_t; ef s="Y": dwvs(1.2)Z_w--Z_y--Z_t; dwv Z_y--Z_g; ef s="Z": dwh Z_q--Z_u; dwvs(1.4)(1.4hP,fP)--(aW-1.4hP,aH-fP); dwh Z_a--Z_d; ef s="a": dw Z_x..Z_o..Z_s..Z_m..cycle; dwv Z_e--Z_t; ef s="b": dw Z_x..Z_o..Z_p..Z_m..cycle; dwv Z_b--(hP,1.3aH) ef s="c": cdw sbp(.06,.94)Z_o..Z_s..Z_m..Z_x..cycle; ef s="d": dw Z_x..Z_o..Z_p..Z_m..cycle; dwv Z_e--(fW,1.3aH); ef s="e": cdw sbp(0,.92)Z_o..Z_s..Z_m..Z_x..cycle; dw Z_o--Z_m; ef s="f": cdw (.4fW,0)--(.4fW,.75aH){up}..(.75aW,fH)..{down}(fW,.8aH); dwh Z_h--Z_v; ef s="g": dw circ_Oa; dw sbp(0,.5)circ_Oh shifted (0,-.5fH); cdw (fW,.7aH)--(fW,-qH); ef s="h": cdw Z_b..(hP,.3aH){up}..(hW,.7fH)..{down}(fW,.3aH)..Z_e; dwv (hP,.3aH)--Z_w; ef s="i": dwv Z_g--(hW,.7aH); ppcs 1.4fP; dw Z_s; ef s="j": cdw (fW,.7aH)--Z_z..(aW/4,-.66fP)..Z_c; ppcs 1.4fP; dw Z_n; ef s="k": dwv Z_b--(hP,1.3fH); cdw .5[Z_b,Z_w]--Z_e; cdw .5[Z_b,Z_w]--Z_u; ef s="m": cdw Z_b..(hP,.3aH){up}..(.28aW,fH)..{down}(hW,.3aH)..Z_g; cdw (hW,.6aH){up}..(.7aW,fH)..{down}(fW,.6aH)..Z_e; dwv (hP,.3aH)--Z_w; ef s="n": cdw Z_b{up}..(hW,.8fH)..{down}Z_o..Z_e; dwv Z_b--(hP,.8aH); ef s="o": dw Z_x..Z_o..Z_s..Z_m..cycle; ef s="p": dw Z_x..Z_o..Z_s..Z_m..cycle; dwv Z_w--(hP,-.3aH); ef s="q": dw Z_x..Z_o..Z_s..Z_m..cycle; dwv Z_t--(fW,-.3aH); ef s="r": cdw (sbp(.33,.72)Z_x..Z_o..Z_s..Z_m..cycle) shifted(0,-hP); dwv Z_b--Z_w; ef s="s": cdw sbp(.05,.45)circ_O; cdw sbp(.55,.95)circ_O; dw (fW,.3aH){up}..{up}(hP,.7aH); ef s="t": dwv Z_g--Z_f; dwh (0,.66aH)--(aW,.66aH); ef s="u": cdw Z_w..(hP,.55aH){down}..Z_x..(fW,.55aH){up}..Z_t; dwv Z_t--Z_e; ef s="v": dwv Z_w--Z_g--Z_t; ef s="w": dwv Z_w--(aW/4,0)--Z_f--Z_l--Z_t; ef s="x": dwvs(1.4)Z_w--Z_e; dwvs(1.4) Z_t--Z_b; ef s="y": dwvs(1.4)(Z_w--Z_y) shifted (0,-.3aH); dwvs(1.4)(Z_t--Z_b) shifted (0,-.3aH); ef s="z": dwh Z_q--Z_u; dwvs(1.4)(1.4hP,fP)--(aW-1.4hP,aH-fP); dwh Z_a--Z_d; ef s="0": dw Z_m...Z_s...Z_o...Z_x...cycle; ef s="1": dwv Z_g--(hW,aH-.3hP)--(hW-fP,aH-fP)--(hW-fP,aH-1.5fP); ef s="5": dwh Z_q--Z_u; dwv Z_r--(hP,.55fH); cdw (qP,.18aH)..(.65aW,1.3hP)..(fW,.4aH)..(hW,.63aH)..(.7hP,.56aH); ef s="6": dw Z_x..(fW,.5fW)..Z_i..(hP,.5fW)..cycle; cdw (.8fP,hH)--Z_f; ef s="7": dwh (0,.fH)--Z_u; dwvs(1.2)(aW-1.2hP,aH-fP)--(.4aW,0); ef s="8": dw circ_Oh; dw (hP,.75aH)...Z_s...(fW,.75aH)...Z_y...cycle; ef s="9": dw (Z_x..(fW,.5fW)..Z_i..(hP,.5fW)..cycle) shifted (0,.32aH); cdw (fW-.45fP,hH)--Z_g; else: fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def warning_bond(expr a)= if addA[a]=0: warning("A"&decimal(a)&" ( "&fsl(8)(str_tbl[strA[a]])&") has"&fdr(2)(bond_cntA)&" bonds"); fi enddef; %------------------------------------------------------------------------------------------------- vardef erase_char(expr s)= sS:=""; if (length(s)>=4)and(s<>"COOH"): for i=1 upto length(s): sC:=subc(i,s); if scan_c(sC,"{}_^+-")=0: sS:=sS&sC; fi endfor sS else: s fi enddef; %------------------------------------------------------------------------------------------------- vardef forbidden_to_underbar(expr t)= sS:=""; for i=1 upto length(t): sC:=subc(i,t); if scan_c(sC,forbiddens)>0: sS:=sS&"_"; else: sS:=sS&sC; fi endfor sS enddef; %================================================================================================= def proc_calc(expr n)= MW_n:=MI_n:=tbl_atom_max:=warning_cnt:=hideH_cnt:=0; nE:=pcode_emb_start; for i=1 upto tbl_atom_end: sumA[i]:=0; endfor for i=1 upto cntA: knownA:=bond_cntA:=0; nS:=strA[i]; for j=1 upto cntB: bond_num[j]:=bond_type(lineB[j]); if (sB[j]=i)or(eB[j]=i): bond_cntA:=bond_cntA+bond_num[j]; fi endfor Bcnt[i]:=bond_cntA; if ((nS=0)or(nS=(C-nE)))and(bond_cntA<4): hideH[i]:=4-bond_cntA; hideH_cnt:=hideH_cnt+hideH[i]; else: hideH[i]:=0; fi if nS=0: if bond_cntA>4: warning_bond(i) fi ef nS=(O-nE): if bond_cntA<>2: warning_bond(i) fi ef nS=(N-nE): if (bond_cntA<>3)and(bond_cntA<>5): warning_bond(i) fi ef nS=(S-nE): if (bond_cntA<>2)and(bond_cntA<>4)and(bond_cntA<>6): warning_bond(i) fi ef nS=(H-nE): if bond_cntA<>1: warning_bond(i) fi ef nS=(OH-nE): if bond_cntA<>1: warning_bond(i) fi ef nS=(COOH-nE): if bond_cntA<>1: warning_bond(i) fi ef nS=(NH2-nE): if bond_cntA<>1: warning_bond(i) fi ef nS=(CN-nE): if bond_cntA<>1: warning_bond(i) fi ef nS=(P-nE): if bond_cntA<>5: warning_bond(i) fi ef nS=(C-nE): if bond_cntA>4: warning_bond(i) fi ef nS=(F-nE): if bond_cntA<>1: warning_bond(i) fi ef nS=(Cl-nE): if bond_cntA<>1: warning_bond(i) fi ef nS=(Br-nE): if bond_cntA<>1: warning_bond(i) fi fi for j=1 upto tbl_group_end: if str_tbl[nS]=tbl_atom_str[j]: if tbl_atom[j]=0: sumA[j]:=sumA[j]+1; if j>tbl_atom_max: tbl_atom_max:=j; fi else: for k=1 upto tbl_atom[j]: sumA[tbl_group[j][k]]:=sumA[tbl_group[j][k]]+1; if tbl_group[j][k]>tbl_atom_max: tbl_atom_max:=tbl_group[j][k]; fi endfor fi knownA:=1; fi exitif knownA=1; endfor if knownA=0: warning(" Unknown Str("&str_tbl[strA[i]]&") is used "&decimal(i)); fi endfor %------------------------------------------------------------------------------------- sumA[2]:=sumA[2]+hideH_cnt; if (tbl_atom_max=1)and(sumA[2]>0): tbl_atom_max:=2; fi for i=1 upto tbl_atom_max: if sumA[i]>=1: MW_n:= MW_n+tbl_atom_wt[i]*sumA[i]; MI_n:= MI_n+tbl_atom_mi[i]*sumA[i]; fm:=fm&erase_char(tbl_atom_str[i]) if sumA[i]>=2: &decimal(sumA[i]) fi; fi endfor mw:=substring(0,8) of decimal(MW_n); MI:=substring(0,10) of decimal(MI_n); enddef; %================================================================================================= def proc_report_out= file_output:=jobname&"-report.txt"; printf "==========================================================================="; printf " No["&decimal(fig_num)&"],Name<"& EN&">,Category<"&CAT&">,File<"&file_input&">"; printf "---------------------------------------------------------------------------"; for i=1 upto mc_row: printf (substring(0,mc_indent[i]) of blanks)&mc[i]; endfor printf "---------------------------------------------------------------------------"; printf " Row["&decimal(mc_row)&"],Length["&decimal(length(mc))&"],Block"& "["&decimal(block_cnt+1)&"]"&",Code pair["&decimal(pcode_cnt[0])& "],Warning["&decimal(warning_cnt)&"]"; printf "---------------------------------------------------------------------------"; printf "" for i=EQU,CLN,QES,AMK,AMP,HSH,GTN,BAR,QUT,TLD,HAT,BQT,LTN: if tbl_asc[i]>=1: &" "&char(i)&"["&decimal(tbl_asc[i])&"]" fi endfor ; printf "---------------------------------------------------------------------------"; printf " Width["&fdr(8)(mol_wd)&"],Height["&fdr(8)(mol_ht)&"],"& " Shift x["& fdr(8)(minX)&"],Shift y["&fdr(8)(minY)&"]"; printf " Bond length["&fdr(8)(blen)&"],Atom size["&fdr(8)(atom_wd)&"]"; printf "---------------------------------------------------------------------------"; printf " Atom["&decimal(cntA)&"],Bond["&decimal(cntB)& "],Ring["&decimal(cntB-cntA+1)&"],Hide H["&decimal(hideH_cnt)&"]"; printf "< NO. >( x axis , y axis )"; for i=1 upto cntA: printf " A"&fdl(6)(i)&fsl(8)(erase_char(str_tbl[strA[i]]))& " ("&fdr(10)(round(xpart(posA[i])/blen))&" , "& fdr(10)(round(ypart(posA[i])/blen))&" ) "&fdr(4)(Bcnt[i])& iif(hideH[i]>0,fdr(6)(hideH[i])," ") if chargeA[i]<>0: &fdr(4)(chargeA[i]) fi; endfor printf "---------------------------------------------------------------------------"; printf "< NO. >< bond (sdt)>"; for i=1 upto cntB: nC:=lenB[i]; if nC=_size_atom: nC:=ratio_atom_bond; elseif nC<0: nC:=-nC; fi nB:=angB[i]; if nB>180: nB:=nB-360; fi printf " B"&fdl(4)(i)&fdr(3)(sB[i])&" -> "&fdr(3)(eB[i])& " ("&fdr(3)(bond_num[i])&")"&fdr(8)(round(angB[i]))& " ("&fdr(6)(round(nB))&")"&fdr(8)(nC)&" ("&fdr(8)(round(nC*blen))&")"; endfor printf "---------------------------------------------------------------------------"; printf "( atom wt )[ mi wt ] < cnt > < sum wt >[ sum mi wt ]"; for i=1 upto tbl_atom_max: if sumA[i]>=1: printf " "&fsl(5)(erase_char(tbl_atom_str[i]))& "("&fdr(9)(tbl_atom_wt[i])&")"&"["&fdr(9)(tbl_atom_mi[i])&"]"&" * "&fdr(8)(sumA[i]) &" "&fdr(7)(tbl_atom_wt[i]*sumA[i])&"["&fdr(12)(tbl_atom_mi[i]*sumA[i])&"]"; fi endfor printf " Molecular Weight [Mono Isotopic] = "&fsr(12)(mw)&"["&fsr(12)(MI)&"]"; printf "---------------------------------------------------------------------------"; printf " Weight Calc: "&mw if MW<>"-": &" - Input: "&MW&" = "&fdr(9)(MW_n-scantokens(MW)) fi; printf " Fomula Calc: "&fm if FM<>"-": &" "&iif(fm=FM,"=","<>")&" Input: "&FM fi; printf "==========================================================================="; enddef; %================================================================================================= def proc_mol_out(expr n)= if EN<>"-": EN_:=forbidden_to_underbar(EN); fi file_output:="m"&fit_zero(fig_num)&"-"&EN_&".mol"; %-V2000--------------------------------------------------------------------------------------- if n=2000: printf ""; printf " -MCFtoMOL- "&fsl(20)(EN); printf ""; printf fdr(3)(cntA)&fdr(3)(cntB)&" 0 0 0 0 0 0 0 0999 V2000"; for i=1 upto cntA: printf fdr(10)(xpart(posA[i])/blen)& fdr(10)(ypart(posA[i])/blen)&fdr(10)(0)&" "& fsl(2)(erase_char(str_tbl[strA[i]]))&" 0"&fdr(3)(bond_charge(chargeA[i]))&" 0 0"; endfor for i=1 upto cntB: if lineB[i]<>0: printf fdr(3)(sB[i])&fdr(3)(eB[i])&fdr(3)(bond_type(lineB[i]))& fdr(3)(bond_stereo(lineB[i]))&" 0 0"; fi endfor printf "M END"; %-V3000--------------------------------------------------------------------------------------- elseif n=3000: printf ""; printf " -MCFtoMOL- "&fsl(20)(EN); printf ""; printf " 0 0 0 0 0 0 0 0 0 0 0 V3000"; printf "M V30 BEGIN CTAB"; printf "M V30 COUNTS "&decimal(cntA)&" "&decimal(cntB)&" 0 0 0"; printf "M V30 BEGIN ATOM"; for i=1 upto cntA: printf "M V30 "&decimal(i)&" "&erase_char(str_tbl[strA[i]])&" "& decimal(xpart(posA[i])/blen)&" "&decimal(ypart(posA[i])/blen)&" 0 0" if chargeA[i]<>0: &" CHG="&decimal(chargeA[i]) fi; endfor printf "M V30 END ATOM"; printf "M V30 BEGIN BOND"; for i=1 upto cntB: if lineB[i]<>0: printf "M V30 "&decimal(i)&" "&decimal(bond_type(lineB[i]))& " "&decimal(sB[i])&" "&decimal(eB[i]) if bond_stereo(lineB[i])<>0: &" CFG="&decimal(bond_config(lineB[i])) fi; fi endfor printf "M V30 END BOND"; printf "M V30 END CTAB"; printf "M END"; fi enddef; %================================================================================================= def proc_mc_out= file_output:="temp-mc.aux"; if mc_length<100: nN:=split_str(mc,",")(arg_s); nA:=0; temps:=""; for i=1 upto nN: if i=nN: temps:=temps&arg_s[i]; printf temps; ef at_char[i+1]-nA>mc_length: nA:=at_char[i]; printf temps&arg_s[i]&","; temps:=""; else: temps:=temps&arg_s[i]&","; fi endfor else: for i=1 upto mc_row: printf (substring(0,mc_indent[i]) of blanks)&mc[i]; endfor fi printf EOF; enddef; %================================================================================================= vardef fit_zero(expr n)= if n<=9: "00" ef n<=99: "0" else: "" fi &decimal(n) enddef; vardef bond_type(expr n)= if (n>=dl)and(n<=dm_):2 ef n=tm:3 ef (n=0)or(n=vf)or(n=vb): 0 else: 1 fi enddef; vardef bond_charge(expr n)= if n=2: 1 ef n=1: 3 ef n=-1: 5 ef n=-2: 6 else: 0 fi enddef; vardef bond_stereo(expr n)= if (n=wf)or(n=zb)or(n=bd): 1 ef (n=zf)or(n=wb)or(n=dt): 6 ef n=wv: 4 else: 0 fi enddef; vardef bond_config(expr n)= if (n=wf)or(n=zb)or(n=bd): 1 ef (n=zf)or(n=wb)or(n=dt): 3 ef n=wv: 2 else: 0 fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% vardef define_atom(expr s,WT,MI)= str_cnt:=str_cnt+1; tbl_cnt:=tbl_cnt+1; pcode_num:=pcode_num+1; pcode_com[pcode_num][1]:=_set_atom; pcode_par[pcode_num][1]:=str_cnt; pcode_cnt[pcode_num]:=1; str_tbl[str_cnt]:=tbl_atom_str[tbl_cnt]:=s; tbl_atom[tbl_cnt]:=0; tbl_atom_wt[tbl_cnt]:=WT; tbl_atom_mi[tbl_cnt]:=MI; pcode_num enddef; %------------------------------------------------------------------------------------------------- vardef define_group_string(expr s)(text t)= str_cnt:=str_cnt+1; tbl_cnt:=tbl_cnt+1; pcode_num:=pcode_num+1; pcode_com[pcode_num][1]:=_set_atom; pcode_par[pcode_num][1]:=str_cnt; pcode_cnt[pcode_num]:=1; str_tbl[str_cnt]:=tbl_atom_str[tbl_cnt]:=s; tbl_atom[tbl_cnt]:=0; for list=t: tbl_group[tbl_cnt][incr tbl_atom[tbl_cnt]]:=list-pcode_emb_start; endfor pcode_num enddef; %================================================================================================= def define_atom_group_parts= save `,``,'; def `=define_atom enddef; def ``=define_group_string enddef; def '= define_parts enddef; pcode_int:=pcode_emi_start; pcode_num:=pcode_emb_start; ?3:=?20:=Ph:=Ph1:=Ph2:=hz:=0; vt:=1; %----------------------------------------------------------------------------------------------- C:= `("C" ,12.0107, 12.0000000); H:= `("H" , 1.00794, 1.00782503223); D:= `("D" ,2.012, 2.01410177812); Ag:=`("{Ag}",107.868, 106.905095); Al:=`("{Al}",26.9815, 26.98153853); As:=`("{As}",74.9216, 74.92159457); B:= `("B" ,10.811, 11.00930536); Ba:=`("{Ba}",137.33, 136.905816); Be:=`("{Be}",9.01218, 0); Bi:=`("{Bi}",208.9804, 208.980338); Br:=`("{Br}",79.904, 78.9183376); Ca:=`("{Ca}",40.078, 39.962590863); Cd:=`("{Cd}",112.41, 110.904182); Cl:=`("{Cl}",35.453, 34.968852); Co:=`("{Co}",58.933194, 58.93319429); Cr:=`("{Cr}",51.9961, 51.94050623); Cs:=`("{Cs}",132.905, 132.90543); Cu:=`("{Cu}",63.546, 62.92959772); F:= `("F" ,18.9984, 18.99840316273); Fe:=`("{Fe}",55.845, 55.93493633); Hg:=`("{Hg}",200.59, 201.97064340); I:= `("I" ,126.90447,126.9044719); K:= `("K" ,39.0983, 38.9637064864); Li:=`("{Li}",6.941, 7.0160034366); Mg:=`("{Mg}",24.305, 23.985041697); Mn:=`("{Mn}",54.938044, 54.93804391); Mo:=`("{Mo}",95.95, 0); N:= `("N" ,14.0067, 14.00307400443); Na:=`("{Na}",22.98977, 22.9897692820); Ni:=`("{Ni}",58.693, 57.93534241); O:= `("O" ,15.9994, 15.99491461957); P:= `("P" ,30.973762, 30.97376199842); Pb:=`("{Pb}",207.2, 205.974455); Pd:=`("{Pd}",106.4, 107.905075); S:= `("S" ,32.065, 31.9720711744); Sb:=`("{Sb}",121.75, 120.90381); Se:=`("{Se}",78.971, 79.9165218); Si:=`("{Si}",28.0855, 27.97692653465); Sn:=`("{Sn}",118.71, 119.90220163); Ta:=`("{Ta}",180.948, 0); Te:=`("{Te}",127.60, 129.90623); Ti:=`("{Ti}",47.867, 47.94794198); U:= `("U", 238.0289, 238.05079); V:= `("V", 50.9415, 50.943957); W:= `("W", 183.85, 181.948225); Zn:=`("{Zn}",65.409, 63.92914201); NO_ATOM:=`("",0,0); tbl_atom_end:=tbl_cnt; %----------------------------------------------------------------------------------------------- if sw_expand=0: CH3:=``("C{H_3_}")(C,H,H,H); CH2:=``("C{H_3_}")(C,H,H); CN:=``("CN")(C,N); OH:=``("OH")(O,H); COOH:=``("COOH")(C,O,O,H); COONa:=``("COO{Na}")(C,O,O,Na); CHO:=``("CHO")(C,H,O); NO:=``("NO")(N,O); NO2:=``("N{O_2_}")(N,O,O); NH2:=``("N{H_2_}")(N,H,H); SH:= ``("SH")(S,H); SO2H:=``("S{O_2_}H")(S,O,O,H); SO3H:=``("S{O_3_}H")(S,O,O,O,H); ONa:=``("O{Na}")(O,Na); SO3Na:=``("S{O_3_}{Na}")(S,O,O,O,Na); fi %----------------------------------------------------------------------------------------------- tbl_group_end:=tbl_cnt; pcode_atm_end:=pcode_num; ?:=(_group_si,NO_ATOM); ?wf:=?w:=(_group_si,NO_ATOM); ?zf:=?z:=(_group_si,NO_ATOM); ?O:=(_group_dm,O); NH:='(N,/H~nl); ?NH:=(_group_dm,NH); %----------------------------------------------------------------------------------------------- ?H:='(/H); ?F:='(/F); ?Cl:='(/Cl); ?OH:='(/OH); ?OH:='(/COOH); ?NH2:='(/NH2); for i=3 upto 20: ?[i]:='((_com,_len_ss),(_get_len,_ring_len),<((-180 DIV i)-90) for j==2 upto i:: ,(360 DIV i) endfor,(_cyc_sB,1-i),(_com,_len_ee)); endfor Ph:=Ph1:='(?6,-2=dl,-4=dl,-6=dl); Ph2:='(?6,-1=dl,-3=dl,-5=dl); for i=5,6,7,8: for j=11 upto 15: ?[i][j]:='((i,j)); endfor endfor %----------------------------------------------------------------------------------------------- !:=!1:='((_mk_bond,_arrange_ang)); !db:=!d:='(!~db); !tm:=!t:='(!~tm); !wf:=!w:='(!~wf); !zf:=!z:='(!~zf); !wb:='(!~wb); !zb:='(!~zb); !dl:='(!~dl); !dr:='(!~dr); !dm:='(!~dm); for i==2 upto 20: ![i]:='((_com,_len_ss),(_get_len,_tmp_len),! for j==2 upto i::,! endfor ,(_com,_len_ee)); endfor ?!:='(/_,!); ?!d:='(/_,!d); ?!2:='(/_,!2); ??!:='(/_,/_^60,60); ??:='(/_^35,/_^-35); !?:='(!,/_); !?!:='(!?,!); !??!:='(!,??,!); ?2:='(/!); !?2:='(!,?2); ?2!:='(?2,!); n_:='((_set_add,MIS)); p_:='((_set_add,PLS)); zero_wf:='(0~wf); zero_zf:='(0~zf); zero_dm:='(0~dm); zero_wv:='(0~wv); mark_adress:='((_com,_mark)); reset_adress:='((_com,_moff)); reset_length:='((_com,_len_e)); %----------------------------------------------------------------------------------------------- if sw_expand=1: CH3:='(/H,/H^60,/H^-60); NH:='(N,/H); NH2:='(N,/H^60,/H^-60); NO2:='(N,//O^60,//O^-60); OH:='(O,!,H); NO:='(N,//O); CONH2:='(//O,!,NH2); SH:='(S,!,H); SO2H:='(S,//O^60,/OH^-60); SO3H:='(S,/OH,//O^60,//O^-60); CHO:='(//O^-60,/H^60); COOH:='(//O^-60,/OH^60); CN:='(!~tm,N); ONa:='(O,!,Na); SO3Na:='(S,/ONa,//O^60,//O^-60); fi %----------------------------------------------------------------------------------------------- ?F!F:='(/F,60,F); ?Cl!Cl:='(/Cl,60,Cl); ?Br!Br:='(/Br,60,Br); ?F?F!F:='(/F,/F^60,60,F); ?Cl?Cl!Cl:='(/Cl,/Cl^60,60,Cl); %----------------------------------------------------------------------------------------------- N!:='(N,!); N?:='(N,/_); N!2:='(N,!3); N!2:='(N,!3); !N:='(!,N); N?!:='(N,?!); N?2:='(N,?2); N?2!:='(N?2,!); N?!2:='(N,?!2); S?O:='(S,?O); S?O!:='(S?O,!); ?O?O:='(?O^-35,?O^35); S?O?O:='(S,?O?O); S?O?O!:='(S?O?O,!); O!:='(O,!); O!2:='(O,!2); O!3:='(O,!3); S!:='(S,!); S!2:='(S,!2); S!3:='(S,!3); %----------------------------------------------------------------------------------------------- ?O!:='(?O,!); ?O!2:='(?O,!2); ?O!3:='(?O,!3); !?O:='(!,?O); !?O!:='(!,?O!); NH!:='(NH,!); NH!2:='(NH,!2); !NH:='(!,NH); !NH!:='(!,NH!); %----------------------------------------------------------------------------------------------- !OH:='(!,OH); !SH:='(!,SH); !NH2:='(!,NH2); !S?O:='(!,S?O); !O:='(!,O); !dO:='(!d,O); !O!:='(!,O!); !O!2:='(!,O!2); !O!3:='(!,O!3); !S!:='(!,S!); !S!2:='(!,S!2); !S!3:='(!,S!3); !COOH:='(!,COOH); ?COOH:='(/COOH); !CH3:='(!,CH3); !CN:='(!,CN); !CHO:='(!,CHO); !NO2:='(!,NO2); !Cl:='(!,Cl); !Br:='(!,Br); !F:='(!,F); !?F!F:='(!,?F!F); !?Cl!Cl:='(!,?Cl!Cl); !?F?F!F:='(!,?F?F!F); !?Cl?Cl!Cl:='(!,?Cl?Cl!Cl); !?3:='(!,?3); !?4:='(!,?4); !?5:='(!,?5); !?6:='(!,?6); !?7:='(!,?7); !?8:='(!,?8); !Ph:='(!,Ph); !?OH:='(!,?OH); ?OH!:='(?OH,!); %----------------------------------------------------------------------------------------------- lr:='(60 for i==1 upto 10:: ,-60,60 endfor); rl:='(-60 for i==1 upto 10:: ,60,-60 endfor); %----------------------------------------------------------------------------------------------- hexose_hp:='(#1.4,-30~wf_r,30~bd_r`1,30~wb_r,120,O,30,&1,##); Pyranose_hp:='(#1.4,-35~wf_r,35~bd_r`1,30~wb_r,130`1.66,O,&1,##); enddef; %------------------------------------------------------------------------------------------------- define_atom_group_parts; %================================================================================================= init_par(parameter_list); %------------------------------------------------------------------------------------------------- for i=pcode_emb_start+1 upto pcode_num: pcode_all:=pcode_all+pcode_cnt[i]; endfor message "pcode_emb =" & decimal(pcode_emb_start) &" => " & decimal(pcode_num) & " [ " & decimal(pcode_all) & " ]"; message "pcode_emi =" & decimal(pcode_emi_start) &" => " & decimal(pcode_int); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% vardef checkm(expr s)= save mc_char,mc_adr,mc_asc,char_cnt,lens,f_depth; string err_type[]; numeric mc_char[],mc_asc[],mc_adr[]; err_cnt:=char_cnt:=block_cnt:=f_depth:=0; nA:=1; lens:=length(s); err_type[0]:="no mc-row "; err_type[1]:="mismatch () "; err_type[2]:="mismatch {} "; err_type[3]:="mismatch [] "; err_type[4]:="missing arg "; err_type[5]:="extra arg "; %--------------------------------------------------------------------------------------------- if mc_row>=1: for i=1 upto 128: tbl_asc[i]:=0; endfor for i=1 upto lens: mc_char[i]:=ASCII(subc(i,s)); endfor forever: temps:=substring (nA-1,nA) of s; if (temps<>",")and(temps<>" "): nF:=0; for j=1 upto rw_cnt: nC:=lenw[j]-1; if substring (nA-1,nA+nC) of s=rw[j]: for k=1 upto nC: mc_char[nA]:=j; mc_char[nA+k]:=BLK; endfor nF:=1; nA:=nA+nC; fi exitif nF=1; endfor fi nA:=nA+1; exitif nA>=lens; endfor for i=1 upto lens: if mc_char[i]<>BLK: mc_asc[incr char_cnt]:=mc_char[i]; mc_adr[char_cnt]:=i; fi endfor mc_asc[0]:=mc_asc[char_cnt+1]:=CMA; %-- argument check ------------------------------------------------------------------------- for i=1 upto char_cnt: nA:=mc_asc[i-1]; nB:=mc_asc[i]; nC:=mc_asc[i+1]; tbl_asc[nB]:=tbl_asc[nB]+1; if nB=CMA: if f_depth=0: block_cnt:=block_cnt+1; fi ef (nB=EQU)or(nB=CLN)or(nB=HAT)or(nB=BQT)or(nB=TLD)or(nB=LTN): % =,:,^,`,~,> if (nA=CMA)or(nC=CMA): proc_err(4,i) fi ef (nB=AMK)or(nB=AMP)or(nB=GTN)or(nB=HSH): % @,&,<,# if nA<>CMA: proc_err(5,nB) fi if nC=CMA: proc_err(4,i) fi ef (nB=SLS)or((nB>=7)and(nB<=11)): % /,*/*,//,/*,*/,** if (nA<>CMA)and(nA<>CLN)and(nA<>PRS): proc_err(5,i) fi if nC=CMA: proc_err(4,i) fi fi if (nB=PRS)or(nB=BRS): f_depth:=f_depth+1; ef (nB=PRE)or(nB=BRE): f_depth:=f_depth-1; fi endfor %-- brackets balance check ----------------------------------------------------------------- if tbl_asc[PRS]<>tbl_asc[PRE]: proc_err(1,0) fi % mismatch () if tbl_asc[BRS]<>tbl_asc[BRE]: proc_err(2,0) fi % mismatch {} if tbl_asc[BKS]<>tbl_asc[BKE]: proc_err(3,0) fi % mismatch [] else: proc_err(0,0) fi %--------------------------------------------------------------------------------------------- %%%%%%% err_cnt>0: readstring; err_cnt enddef; %------------------------------------------------------------------------------------------------- def proc_err(expr e,n)= err_cnt:=err_cnt+1; message "["&decimal(fig_num)&"]:"&err_type[e] if n>=1: &"("&fdr(3)(n)&") "&substring(mc_adr[n]-2,mc_adr[n]+3) of mc fi ; enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def savem(expr s)= file_output:=s; for i=1 upto ucount: for j=1 upto unit_lines[i]: printf row[i][j]; endfor endfor closefrom file_output; enddef; %------------------------------------------------------------------------------------------------- def loadm(text s)= begingroup save f_mcf,f_line,lines,unit_cnt,row_s,row_cnt,semic_cnt,info_cnt,order,min_n,max_n,firstc, sign_at,sign_n,filter_n,filter_tag,filter_var,filter_sign,filter_cnt,filter_p,lib_unit_cnt, at_colon,at_equal,at_less,at_greater,at_n,sort_tbl,key_s,sort_s,sign_s,sV,sS,sT,sort_oder, tag_s,val_s; string row_s[][],sort_s,sort_tbl[],key_s,filter_tag[],filter_var[],sign_s[],sV,sS,sT,firstc, tag_s[][],val_s[][]; numeric row_cnt[],order[],order_tbl[],filter_sign[],filter_p[]; lines:=f_mcf:=mc_row:=info_cnt:=filter_cnt:=lib_unit_cnt:=0; unit_cnt:=1; file_input:=default_library; sign_s1:="="; sign_s2:="<>"; sign_s3:="<"; sign_s4:=">"; sign_s5:="<="; sign_s6:=">="; %----------------------------------------------------------------------------------------------- for list=s: at_colon:=scan_c(":",list); at_equal:=scan_c("=",list); at_less:=scan_c("<",list); at_greater:=scan_c(">",list); key_s:=""; %--------------------------------------------------------------------------------------------- if at_colon>=2: sign_at:=at_colon; sign_n:=0; at_n:=1; ef at_equal>=2: if (at_equal-1)=at_less: sign_at:=at_equal; sign_n:=5; at_n:=2; ef (at_equal-1)=at_greater: sign_at:=at_equal; sign_n:=6; at_n:=2; else: sign_at:=at_equal; sign_n:=1; at_n:=1; fi ef at_greater>=2: if (at_greater-1)=at_less: sign_at:=at_greater; sign_n:=2; at_n:=2; else: sign_at:=at_greater; sign_n:=4; at_n:=1; fi ef at_less>=2: sign_at:=at_less; sign_n:=3; at_n:=1; fi sT:=substring(0,sign_at-at_n) of list; sV:=substring(sign_at,length(list)) of list; %--------------------------------------------------------------------------------------------- if sign_n=0: if sT="f": if scan_c(".",sV)=0: file_input:=sV&".mcf"; else: file_input:=sV; fi ef sT="a": key_s:=sV; sort_oder:=0; ef sT="d": key_s:=sV; sort_oder:=1; fi else: filter_tag[incr filter_cnt]:=sT; filter_sign[filter_cnt]:=sign_n; if (sign_n>=3)and(is_num(sV)=1): filter_var[filter_cnt]:=fix_num(sV); else: filter_var[filter_cnt]:=sV; fi fi endfor %----------------------------------------------------------------------------------------------- forever: temps:=readfrom file_input; exitif temps=EOF; firstc:=subc(1,temps); if (firstc<>"%")or(sw_comment=1): row_s[unit_cnt][incr lines]:=temps; if firstc=";": row_cnt[unit_cnt]:=lines; f_mcf:=lines:=0; filter_n:=1; for i=1 upto filter_cnt: filter_p[i]:=0; endfor sort_s:=""; for i=1 upto info_cnt: get_tag_var(arg_s[i])(sT,sV); tag_s[unit_cnt][i]:=sT; val_s[unit_cnt][i]:=sV; if sT=key_s: if is_num(sV)=1: sort_s:=fix_num(sV); else: sort_s:=sV; fi fi for j=1 upto filter_cnt: if filter_tag[j]=sT: filter_p[j]:=1; if (filter_sign[j]>=3)and(is_num(sV)=1): temps:=fix_num(sV); else: temps:=sV; fi if filter_sign[j]=1: if not(temps= filter_var[j]): filter_n:=0; fi ef filter_sign[j]=2: if not(temps<>filter_var[j]): filter_n:=0; fi ef filter_sign[j]=3: if not(temps< filter_var[j]): filter_n:=0; fi ef filter_sign[j]=4: if not(temps> filter_var[j]): filter_n:=0; fi ef filter_sign[j]=5: if not(temps<=filter_var[j]): filter_n:=0; fi ef filter_sign[j]=6: if not(temps>=filter_var[j]): filter_n:=0; fi fi fi endfor endfor for i=1 upto filter_cnt: if filter_p[i]=0: filter_n:=0; fi endfor info_cnt:=0; lib_unit_cnt:=lib_unit_cnt+1; if filter_n=1: if key_s<>"": sort_tbl[unit_cnt]:=sort_s; fi unit_cnt:=unit_cnt+1; fi ef (firstc=":")or(firstc="="): f_mcf:=1; mc_row:=1; ef (firstc<>"%")or(sw_comment=1): if f_mcf=1: mc_row:=mc_row+1; else: info[unit_cnt]:=info_cnt:=split_str(temps,";")(arg_s); fi fi fi endfor ucount:=unit_cnt:=unit_cnt-1; %============================================================================================= message "* Input : "&file_input&" ["&decimal(lib_unit_cnt)&"]"; message "* Output : ucount ["&decimal(ucount)&"]"; if filter_cnt>=1: for i=1 upto filter_cnt: message "* Filter("&decimal(i)&"): "&filter_tag[i]&" "&sign_s[filter_sign[i]]&filter_var[i]; endfor if key_s<>"": message "* Sort key : "&key_s&iif(sort_oder=0," (ascending)"," (descending)"); fi fi %----------------------------------------------------------------------------------------- if key_s<>"": for i=1 upto unit_cnt: order[i]:=0; endfor for i=1 upto unit_cnt: if sort_oder=0: temps:="~"; for j=1 upto unit_cnt: if order[j]=0: if sort_tbl[j]temps: temps:=sort_tbl[j]; max_n:=j; fi fi endfor order[max_n]:=i; order_tbl[i]:=max_n; fi endfor %--------------------------------------------------------------------------- for i=1 upto unit_cnt: for j=1 upto info[order_tbl[i]]: lib_tag[i][j]:=tag_s[order_tbl[i]][j]; lib_val[i][j]:=val_s[order_tbl[i]][j]; endfor unit_lines[i]:=row_cnt[order_tbl[i]]; for j=1 upto row_cnt[order_tbl[i]]: row[i][j]:=row_s[order_tbl[i]][j]; endfor endfor %------------------------------------------------------------------------- else: for i=1 upto unit_cnt: for j=1 upto info[i]: lib_tag[i][j]:=tag_s[i][j]; lib_val[i][j]:=val_s[i][j]; endfor unit_lines[i]:=row_cnt[i]; for j=1 upto row_cnt[i]: row[i][j]:=row_s[i][j]; endfor endfor fi closefrom file_input; endgroup; enddef; %============================================================================================= vardef fix_num(expr s)= sS:=s; nN:=scan_c(".",sS); if nN=0: sS:=fsr(4)(sS); ef nN=1: sS:=" 0"&sS; ef nN=2: sS:=" "&sS; ef nN=3: sS:=" "&sS; ef nN=4: sS:=" "&sS; fi sS enddef; %------------------------------------------------------------------------------------------------- vardef is_num(expr s)= for i=1 upto length(s): if ((subc(i,s)>="0")and(subc(i,s)<="9"))or(subc(i,s)="."): nN:=1; else: nN:=0; fi endfor nN enddef; %------------------------------------------------------------------------------------------------- vardef scan_bit(expr n,b)= if b>=1: odd(floor(n/b)) else: odd(floor((frac n)/b)) fi enddef; %------------------------------------------------------------------------------------------------- vardef scan_char(expr c,s,d,n)= nN:=0; if d=0: for i=n upto length(s): if subc(i,s)=c: nN:=i; fi exitif nN>0; endfor ef d=1: for i=n upto length(s): if subc(i,s)<>c: nN:=i; fi exitif nN>0; endfor ef d=-1: for i=length(s) downto n: if subc(i,s)<>c: nN:=i; fi exitif nN>0; endfor fi nN enddef; %------------------------------------------------------------------------------------------------- def scan_c(expr c,s)= scan_char(c,s,0,1) enddef; %------------------------------------------------------------------------------------------------- vardef split_str(expr s,c)(suffix v)= at_char[0]:=nN:=0; for i=1 upto length(s): if subc(i,s)=c: at_char[incr nN]:=i; fi endfor nN:=nN+1; at_char[nN]:=length(s)+1; for i=1 upto nN: v[i]:=substring (at_char[i-1],at_char[i]-1) of s; endfor nN enddef; %------------------------------------------------------------------------------------------------- vardef get_tag_var(expr s)(suffix t,v)= nN:=scan_c(":",s); t:=substring(0,nN-1) of s; v:=substring(nN,length(s)) of s; enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%