diff options
Diffstat (limited to 'Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf')
| -rw-r--r-- | Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf | 330 |
1 files changed, 142 insertions, 188 deletions
diff --git a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf index af136209e34..0ebece8405f 100644 --- a/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf +++ b/Master/texmf-dist/metapost/mcf2graph/mcf2graph.mf @@ -1,5 +1,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% mcf2graph ver 4.56 Copyright (c) 2013-2021 Akira Yamaji +% mcf2graph ver 4.57 Copyright (c) 2013-2021 Akira Yamaji % % Permission is hereby granted, free of charge, to any person obtaining a copy of this software % and associated documentation files (the "Software"), to deal in the Software without restriction, @@ -37,12 +37,12 @@ % Set to use plain.mp (label,arrow,atom) : mpost -s labeloffset=2 FILENAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% tracingstats:=1; -message "* This is mcf2graph ver 4.56 2021.01"; +message "* This is mcf2graph ver 4.57 2021.02.11"; %------------------------------------------------------------------------------------------------- newinternal cntA,cntB,cntM,minX,minY,maxX,maxY,sftX,sftY,com,par,envT,envB,lenT,lineT,angT,rotT, crR,nA,nB,nC,nD,nE,nF,nN,nP,nU,nP,nL,nR,nS,nW,xpos,ypos,markA,markB,saveA,saveB,bondL; numeric save_num[],comD[][],parD[][],adrD[][],cntD[],tbl_atom[],tbl_group[][],f_char[], - tbl_atom_wt[],tbl_atom_mi[],tbl_char_wd[],tbl_char_ht[],andA[],and_rot[],chargeA[], + tbl_atom_wt[],tbl_atom_mi[],tbl_char_wd[],tbl_char_ht[],addA[],add_rot[],chargeA[], com_group[][],par_group[][],cnt_group[],colorA[],colorB[],sumA[],bondC[],hideH[], lineB[],sB[],eB[],angB[],angA[],lenB[],angX[],numS[],wdM[],htM[],wdA[],dxA[]; string info[],save_str[],tbl_atom_str[],strD[],tag[],out_file_name,out_file_aux, @@ -191,8 +191,8 @@ def def_com(expr n)(text tx)= nA:=n; forsuffixes list=tx:: list:=nA; nA:=nA+1; e 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,_set_adr,_mk_bond,_set_atom,_arg_ang,_chg_atom,_tmp_rot,_fuse,_size_atom,_numeric, - _jump_at,_connect_at,_set_and,_chg_and,_nop,_mark,_moff,_term,_len_s,_len_e,_len_ss,_len_ee, - _group_s,_group_e,_rest, + _jump_at,_set_add,_chg_add,_nop,_mark,_moff,_term,_len_s,_len_e,_len_ss,_len_ee, + _group_s,_group_e,_rest,_charge, si,dl,dr,db,dm,tm,wf,wb,bd,bz,zf,zb,dt,wv,nl,vf,vb,nb,si_,dl_,dr_,dm_,wf_,wb_,zf_,zb_,wv_,bd_); %-------------------------------------------------------------------------------------------------- def parameter_list= @@ -319,38 +319,29 @@ def endfont= enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def set_def_MC= - save /,//,/*,*/,**,*/*,~,^,',`,``,<,>,&,:,=,\,\\,*\,\*,*\*,@,#,@#,$, - {,},|,||,|||,|=,=|,|<,>|,|<<,>>|,:|,_,d,w,z,CP,CPe,CPx,inside_def_MC; + save /,//,/*,*/,**,*/*,~,^,',`,<,>,&,:,=,\,\\,*\,\*,*\*,@,$,&,#,##,{,},|,||,_,inside_def_MC; inside_def_MC:=1; - _:=Me; d:=db; w:=wf; z:=zf; + _:=Me; tertiarydef a=b == if (known a)and(known b):: change_bond(a,b) else:: _nop fi enddef; tertiarydef a:b == if (known a)and(known b):: change_atom(a,b) else:: _nop fi enddef; - def { == read_number( enddef; let } == ); - def &primary s == (_set_and,ASCII(s)) enddef; - vardef $primary a == a-4095 enddef; - def <primary n == (_rot_ang,n) enddef; - def ``primary n == (_chg_len,n) enddef; + def { == read_number( enddef; let } == ); def <primary n == (_rot_ang,n) enddef; tertiarydef a^b == if known b:: (_tmp_rot,b),a else:: _nop,a fi enddef; tertiarydef a`b == if known b:: (_tmp_len,b),a else:: _nop,a fi enddef; tertiarydef a~b == if known b:: (_tmp_line,b),a else:: _nop,a fi enddef; tertiarydef a>b == if known b:: (_tmp_env,b),a else:: _nop,a fi enddef; - def # == _connect_at enddef; def @ == _jump_at enddef; primarydef a@#b == a:@,b:# enddef; - def \ == @,0 enddef; def \\ == \~dm enddef; def *\ == \~wf enddef; def \* == \~zf enddef; + def @primary n == (_jp_atom,n) enddef; def &primary n == (_cyc,n) enddef; + def \ == 0 enddef; def \\ == \~dm enddef; def *\ == \~wf enddef; def \* == \~zf enddef; def *\* == \~wv enddef; - def | == (_com,_mark) enddef; def || == (_com,_moff) enddef; def ||| == (_com,_term) enddef; - def |< == (_com,_len_s) enddef; def >| == (_com,_len_e) enddef; - def |<< == (_com,_len_ss) enddef; def >>| == (_com,_len_ee) enddef; - def |=primary n == |<,(_chg_len,n) enddef; def =| == >| enddef; def :| == (_com,_rest) enddef; + def | == (_com,_mark) enddef; def || == (_com,_moff) enddef; + def #primary n == (_com,_len_s),(_chg_len,n) enddef; def ## == (_com,_len_e) enddef; def /secondary n == if known n:: (_group_si,n) else:: _nop fi enddef; - def //secondary n == /n~dm enddef; def */secondary n == /n~wf enddef; - def /*secondary n == /n~zf enddef; def */*secondary n == /n~wv enddef; - def **secondary n == /n~nb enddef; - vardef '(text TXT)== read_mcf(incr parts_cnt)(|,``crR,TXT,:|); parts_cnt enddef; - def CP == com_par enddef; - def CPe == com_par_ex(0) enddef; - def CPx == com_par_ex(1) enddef; + def //secondary n == /n~dm enddef; def */secondary n == /n~wf enddef; + def /*secondary n == /n~zf enddef; def */*secondary n == /n~wv enddef; + def **secondary n == /n~nb enddef; vardef $primary a == a-4095 enddef; + vardef '(text TXT)==read_mcf(incr parts_cnt)(|,#crR,TXT,##,(_com,_rest)); parts_cnt enddef; enddef; %------------------------------------------------------------------------------------------------- +def CP == com_par enddef; def CPe == com_par_ex(0) enddef; def CPx == com_par_ex(1) enddef; vardef '(text TXT)= parts_cnt:=parts_cnt+1; read_mcf(parts_cnt)(TXT); parts_cnt enddef; %================================================================================================= def read_mcf(expr n)(text TXT)= @@ -371,8 +362,12 @@ def read_mcf(expr n)(text TXT)= else:: nCP:=nCP+1; comD[n][nCP]:=_mk_bond; parD[n][nCP]:=list; fi elseif string list:: - str_cnt:=str_cnt+1; strD[str_cnt]:=list; - nCP:=nCP+1; comD[n][nCP]:=_set_atom; parD[n][nCP]:=str_cnt; + if (list=="+")or(list=="-"):: + nCP:=nCP+1; comD[n][nCP]:=_set_add; parD[n][nCP]:=ASCII(list); + else:: + str_cnt:=str_cnt+1; strD[str_cnt]:=list; + nCP:=nCP+1; comD[n][nCP]:=_set_atom; parD[n][nCP]:=str_cnt; + fi fi else:: message "unknown command in "AND decimal(n); fi @@ -440,8 +435,6 @@ vardef change_bond(expr a,b) = CP(_set_adr,-4) CP(_set_line,dl) elseif b==Ph2:: fuse_ring(a,6) CP(_set_adr,-1) CP(_set_line,dl) CP(_set_adr,-3) CP(_set_line,dl) CP(_set_adr,-5) CP(_set_line,dl) - elseif b==_jump_at:: CP(_jp_bond,a) - elseif b==_connect_at:: CP(_cyc_sB,a) elseif comD[b][1]==_fuse:: if comD[b][2]<=6:: fuse_ring_bonds(a,parD[b][1],comD[b][2]) elseif (comD[b][2]>=11)and(comD[b][2]<=15):: fuse_ring_size(a,parD[b][1],comD[b][2]) @@ -461,7 +454,7 @@ vardef change_atom(expr a,b)= nCP:=0; if numeric b:: if (b GT parts_emb_start)and(b<=parts_atom_end):: CPe(a)(_chg_atom,b) - ef b==NH:: CPe(a)(_chg_atom,N) CP(_tmp_line,nl) + ef b==NH:: CPe(a)(_chg_atom,N) if NH<>xNH:: CP(_tmp_line,nl) fi CP(_com,_group_s) CPx(a)(_group_si,H) CP(_com,_group_e) ef b==N!:: CPe(a)(_chg_atom,N) CP(_com,_group_s) CPx(a)(_group_si,_) CP(_com,_group_e) ef b==N!2:: CPe(a)(_chg_atom,N) CP(_com,_group_s) CPx(a)(_group_si,!) CP(_com,_group_e) @@ -472,14 +465,10 @@ vardef change_atom(expr a,b)= CP(_tmp_line,dm) CP(_tmp_rot,-35) CPx(a)(_group_si,O) CP(_com,_group_e) ef b==SO:: CPe(a)(_chg_atom,S) CP(_com,_group_s) CP(_tmp_line,dm) CPx(a)(_group_si,O) CP(_com,_group_e) - ef b==_jump_at:: CP(_jp_atom,a) - ef b==_connect_at:: CP(_cyc,a) - fi - ef pair b:: - if xpart(b)==_set_and:: CP(_set_and,ypart(b)) CP(_chg_and,a) - else:: CP(_com,_group_s) CPx(a)(xpart(b),ypart(b)) CP(_com,_group_e) fi - ef color b:: color_list[incr cntC]:=b; CPe(a)(_set_colorA,cntC) + ef pair b:: CP(_com,_group_s) CPx(a)(xpart(b),ypart(b)) CP(_com,_group_e) + ef string b:: CP(_com,_group_s) CP(_set_add,ASCII(b)) CP(_chg_add,a) CP(_com,_group_e) + ef color b:: color_list[incr cntC]:=b; CPe(a)(_set_colorA,cntC) fi cntD[parts_int]:=nCP; parts_int %------- Retern value ------- @@ -740,21 +729,21 @@ enddef; %------------------------------------------------------------------------------------------------- def MC(text TXT)= begingroup - save f_bra,strAT,cnt_group,temp_lenE,temp_lenF,temp_cntB,f_end,f_term,f_at,f_lineT,f_rotT, + save f_bra,strAT,cnt_group,temp_lenE,temp_lenF,temp_cntB,f_term,f_at,f_lineT,f_rotT, f_lenT,f_envT,sA,factor,m_wd,m_ht,temp_p,defaultsize,defaultscale; string sA; pair temp_p; %----------------------------------------------------------------------------------------------- if (sw_numberA>=1)or(sw_numberB>=1): ratio_atom_bond:=0.25; fi - if (sw_expand=1)or(sw_mol_out>=1): expand_set; fi - cntA:=cntB:=cnt_group:=cntC:=0; strD[0]:="C"; str_cnt:=2000; crR:=-ratio_chain_ring; + if (sw_expand=1)or(sw_mol_out>=1): expand_set; crR:=1; else: crR:=-ratio_chain_ring; fi + cntA:=cntB:=cnt_group:=cntC:=0; strD[0]:="C"; str_cnt:=2000; %----------------------------------------------------------------------------------------------- font_wd:=xpart(fsize); font_ht:=ypart(fsize); margin_lr:=xpart(fmargin); margin_tb:=ypart(fmargin); %=============================================================================================== - read_mcf(0)(TXT,|||); + read_mcf(0)(TXT,(_com,_term)); proc_bond_atom(0)(1); if (cnt_group>0)and(sw_group_off=0): read_group(0)(1); fi char_use_check; @@ -777,28 +766,24 @@ def MC(text TXT)= else: factor:=((font_wd-2margin_lr)*xpart(msize))/mol_wd; fi fi - exitif (factor>=1-eps)and(factor<=1+eps); - blen:=blen*factor; - proc_size_setup; + 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 + if blen>max_blength: blen:=max_blength; proc_size_setup; proc_skeleton(0); proc_scaling; fi fi - %-draw atom-------------------------------------------------------------------------------------- + %-draw atom------------------------------------------------------------------------------------- if (sw_numberA=0)and(sw_numberB=0): for i=1 upto cntA: draw_atom(i); endfor fi - %-draw charge------------------------------------------------------------------------------------ + %-draw add to atom------------------------------------------------------------------------------ for i=1 upto cntA: - if andA[i]<>0: - sA:=char(andA[i]); nA:=angX[i]+and_rot[i]; nC:=nA mod 90; + if addA[i]<>0: + sA:=char(addA[i]); nA:=angX[i]+add_rot[i]; nC:=nA mod 90; + if sA="+": chargeA[i]:=1; elseif sA="-": chargeA[i]:=-1; else: chargeA[i]:=0; fi if numS[i]=0: nB:=.5atom_wd; - else: nB:=.85atom_wd+iif(nC<45,sind(nC),cosd(nC))*.5atom_wd; + else: nB:=.85wdA[i]+iif(nC<45,sind(nC),cosd(nC))*.5wdA[i]; fi temp_p:=sfrt(posA[i]-(.35atom_wd,.35atom_wd),nB,nA); draw_char(sA,temp_p,atom_wd,bond_pen_wd*ratio_char_bond,0); - else: sA:=""; + else: chargeA[i]:=0; fi - if sA="+": chargeA[i]:=1; elseif sA="-": chargeA[i]:=-1; else: chargeA[i]:=0; fi endfor %-draw bond------------------------------------------------------------------------------------- for i=1 upto cntB: if lineB[i]<si_ : draw_bond(i); fi endfor @@ -950,12 +935,12 @@ def char_use_check= enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def proc_bond_atom(expr a)(expr n)= - f_bra:=f_end:=f_term:=rotT:=f_lineT:=f_rotT:=f_lenT:=f_envT:=envT:=envB:=strAT:=f_at:=0; + f_bra:=f_term:=rotT:=f_lineT:=f_rotT:=f_lenT:=f_envT:=envT:=envB:=strAT:=f_at:=0; bondL:=crR; lenT:=crR; sB[0]:=0; eB[0]:=1; lineT:=si; - andAT:=markA:=markB:=saveA:=saveB:=0; + addAT:=markA:=markB:=saveA:=saveB:=0; %----------------------------------------------------------------------------------------------- for i=n upto cntD[a]: com:=comD[a][i]; par:=parD[a][i]; - if com=_mk_bond: if (par=0)and(rotT<>0): rotT:=0; fi add_atom; + if com=_mk_bond: if (par=0)and(rotT<>0): rotT:=0; fi add_atom(0); ef com=_set_adr: adrT:=par; ef com=_com: if par=_mark: saveA:=markA; saveB:=markB; markA:=cntA; markB:=cntB; ef par=_rest: markA:=saveA; markB:=saveB; @@ -982,28 +967,29 @@ def proc_bond_atom(expr a)(expr n)= ef com=_set_line: lineB[getB(adrT)]:=par; ef com=_tmp_line: lineT:=par; ef com=_tmp_rot: rotT:=par; - ef com=_cyc: f_end:=getA(par); check_adrA(f_end); add_atom; - ef com=_cyc_eB: f_end:=eB[getB(par)]; add_atom; - ef com=_cyc_sB: f_end:=sB[getB(par)]; add_atom; + ef com=_cyc: check_adrA(getA(par)); add_atom(getA(par)); + ef com=_cyc_eB: add_atom(eB[getB(par)]); + ef com=_cyc_sB: add_atom(sB[getB(par)]); ef com=_chg_env: envB:=par; ef com=_tmp_env: envT:=par; ef com=_set_colorA: colorA[getA(adrT)]:=par; ef com=_set_colorB: colorB[getB(adrT)]:=par; - ef com=_set_and: andAT:=par; - ef com=_chg_and: andA[getA(par)]:=andAT; andAT:=0; if rotT<>0: and_rot[getA(par)]:=rotT; fi + ef com=_set_add: addAT:=par; + ef com=_chg_add: addA[getA(par)]:=addAT; addAT:=0; if rotT<>0: add_rot[getA(par)]:=rotT; fi else: fi endfor enddef; %------------------------------------------------------------------------------------------------- -def add_atom= +def add_atom(expr n)= cntB:=cntB+1; lineB[cntB]:=lineT; lineT:=si; if lenT=crR: lenB[cntB]:=bondL; else: lenB[cntB]:=lenT; lenT:=crR; fi if f_bra=0: cntA:=cntA+1; sB[cntB]:=cntA; numS[cntA]:=strAT; - andA[cntA]:=andAT; andAT:=strAT:=and_rot[cntA]:=0; - if rotT<>0: and_rot[cntA]:=rotT; rotT:=0; fi - if f_MP=1: colorA[cntA]:=colorB[cntA]:=0; fi else: f_bra:=0; fi - if f_end=0: eB[cntB]:=cntA+1; f_term:=0; else: eB[cntB]:=f_end; f_end:=0; f_term:=1; fi + addA[cntA]:=addAT; addAT:=strAT:=add_rot[cntA]:=0; + if rotT<>0: add_rot[cntA]:=rotT; rotT:=0; fi + if f_MP=1: colorA[cntA]:=colorB[cntA]:=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)= @@ -1012,20 +998,20 @@ enddef; def check_adrB(expr n)= if (n>cntB)or(n<=0): errmessage("cntB=[ "&decimal(n)&" ]"); fi enddef; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% def proc_skeleton(expr a)= - markA:=markB:=cntA:=cntB:=f_end:=f_bra:=rotT:=f_term:=0; + 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 cntD[a]: com:=comD[a][i]; par:=parD[a][i]; - if com=_mk_bond: if (par=0)and(rotT<>0):par:=rotT; rotT:=0; fi add_bond(par); + if com=_mk_bond: if (par=0)and(rotT<>0):par:=rotT; rotT:=0; fi add_bond(par,1); ef com=_com: if par=_mark: saveA:=markA; saveB:=markB; markA:=cntA; markB:=cntB; ef par=_rest: markA:=saveA; markB:=saveB; ef par=_moff: markA:=markB:=0; ef par=_term: termB; ef par=_group_e: lineT:=si; lenT:=crR; rotT:=envT:=0; fi - ef com=_jp_bond: termB; nA:=getB(par); posBs:=posA[sB[nA]]; angT:=angB[nA]; f_bra:=1; rotT:=0; + ef com=_jp_bond: termB; nA:=getB(par); posBs:=posA[sB[nA]]; angT:=angB[nA]; f_bra:=1; rotT:=0; ef com=_jp_atom: termB; adrT:=getA(par); posBs:=posA[adrT]; angT:=angX[adrT]; f_bra:=1; rotT:=0; ef com=_jp_absA: adrT:=par; posBs:=posA[adrT]; - angT:=angX[adrT]; f_bra:=1; rotT:=0; temp_cntB:=cntB; + angT:=angX[adrT]; f_bra:=1; rotT:=0; temp_cntB:=cntB; ef com=_adj_ang: if (angT<40)or(angT>320): angT:=0; ef angT<140: angT:=90; ef angT<220: angT:=180; else: angT:=270; fi ef com=_rot_ang: angT:=(angT+par) mod 360; @@ -1033,49 +1019,44 @@ def proc_skeleton(expr a)= ef com=_group_si: rotT:=0; ef com=_chg_env: envB:=par; ef com=_tmp_env: envT:=par; - ef com=_cyc: f_end:=1; proc_cyc(getA(par)); - ef com=_cyc_sB: f_end:=1; proc_cyc(sB[getB(par)]); - ef com=_cyc_eB: f_end:=1; proc_cyc(eB[getB(par)]); + ef com=_cyc: add_bond(angle(posA[getA(par)]-posBs)-angT,0); + ef com=_cyc_sB: add_bond(angle(posA[sB[getB(par)]]-posBs)-angT,0); + ef com=_cyc_eB: add_bond(angle(posA[eB[getB(par)]]-posBs)-angT,0); else: fi endfor enddef; %------------------------------------------------------------------------------------------------- -def add_bond(expr ROT)= - if ROT=_arg_ang: - if cntB=0: angT:=(angT-180) mod 360; nA:=180; - else: - nB:=(angT mod 360); - if envB>=parts_emb_start: nA:=parD[envB][cntB-temp_cntB+2]; - else: - if envB=hz: - if nB=0:nA:= 60;ef nB<=90:nA:=-60;ef nB<=180:nA:= 60;ef nB<270:nA:=-60;else:nA:= 60; fi - ef envB=vt: - if nB=0:nA:=-60;ef nB<90: nA:= 60;ef nB<=180:nA:=-60;ef nB<=270:nA:=60;else:nA:=-60; fi - ef (envB>=-180)and(envB<=180): nA:=envB; - fi - fi - fi - else: nA:=ROT; - fi +def add_bond(expr ROT,FLG)= + if ROT=_arg_ang: nA:=arrange_ang(angT mod 360); else: nA:=ROT; fi if f_bra=0: adrT:=cntA:=cntA+1; posA[cntA]:=posBs; angA[cntA]:=angT; angX[cntA]:=(angT+nA/2+iif(nA>=0,-90,90)) mod 360; else: f_bra:=0; fi - angB[cntB+1]:=angT:=(angT+nA) mod 360; - if f_end=0: - if lenB[cntB+1]=_size_atom: posBe:=sfrt(posBs,atom_wd,angT); + cntB:=cntB+1; angB[cntB]:=angT:=(angT+nA) mod 360; + if FLG=1: + if lenB[cntB]=_size_atom: posBe:=sfrt(posBs,atom_wd,angT); else: - nA:=lenB[cntB+1]; + 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: - f_end:=0; f_term:=1; + if envB>=parts_emb_start: parD[envB][cntB-temp_cntB+2] + 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 - cntB:=cntB+1; posBs:=posBe; enddef; %================================================================================================= vardef getA(expr n)= if n>=0: markA+n ef n>=-999: cntA+n+1 else: n+4095 fi enddef; @@ -1084,8 +1065,8 @@ vardef getB(expr n)= if n>=0: markB+n ef n>=-999: cntB+n+1 else: n+4095 fi endde def termA= if f_term=0: if f_bra=0: - cntA:=cntA+1; numS[cntA]:=strAT; andAT:=strAT:=and_rot[cntA]:=andA[cntA]:=0; - if rotT<>0: and_rot[cntA]:=rotT; rotT:=0; fi + cntA:=cntA+1; numS[cntA]:=strAT; addA[cntA]:=addAT; add_rot[cntA]:=rotT; + addAT:=strAT:=rotT:=0; if f_MP=1: colorA[cntA]:=0; fi else: f_bra:=0; fi @@ -1094,11 +1075,9 @@ def termA= enddef; %------------------------------------------------------------------------------------------------- def termB= - if f_term=0: if f_bra=0: cntA:=cntA+1; angX[cntA]:=angT mod 360; else:f_bra:=0; fi f_term:=1; fi + if f_term=0: if f_bra=0:cntA:=cntA+1; angX[cntA]:=angT mod 360; else:f_bra:=0; fi f_term:=1; fi enddef; %------------------------------------------------------------------------------------------------- -def proc_cyc(expr n)= add_bond(angle(posA[n]-posBs)-angT); enddef; -%------------------------------------------------------------------------------------------------- vardef glu_atom(expr NUM)= if numS[NUM]<>0: nE:=angT mod 90; nF:=0.5atom_wd;(iif(nE<45,sind(nE),cosd(nE))*nF)++nF else: 0 fi enddef; @@ -1407,7 +1386,7 @@ vardef fdl(expr n)(expr s)=fixed_l(n)(decimal(s)) enddef; def warning(expr s)= message "% "&decimal(char_num)&fdr(3)(incr warning_cnt)&")"&s; enddef; %------------------------------------------------------------------------------------------------- def warning_bond(expr a)= - if andA[a]=0: + if addA[a]=0: warning("A"&decimal(a)&" ( "&fixed_l(8)(strD[numS[a]])&") has"&fdr(2)(bond_cnt)&" bonds"); fi enddef; @@ -1419,7 +1398,9 @@ vardef cut_paren(expr ATOM)= if (length(ATOM)>=4)and(ATOM<>"COOH"): for i=0 upto length(ATOM)-1: temp_c:=subc(i,ATOM); - if (temp_c<>"{")and(temp_c<>"}")and(temp_c<>"_")and(temp_c<>"^"): temp_s:=temp_s&temp_c; fi + if (temp_c<>"{")and(temp_c<>"}")and(temp_c<>"_")and(temp_c<>"^") + and(temp_c<>"+")and(temp_c<>"-"): + temp_s:=temp_s&temp_c; fi endfor temp_s else: ATOM @@ -1433,9 +1414,6 @@ def proc_calc= nE:=parts_emb_start; for i=1 upto tbl_atom_end: sumA[i]:=0; endfor for i=1 upto cntA: - if (numS[i]>str_plus)and(numS[i]<=str_minus): chargeA[i]:=1; - elseif (numS[i]>str_minus)and(numS[i]<=str_minus_end): chargeA[i]:=-1; - fi knownA:=bond_cnt:=0; nS:=numS[i]; for j=1 upto cntB: @@ -1502,9 +1480,9 @@ def proc_calc= else: num_MW:=cen_MW; cal_MW:=fdr(6)(cen_MW)&"*100"; fi if cen_MI<40: cal_MI:=substring (0,10) of decimal(num_MI); else: num_MI:=cen_MI; cal_MI:=fdr(8)(cen_MI)&"*100"; fi - if sw_aux_out>=1: proc_auxfile_out; fi - if sw_rep_out=1: proc_report_out; fi - if sw_mol_out>=1: proc_mol_out; fi + if (sw_aux_out>=1)and(cntM=1): proc_auxfile_out; fi + if (sw_rep_out=1)and(cntM=1): proc_report_out; fi + if (sw_mol_out>=1)and(cntM=1): proc_mol_out; fi endgroup enddef; %================================================================================================= @@ -1606,76 +1584,59 @@ def proc_report_out= enddef; %================================================================================================= def proc_mol_out= - begingroup - save chg_cnt,chg_atm,chg_chg; - nA:=nB:=chg_cnt:=0; message "["&decimal(char_num)&"]:"&inf_EN; out_file_name:=out_file_mol; - if sw_mol_out<=2: - out_file_name:=out_file_mol; - if sw_mol_out=1: proc_vdk; elseif sw_mol_out=2: proc_vtk; fi - fi - endgroup -enddef; -%-V2000------------------------------------------------------------------------------------------ -def proc_vdk= - printf ""; printf " -MCFtoMOL- "&fixed_l(20)(info[1]); - 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)&" "&fixed_l(2)(cut_paren(strD[numS[i]]))&" 0 0 0 0"; - if chargeA[i]<>0: chg_atm[incr chg_cnt]:=i; chg_chg[chg_cnt]:=chargeA[i]; fi - endfor - for i=1 upto cntB: - if lineB[i]<>0: - proc_bond_class(lineB[i]); - printf fdr(3)(sB[i])&fdr(3)(eB[i])&fdr(3)(nA)&fdr(3)(nB)&" 0 0"; - fi - endfor - if chg_cnt>0: - printf "M CHG"&fdr(3)(chg_cnt) - for i=1 upto chg_cnt: &fdr(4)(chg_atm[i])&fdr(4)(chg_chg[i]) endfor; + %-V2000--------------------------------------------------------------------------------------- + if sw_mol_out=1: + printf ""; printf " -MCFtoMOL- "&fixed_l(20)(info[1]); 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)&" "& + fixed_l(2)(cut_paren(strD[numS[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 sw_mol_out=2: + printf ""; printf " -MCFtoMOL- "&fixed_l(20)(info[1]); printf ""; + printf " 0 0 0 0 0 999 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)&" "&cut_paren(strD[numS[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 - printf "M END"; -enddef; -%-V3000--------------------------------------------------------------------------------------- -def proc_vtk= - printf ""; printf " -MCFtoMOL- "&fixed_l(20)(info[1]); - printf ""; - printf " 0 0 0 0 0 999 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)&" "&cut_paren(strD[numS[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: - proc_bond_class(lineB[i]); - printf "M V30 "&decimal(i)&" "&decimal(nA)&" "&decimal(sB[i])&" "&decimal(eB[i]); - fi - endfor - printf "M V30 END BOND"; - printf "M V30 END CTAB"; - printf "M END"; enddef; %------------------------------------------------------------------------------------------------- vardef fit_zero(expr n)=if n<=9: "00" elseif n<=99: "0" else: "" fi &decimal(n) enddef; %------------------------------------------------------------------------------------------------- -def proc_bond_class(expr n)= - if (n=dl)or(n=dr)or(n=dm): nA:=2; - ef n=tm: nA:=3; - ef (n=wf)or(n=zb)or(n=bd): nB:=1; - ef (n=zf)or(n=wb)or(n=dt): nB:=6; - ef n=wv: nB:=4; - else: nA:=1; nB:=0; - fi -enddef; +vardef bond_type(expr n)= + if (n=dl)or(n=dr)or(n=dm)or(n=db)or(n=dl_)or(n=dr_)or(n=dm_): 2 ef n=tm: 3 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 STa(expr ATOM,WT,MI)= str_cnt:=str_cnt+1; tbl_cnt:=tbl_cnt+1; parts_cnt:=parts_cnt+1; @@ -1717,10 +1678,10 @@ N:= STa("N" ,14.0067, 14.00307400443); Na:=STa("{Na}",22.98977, 22.989769 Ni:=STa("{Ni}",58.693, 57.93534241); O:= STa("O" ,15.9994, 15.99491461957); P:= STa("P" ,30.973762, 30.97376199842); Pb:= STa("Pb" ,207.2, 205.974455); Pd:=STa("Pd" ,106.4, 107.905075); -S:= STa("S" ,32.065, 31.9720711744); Sb:= STa("Sb" ,121.75, 0.0); +S:= STa("S" ,32.065, 31.9720711744); Sb:= STa("Sb" ,121.75, 120.90381); Se:=STa("{Se}",78.971, 79.9165218); Si:=STa("{Si}",28.0855, 27.97692653465); Sn:=STa("{Sn}",118.71, 119.90220163); Ti:=STa("{Ti}",47.867, 47.94794198); -U:= STa("U", 238.0289, 238.05079); V:= STa("V", 50.9415, 0.0); +U:= STa("U", 238.0289, 238.05079); V:= STa("V", 50.9415, 50.943957); W:= STa("W", 183.85, 181.948225); Zn:=STa("{Zn}",65.409, 63.92914201); tbl_atom_end:=tbl_cnt; %------------------------------------------------------------------------------------------------- @@ -1730,23 +1691,16 @@ NO:=STb("NO")(N,O); NO2:=STb("N{O_2_}")(N,O,O); NH2:=STb("N{H_2_}")(N,H,H); SO2H:=STb("S{O_2_}H")(S,O,O,H); SO3H:=STb("S{O_3_}H")(S,O,O,O,H); ONa:=STb("O{Na}")(O,Na); SO3Na:=STb("S{O_3_}{Na}")(S,O,O,O,Na); %------------------------------------------------------------------------------------------------- -str_plus:=str_cnt; -N[1]:=STb("{N^+^}")(N); H[1]:=STb("{H^+^}")(H); Na[1]:=STb("{Na^+^}")(Na); K[1]:=STb("{K^+^}")(K); -NH3[1]:= STb("{N^+^}{H_3_}")(N,H,H,H); NH4[1]:= STb("{N^+^}{H_4_}")(N,H,H,H,H); -S[1]:= STb("{S^+^}")(S); -str_minus:=str_cnt; -O[-1]:=STb("{O^-^}")(O); COO[-1]:=STb("COO^-^")(C,O,O); SO3[-1]:=STb("S{O_3_}^-^")(S,O,O,O); -Cl[-1]:=STb("{Cl^-^}")(Cl); Br[-1]:=STb("{Br^-^}")(Br); I[-1]:=STb("{I^-^}")(I); -%------------------------------------------------------------------------------------------------- -str_minus_end:=str_cnt; tbl_group_end:=tbl_cnt; parts_atom_end:=parts_cnt; %================================================================================================= -for i==3 upto 20: ?[i]:='(|<<,(_get_len,_ring_len),<((-180 DIV i)-90) - for j==2 upto i:: ,(360 DIV i) endfor,(_cyc_sB,1-i),>>|); endfor +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); !:=!1:='((_mk_bond,_arg_ang)); !!:='(!~db); !!!:='(!~tm); -for i==2 upto 20: ![i]:='(|<<,(_get_len,_tmp_len),! for j==2 upto i::,! endfor ,>>|); endfor +for i==2 upto 20: + ![i]:='((_com,_len_ss),(_get_len,_tmp_len),! for j==2 upto i::,! endfor ,(_com,_len_ee)); +endfor Me:='(); Et:='(!); iPr:=?!:='(/_,!); tBu:=??!:='(/_,/_^60,60); !?!:='(!,?!); !??!:='(!,??!); %------------------------------------------------------------------------------------------------- NH:='(N,/H~nl); N!:='(N,/_); N!2:='(N,/!); SO:='(S,//O); SOO:='(S,//O^-35,//O^35); |