******************************************************************************* Changelog of mcf2graph software package by Akira Yamaji 2024-02-25 ******************************************************************************* [ver. 5.12 / 2024-02-25] -add command `(),``() define group "string" `("{string}") ``("{string}")(atom list) -update mcf2graph.mp -update main_lib.mcf -update MCF manual,example [ver. 5.11 / 2024-01-21] -change command name !! => !db,!d !!! => !tm,!t -change group name CCl2=> ?Cl!Cl CCl3=> ?Cl?Cl!Cl CF2 => ?F!F CF3 => ?F?F!F -add abbreviated form command !wf,!w : !~wf !zf,!z : !~zf !db,!d : !~db !wb : !~wb !zb : !~zb !dl : !~dl !dr : !~dr !dm : !~dm -update main_lib.mcf,template_lib.mcf -update MCF manual,example [ver. 5.10 / 2024-01-03] -add binary operator + a + b : '(a,b) -change group name CO => ?O, COO => ?O!O SO => S?O, SOO => S?O?O N! => N?, N!2 => N?2 -change command name of add(),ext() ** => # -fix bug in expand mode -update MCF manual,example [ver. 5.02 / 2023-05-28] -change command name cv() => drawm() -add abbreviated form command '',$,@,#,#@,##,|=,|<,_,\,\*,\\ -delete command cvat() -update MCF manual,example [ver. 5.01 / 2023-05-15] -change command name cv_at() => cvat() -update MCF manual,example [ver. 5.00 / 2023-05-07] -change syntax of beginfigm() beginfigm() => beginfigm -change command name MC() => cv() mc_check() => checkm() -change library name mcf_library.mcf => main_lib.mcf -add command loadm(),readm(),getm(),putm -delete command mc_query() -delete aux-file output -add MCF template file template_lib.mcf -add batch file mcf_to_graph.cmd >mcf_to_graph template_lib.mcf drag and drop library files on this batch create svg(default) files in ./template_lib -update mcf2graph.mp -update mcf_exa_soc.mp -update MCF manual,example [ver. 4.92 / 2023-01-29] -change default output eps => svg -update MCFexample include mcf_exa_code.tex -delete mcf_exa_code.tex -delete mcf_exa_code.pdf [ver. 4.91 / 2023-01-09] -update MCF manual from this version typeset with LuaTeX include mcf_man_soc.mp,mcf_mplib_exa.tex -delete mcf_man_soc.mp -delete mcf_mplib_exa.tex -delete mcf_mplib_exa.pdf [ver. 4.90 / 2022-11-12] -change syntax of fused ring {a--b}=?n => a--b=?n (n:4,5,6) {a---b}=?n => a---b=?n (n:5,6) {a----b}=?6 => a----b=?6 -update MCF manual -update mcf_library.mcf [ver. 4.89 / 2022-11-06] -change syntax of fused ring (a,b)=?n => {a--b}=?n {(a,b), ..}=?n => {a--b, ..}=?n {(a',b), ..}=?n => {a---b, ..}=?n {(a',b'), ..}=?n => {a----b, ..}=?n -fix bug in MOL(V3000) file output -update MCF manual,example -update mcf_library.mcf [ver. 4.88 / 2022-10-10] -change format of mcf_library.mcf -update MCF manual,example -update mcf_library.mcf [ver. 4.87 / 2022-08-22] -change format of mcf_library.mcf -change output file name -update MCF manual,example [ver. 4.86 / 2022-07-18] -fix bug in function mc_query() -update mcf_library.mcf [ver. 4.85 / 2022-06-12] -fix bug in function mc_query() -update mcf_library.mcf -update MCF manual [ver. 4.84 / 2022-05-08] -fix bug in atom drawing -improve report output -update mcf_library.mcf [ver. 4.83 / 2022-03-27] -fix bug in bond check -change fuction name check() => mc_check() query() => mc_query() -improve report output -update mcf_library.mcf -update MCF manual [ver. 4.82 / 2022-03-13] -add new example file mcf_exa_code.tex (example include code) mcf_exa_code.pdf -change file name mf_data_base.mcf => mcf_library.mcf -update mcf2graph.mp -update mcf_library.mcf -update MCF example [ver. 4.81 / 2022-02-27] -update mcf2graph.mp -update MCF manual [ver. 4.80 / 2022-02-20] -update mcf2graph.mp -update mcf_data_base.mcf -update MCF manual,example [ver. 4.79 / 2022-01-22] -fix bug in numbering atom,bond [ver. 4.78 / 2022-01-17] -from this version use MetaPost only -change file name mcf2graph.mf => mcf2graph.mp mcf_exa_soc.mf => mcf_exa_soc.mp mcf_man_soc.mf => mcf_exa_soc.mp -change function name beginfont => beginfigm endfont => endfigm -delete style file mcf_setup.sty -update mcf_example.tex typeset with LuaLaTeX -update mcf_data_base.mcf -update MCF manual,example [ver. 4.77 / 2022-01-02] -change syntax of add group {a'}:*/_ : {a}:/*_ {a'}:/*_ : {a}:*/_ -update mcf_data_base.mcf -update MCF manual,example [ver. 4.76 / 2022-12-20] -change syntax of bond type {a<}=dl => {a'}=dr {a<}=dr => {a'}=dl -change syntax of fused ring {(a<,b)}=?6 => (a',b)=?6 {(a<,b)}=?5 => (a',b)=?5 {(a<,b<)}=?6 => (a',b')=?6 -change syntax of serial number' {a--b} => {a:b} -update mcf_data_base.mcf -update MCF manual,example [ver. 4.75 / 2022-12-12] -change syntax of bond type {a<}=dl : {a}=dr {a<}=dr : {a}=dl -change syntax of fused ring {(a<,b)}=?6 : (a,b)=?6[3] {(a<,b)}=?5 : (a,b)=?5[2] {(a<,b<)}=?6 : (a,b)=?6[2] -update mcf_data_base.mcf -update MCF manual,example [ver. 4.74 / 2021-11-23] -change syntax of fused ring (a,b)=?6[4] => (a,b)=?6 (a,b)=?5[3] => (a,b)=?5 (a,b)=?4[2] => (a,b)=?4 -update mcf_data_base.mcf -update MCF manual,example [ver. 4.73 / 2021-10-10] -update mcf_data_base.mcf -update MCF manual,example [ver. 4.72 / 2021-09-20] -change syntax of beginfont() keep file open 'f+' => 'v+' enable to use default input file name -change syntax of query() input file name 'i:' => 'f:' -fix bug in beginfont(),endfont -fix bug in query() -fix bug in expand mode -update mcf_data_base.mcf -update MCF manual,example [ver. 4.71 / 2021-09-05] -add function query() for data base file -update mcf_data_base.mcf -update MCF manual,example [ver. 4.70 / 2021-08-01] -change syntax of @(x,y) @(x,y) : Move (x,y) from current position @$(x,y) : Move (x,y) from origin(@1) -add bond type for glycan arc_lb : arc left > bottom arc_br : arc bottom > right arc_lbr : arc left > bottom > right arc_ltr : arc left > top > right -update mcf_data_base.mcf -update MCF manual,example [ver. 4.69 / 2021-07-18] -add bond type wf_r,wb_r,bd_r for steric ring -update mcf_data_base.mcf -update MCF manual,example [ver. 4.68 / 2021-06-28] -fix bug in data base file handling -update mcf_data_base.mcf -update MCF manual,example [ver. 4.67 / 2021-06-13] -fix bug in bond color -update mcf_data_base.mcf -update MCF manual,example [ver. 4.66 / 2021-06-06] -add binary operator in {...} { a -- b , ...} : { a,a+1,...,b , ...} (a sw_numbering=Atom sw_numberA=2 => sw_numbering=Atom+Brock sw_numberA=3 => sw_numbering=Atom+Inverse sw_numberB=1 => sw_numbering=Bond sw_numberB=2 => sw_numbering=Bond+Brock sw_numberB=3 => sw_numbering=Bond+Inverse sw_fframe=1 => sw_frame=Outside sw_fframe=2 => sw_frame=Inside sw_fframe=3 => sw_frame=Outside+Inside=Bothside sw_aframe=1 => sw_frame=sw_frame+Atom sw_mframe=1 => sw_frame=sw_frame+Mol numberA_start,numberB_start => numbering_start numberA_end,numberB_end => numbering_end Info1 => Info Info2 => Info+Table Info_t => Info+Temp Mcode_t => Mcode+Temp Report_t => Report+Temp None_Info_t => Font+Info+Temp None_Mcode_t => Font+Mcode+Temp None_Report_t => Font+Report+Temp None_Info_Mcode_t => Font+Info+Mcode+Temp -delete option parameters sw_numberA,sw_numberB,numberA_start,numberA_end, numberB_start,numberB_end, sw_fframe,sw_aframe,sw_mframe -update mcf_data_base.mcf -update MCF manual,example [ver. 4.65 / 2021-05-23] -add parameter for sw_output None_Info_t : output font,'temp-info.aux' None_Mcode_t : output font,'temp-mc.aux' None_Report_t : output font,'temp-report.aux' None_Info_Mcode_t : output font,'temp-info.aux','temp-mc.aux' -update mcf_data_base.mcf -update MCF manual,example [ver. 4.64 / 2021-05-05] -add parameter for sw_output Mcode : output MCF aux files Mcode_t : output 'temp-mc.aux' Info_t : output 'temp-info.aux' -update MCF manual,example [ver. 4.63 / 2021-04-18] -add option parameter sw_output sw_calc =1 => sw_output=None sw_aux_out=1 => sw_output=Info1 sw_aux_out=2 => sw_output=Info2 sw_rep_out=1 => sw_output=Report sw_mol_out=1 => sw_output=MOL2k sw_mol_out=2 => sw_output=MOL3k -delete option parameters sw_calc,sw_aux_out,sw_rep_out,sw_mol_out, sw_file_open -change molecular data base format end MCF : "-" => "+" -update MCF manual,example [ver. 4.62 / 2021-04-04] -add molecular data base file 'mcf_data_base.mcf' -improve function beginfont() able to use molecular data base file -add option parameter sw_file_open -improve function check() -update MCF manual,example [ver. 4.61 / 2021-03-21] -change syntax @.$n => @$n &.$n => &$n -change function name check_mc() => check() -improve function check() -update MCF manual,example [ver. 4.60 / 2021-03-07] -$n (0<=n<360) can use as absolute angle -change option parameter name ratio_zebragap_bond => ratio_hashgap_bond offset_zebra_gap => offset_hash_gap -improve function check_mc() -update MCF manual,example pk font => eps(mps) file [ver. 4.59 / 2021-02-28] -add command @(x,y) : move to (x,y) -improve function check_mc() -improve report output -delete option parameter sw_indent_off -update MCF manual,example [ver. 4.58 / 2021-02-21] -change syntax "+" => p_ "-" => n_ -add function check_mc() -update MCF manual,example [ver. 4.57 / 2021-02-11] -change syntax n:@ => @n n:# => &n &"+" => "+" &"-" => "-" |=n => #n =| => ## -delete command `` -delete command a@#b -delete command A[1],A[-1] -delete bond type d,w,z -fix bug in MOL file output -update MCF manual,example [ver. 4.56 / 2021-01-31] -fix bug in molecular weight calculation -fix bug in report output -fix bug in MOL file output -improve parts definition -improve global ext() setting -update MCF manual,example [ver. 4.55 / 2021-01-03] -fix bug in molecular weight calculation -fix bug in charged atom calculation -add commands ?! : /_,! ?? : /_^35,/_-35 /?! : isopropyl /??! : tert-butyl -change syntax /N!_ => /N?! : dimethylamino -update MCF manual,example [ver. 4.54 / 2020-12-12] -fix bug in report output -update MCF manual,example [ver. 4.53 / 2020-11-03] -improve inline definition -update MCF manual(add index),example [ver. 4.52 / 2020-08-30] -improve aux file output,input -update MCF manual,example [ver. 4.51 / 2020-08-10] -improve aux file output,input -add style file mcf_setup.sty -update MCF manual,example [ver. 4.50 / 2020-07-26] -fix bug in function add() -delete file mcf_man_soc-064.mps -update MCF manual,example [ver. 4.49 / 2020-07-09] -improve command !,!n -delete command !0 -improve function ext() -add command ext_clear: reset global ext() -fix bug in environment setting -update MCF manual,example [ver. 4.48 / 2020-01-26] -add command a@#b : a:@,b:# -update MCF manual [ver. 4.47 / 2019-12-15] -fix bug in fused ring -change option parameter name sw_subst_off => sw_group_off -update MCF manual [ver. 4.46 / 2019-12-08] -miner update mcf2graph.mf -update MCF manual [ver. 4.45 / 2019-10-05] -improve function ext() -delete option parameter sw_auxfix sw_auxfix=1 => sw_aux_out=2 -update MCF manual,example [ver. 4.44 / 2019-07-07] -improve to ignore unknown command [ver. 4.43 / 2019-06-23] -add binary operator for add() a << b : a rotated b -improve embedded font -update MCF manual [ver. 4.42 / 2019-05-26] -add function for add() plus : circled plus minus : circled minus lonepair : lonepair -add binary operator for add() a ** b : a scaled b a /* b : point of b scaled a -add variable for add() A[n]up : dir An A[n]left : dir An+90 A[n]right : dir An-90 A[n]down : dir An+180 B[n]up : dir Bn B[n]left : dir Bn+90 B[n]right : dir Bn-90 B[n]down : dir Bn+180 -change variable for add() A[n]dir => A[n]ang A[n]ang : angle of An B[n] => Bm[n] B[n] : bond position => path -improve label emulation -update MCF manual [ver. 4.41 / 2019-05-11] -change syntax |<=,=>| => |=,=| ext() => add() EXT() => ext() -update MCF manual [ver. 4.40 / 2019-03-21] -add function MC() -change function name MCa() => MCat() -delete function MCc(),MCd(),MCf() -add angle parameter mangle -add size parameter thickness_mframe -change size parameter name bond_len => blength max_bond_length => max_blength font_wd,font_ht => fsize(w,h) margin_left_right,margin_top_bottom => fmargin(w,h) thickness_font_frame => thickness_fframe thickness_atom_frame => thickness_aframe -delete ratio parameter ratio_bond_width -delete option parameter sw_solid -change option parameter name sw_clip => sw_trimming sw_bond_single => sw_single sw_fomt_frame => sw_fframe sw_mol_frame => sw_mframe sw_atom_frame => sw_aframe -update MCF manual [ver. 4.36 / 2019-02-11] -fix bug in draw atom,draw bond -delete size parameter atomfontsize -update MCF manual [ver. 4.35 / 2019-01-03] -fix bug in numbering bond -update MCF manual [ver. 4.34 / 2018-11-11] -change default driver(graphicx,hyperref) dvipdfmx => pdftex -change file name mcf_man_soc-064.eps => mcf_man_soc-064.mps -change command-line parameter settings -change option parameter name sw_report => sw_rep_out -update MCF manual [ver. 4.33 / 2018-06-18] -change syntax n:& n:& => n:# -add command &"c" -update MCF manual and examples [ver. 4.32 / 2018-06-03] -add commands C[],N[],O[],S[] X[1] : "{X^+^}" X[-1] : "{X^-^}" -change option parameter name sw_MOLout => sw_mol_out sw_auxout => sw_aux_out -improve MOL file output sw_mol_out=0 : no MOL file sw_mol_out=1 : MOL file V2000 sw_mol_out=2 : MOL file V3000 -update MCF manual and examples [ver. 4.31 / 2018-04-16] -add command */*n , n:*\* , |<=n */*n : /n~wv n:*\* : n:\~wv |<=n : |<,``n -update MCF manual and examples [ver. 4.30 / 2018-01-03] -change syntax &n &n => n:& -improve address error detection -improve expand mode -update MCF manual and examples [ver. 4.29 / 2017-10-29] -miner update mcf2graph.mf [ver. 4.28 / 2017-09-15] -change syntax #n #n => $n -update MCF syntax manual [ver. 4.27 / 2017-09-03] -improve function ext(),EXT() -update MCF syntax manual [ver. 4.26 / 2017-08-13] -improve label emulation -update MCF syntax manual [ver. 4.25 / 2017-07-23] -improve label,arrow emulation -change variable name Bs[] => B[]s Be[] => B[]e B[]ang => B[]dir A[]bra => B[]dir -update MCF syntax manual [ver. 4.24 / 2017-07-17] -atom font can be changed -update MCF syntax manual [ver. 4.23 / 2017-06-04] -change syntax n*,n\ n* => n:@ n\ => n:\ -update MCF syntax manual [ver. 4.22 / 2017-05-27] -change syntax @(),$() @(a,b,...)c => {a,b,...}:c $(a,b,...)c => {a,b,...}=c -improve function ext() add variable Bs[],Be[] -update MCF syntax manual [ver. 4.21 / 2017-05-03] -change brock making commands '{','}' => '|<','>|' -improve report output -update MCF syntax manual [ver. 4.20 / 2017-03-26] -change length expression length# => length -add emulation commands dotlabel,drawarrow,drawdblarrow -add function MCa(),MCc() -delete function draw_vector() -update MCF syntax manual [ver. 4.11 / 2017-03-06] -improve function EXT(),ext() -update MCF syntax manual [ver. 4.10 / 2017-02-13] -improve function EXT(),ext() -update MCF syntax manual [ver. 4.09 / 2017-01-29] -add new function puts() put string in EXT(),ext() -add new function use_font() make font for puts() -change option parameter name sw_checklist => sw_report -update MCF syntax manual [ver. 4.08 / 2017-01-15] -add monoisotopic mass calculation -update MCF syntax manual [ver. 4.07 / 2017-01-09] -add new command '!!' : '!~db' -add new command '!!!' : '!~tm' -add new substituent '/_' : '/Me' -improve molecular weight calculation -update MCF syntax manual [ver. 4.06 / 2017-01-03] -miner update -corrected molecular examples -update MCF syntax manual [ver. 4.05 / 2016-11-15] -improve molecular checklist -update MCF syntax manual [ver. 4.04 / 2016-11-05] -improve clipping mode -update MCF syntax manual [ver. 4.03 / 2016-11-03] -miner update -update MCF syntax manual [ver. 4.02 / 2016-10-30] -add function EXT(),ext() -delete option parameter sw_start_vector -update MCF syntax manual [ver. 4.01 / 2016-10-23] -many fixes for robustness -update MCF syntax manual [ver. 4.00 / 2016-10-19] -change solid mode parameter 1:solid ratio,2:solid length -update MCF syntax manual [ver. 3.99 / 2016-10-14] -miner update -update MCF syntax manual fixed page number of contents [ver. 3.98 / 2016-10-10] -add option parameter sw_clip (clipping font) -add max_bond_length , delete max_bond_width -update MCF syntax manual [ver. 3.97 / 2016-08-21] -change bond type name 'ov' to 'si_' -add bond type 'wf_','wb_','bd_' -update MCF syntax manual [ver. 3.96 / 2016-08-06] -large scaled rings can fuse 5,6,7,8 membered ring scaled 11/10,12/10,13/10,14/10,15/10 -update MCF syntax manual [ver. 3.95 / 2016-07-10] -improve bond type 'ov' -update MCF syntax manual and example [ver. 3.94 / 2016-06-19] -set maximum ratio atom size / bond length to 0.8 for avoid error when font size is very small [ver. 3.93 / 2016-06-11] -improve font frame -update MCF syntax manual [ver. 3.92 / 2016-05-05] -miner update -update MCF syntax manual [ver. 3.91 / 2016-05-01] -add information tag and var for fixed aux file -update MCF syntax manual [ver. 3.90 / 2016-04-28] -add parameter 'sw_auxfix' fixed aux information format is added It is easy to use with spreadsheet software [ver. 3.89 / 2016-04-10] -add new bond type bz (broad dotted) [ver. 3.88 / 2016-04-06] -rename variable 'aux_separater' => 'aux_delimiter' [ver. 3.87 / 2016-04-04] -change aux information delimiter(, => ;) a lot of molecular name include ',' [ver. 3.86 / 2016-04-02] -change aux output format(command => csv) -update MCF syntax manual [ver. 3.85 / 2016-03-24] -change aux output control -update MCF syntax manual [ver. 3.84 / 2016-03-19] -improve efficiency of command @,: -update MCF syntax manual [ver. 3.83 / 2016-03-05] -change option parameter name sw_logout => sw_auxout sw_MOLfile => sw_MOLout -update MCF syntax manual [ver. 3.82 / 2016-02-14] -add new commands ~~,^^,'`,:> -update MCF syntax manual [ver. 3.81 / 2016-02-11] -add parameter sw_subst_off,sw_bond_single -delete constant _skeltonA_end -update MCF syntax manual [ver. 3.80 / 2016-02-06] add new command || , divide CHANGELOG from README change e-mail address [ver. 3.78 / 2016-01-16] update MCF syntax manual and MCF luamplib example [ver. 3.76 / 2015-11-28] update MCF syntax manual and MCF example [ver. 3.75 / 2015-10-17] fix bug in command ** [ver. 3.74 / 2015-10-03] improve bond infomation of checklist [ver. 3.72 / 2015-09-22] change command ^^ to < and delete ^^ [ver. 3.71 / 2015-09-18] delete command !!,?? [ver. 3.70 / 2015-09-16] add new command | ,change syntax of !,!!,?,?? [ver. 3.63 / 2015-09-14] add command option of numbering address,update MCF syntax manual [ver. 3.62 / 2015-09-07] improve numbering bond, numbering atom, update MCF syntax manual [ver. 3.61 / 2015-09-01] fix bug in local setting of font_wd# and font_ht# [ver. 3.59 / 2015-08-23] update MCF syntax manual [ver. 3.58 / 2015-08-18] improve calculation of molecular formula and weight [ver. 3.57 / 2015-08-14] improve AUX file format [ver. 3.55 / 2015-08-04] support luamplib(v2.11), renew mcf_mplib_exa.tex [ver. 3.54 / 2015-08-03] maximum item number of MOLinfo can be changed [ver. 3.53 / 2015-07-29] support luamplib(LuaLaTeX) [ver. 3.52 / 2015-07-20] '!!4`2' can use as '{,``2,!4,}' [ver. 3.51 / 2015-07-19] '?6`2' can use as '{,``2,?6,}' [ver. 3.50 / 2015-07-11] first version uploaded to ctan. ******************************************************************************