#!/bin/sh # Collect -D & -m options as java arguments command=java while [ `echo $1 | egrep '^-D|^-m' | wc -l` != 0 ]; do command="$command $1" shift done # Determine installation location if [ "$JMOL_HOME" = "" ]; then binDir=${0%/*} if [ "$binDir" = "$0" ]; then # Ran from local directory binDir=$PWD fi # Resolve symlinks. program="$0" while [ -L "$program" ]; do ls=`/bin/ls -ld "$program"` link=`/usr/bin/expr "$ls" : '.*-> \(.*\)$'` if /usr/bin/expr "$link" : '.*/.*' > /dev/null; then program="$link" else program="`/usr/bin/dirname $program`/$link" fi done binDir=`dirname $program` fi JMOL_HOME=${JMOL_HOME:-$binDir} libDir=${JMOL_HOME}/jars if [ ! -e ${JMOL_HOME}/Jmol.jar ]; then echo "Jmol could not find its installed files." exit fi $command -Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar "$@" ^%ܐߧ [Rk|9aK ,t í7%(7D9K7ǰ'r_YSWu_'bf!.ȿ?=V2+hr'S֛,q(5Ҵ` R+DĎStB7\FCE = D >#60D>Wm$Xfdz[(_vV$E'&YW$ ϤނGF1k"Mp*ų]/$T~h9zٞ 7SZD..UH_w:SͶa*MU~DB!҆uɭB 'h @p4Rm(wbF*I"̠A͌> th.mR7gK$ϯJ)Lq VLcrq燀2T~>:rG֑ۜ"MT4?ѪI3@O^I z-NX[(׮(.\Ɛ%>QH7q>XDD1FGT06͖\.vTtMv)M0#0[N"iUa wW|lclko-wi$-qaUp~'&9?}3,h iݕT[~Dw2;D}OSܶun2J.qVQxv^s%;:D1%מeI = .a ] /G[f=V^sk*%wnW?qX FWp&;V?b!KVAOz KzU-OD_\wˠ4$Ekj}C8sX 4ov~fPgMedE㌳$Xw`N~J!@~ 1*`O{qiCW }=OkG LuL+tmeM s PY#Oh{rƙeȿʑL*E'7abN+-4vF%۷L%ֺigmBFDHea=z}}6Hd#Ԣ/ ޿_2%}+" - ]F#hV:`5X SL`GؒGPRa|RӊۆX7+]) 6%g7yӌb-FwKrP֥ ghBJ{뾷{2i#wMVO~f\tB+!A5;bޡ]jY E6UˀE˝w};E5\c,rĘ7Rxw_`0L "Re(z-kQ:3x~ђv}${MoX{RE)*VEoX3kƦv 6ޫRM7RE%Qk/P>9matig>)du|˭ t :wVc=a}ž' T5Z] /6?Z[pRp~ʹe峲"xd*Λ5ݨOKVUs-2uas)λQ4EH_9R56-uTBȯtP`E|?HUwDGN;ABRۂ#7IC(Z{GIї};ׄR̳NcF)/iUCԧO#xB,0ImnwN. %\Z%jKK/qx -%TL=䭍 F$Ŗy|#_;,k%c'Ye^,\z;+ĸbsJe#`<,,fo ;NOTTY- Z@@~i Md%2IН(Z!jK(`+äyCƵJ si!޲&WL+^ɦtX%4v*.,5[v>-^X'&1Ѓ8CeS8ԩr7$I.y|of]e٥b̴b5YHvcp럡{6 /- yjI Ӎ5lu gr+\k}k,Dʹ&S^-.1| `Lzgyl=Qz1vXy^8vc { iqdpu,%ehH7a\z5M9ՇZCG?F8{O?I[%ٛJ4v C_8r &{ 0^j!o-aDHpQn5LFC⚴)`E&R6gx!zXY{8{̜݋2ha.~j(%NpRۡÕɯ St1(x۞>vr6A6Qd׹J̽0gc76мn7F7/ 9FH|֍TީGV޸w*"F2$v,;EMylO9%yC^5;{y/w|@nVS\ӉqeЂeY_7" E\0P5(er^2K@dKloh~_m-1^wQ9/Ӭc$,fFeQ|2ojjPzY$4 {h6/ qqyftGfLj:d"I$:U]I[G8S.l3.L: Z\n==19~ SM؏KL,8fצa%!we;!MU 'іPL!J)9Qb_@R2œ]yX:Y KKw{AqQXq2R GƭșjDκso(u{8v+֕xXk }n,Ukxm8ċ#"Aye}r%ΞKiR]¦>,cU8~ 69$ a X s<ҞcK/##R+Z]\\Ao @퍳[cp?@H1N]=+}  $L.p.of!X p&B] i~|wFx+{iZoaQNlS"ڴdDNFkx2$r);LGnI|Hsۺ wz.QxW=+|K+XoM7rҙ4`*b–<"̐-}N;jq1!G-2j!̈́=4tvI ]l$\Bܑq=V/ eRV3 ^Np-+x!/qI?.pNeXڋѸ*$2ssUq L.o?0]k(u<+Є%h- fX^)H"ڶ'4?UMZfb`'iz!S,ZuZfK< uSKܩ{☵ݦq"ѸBIGְmGDUZNStiDu?'4{^f`td_: O9sAt9yA2 Pq03 g~ȹ+$Bi.*Fи!:t SjHv8ii.:Ns!)JbZ˩ojmd8LVy]rDv8vIwX Uח,4>I\mEzۛzG^Z[P3\۳꠫*y 0@P (}" Bg0r?%p )\5 /F"3l< !IQ~p`E[ɭJr V۲hcͦ»/_?~QUSaʙe&Qœjht^=Uz .f_K\>Z+, 2Z[M)`mގ̱ ;\xvyya%E?r>9ĺ v?(zN-1о ı`A<͍8U(Z=xz]4or;-8=j* {7PG%黳~(d7)xU1]QTf"#bC,,}rC'5IׯJh{Ho"e֩,WCVR Ŷ6J|)eaFCt܄]O֥Fg9Ѝ&'ϼ"[۵ z#8v"#buhv9`|P!{-fOgSdR)"t9(ڡܜ7.ȵfiAvaXKL#f`+Mb2[7s0˾3fﯘJ1:'28T%斨xsKК0$kީ5$"i r"ԍ)ygXmicgT./CJK"8Tn.1%v<.سfz\nӴ |+S̺_ њd'czvD))؆1kL#=`o Ef*$OҨͳЂe_ Ht%ߚO(~y]Q0^?|`TB{ۡ5ց–DEn9/v~_a]@桊|-R\Me]XGKC2.޴+Z&L3=`3@Q4rdtbvOWOEńp&b?#H*zԜi#׮O rM(mo%QＹm ,8_صJ+ N%a VkX辈QDB7A /,5F%q'ĤAL{{gzJ[^ dKGz$Mh.Ĉ+TO`~dRkjoDh2k+ eK@`E{59I9 BsO"$%cg<식]_u:h)۸o^c4@!&7Vdէɕ^#QahĽ-7q۷}ݖ}`X_ayeMPW8A+k>s}/nR9:g֟-+ZZBx1ؔ֍`dy2$aңz&!Q#(LԒtA۝C\45=#l[IƢ "/gA!@2_1q|U\ UY[: &PDpIٯ<{Zy]Qr_N3桮:͞N tݴ&yg8QZsq~r-5uː g]OGZ(rT(Fa.&D?95rZwoXp&}`Cx|1qЇ=uH9\KcqzWu4#O B$28y ;ERChQCBաo'==Xg"? ං'垩I[{TX^}p+zQ8 QM&̈X}F[dŠUc珥)வx *ǰ5tbP<$]츱_&h'o2B~W(;r7&E8 x 鯁~iY!\&:V^L~B<ѼҪ{m)dáO^HLJ1"&yY2{Ҥ0=1c=-1ąJ-4 :p4\1!um g;A&NH^G bVpIpT$>2G+vz=a莕\(f <q0Z&<Y{լi0AclU2Vh7TA8J0Xm<1zzeϠƿP%GPP&Uf8/[!0tcY F]{iwY 2MȷoXka|UaFjvyHlToT7PNŢ8073]R7H46m7Bp863 Yd7u)s]) r:??)Aĝh[QpZ F]"=^1ȸ|vJLFD/(/449_2.׆̴Z-e{T!Wy%ӳo"`~uSVJx&G+w,n颁-Ї;B|`h k3a0:Xq@jg%+6S0 I<7`rIkRɎ@)FٞR"Ĩ{R< ihU6.*hm?Ngg;Lj`5tj秸E@|R* 2 9p{Y9m-KBj* Rd/6Qbp>49RzY?-MLG}11eb:4=,VWuRuZ;{ʻ,מ!ڰœSמ.`%I]:@}Ke|ZlRVrn2[]nr>X!aw<*c5Z1?#yqBpasKIu=\ eer4<Oι2_ yQ_wk*Nğ&2-{龮*"pQT0lf- Ҍ 0#ZCU9p5V&j7N90(L$FI"cH()꺩5)c]`tSGݐ -SCm(uy>Qc>*>?q<:uny?nHxqzS%e1<9#Q%̓zk&cv&e[@j<@Vv@iXpߡa7 wR&?oΔua]u U$.J|i#.a~bK͛Į}T!˧[RdٴFxYs_bnRһ:%h *#$l5P \i/Ul3p7ŧ/w%܏O2A=,1~QsKG`&$3‡eߠHbtZgH||~Zc@NftgcMawh /p% 9Qu4R20g;f^*zL"0"coZX"b,.F&Yq26%$0l 4R54t!Lˆ +58 N ̩J8g4?bVBZ!YGNcyXGIuoѬ"%ꦅ 4|U$D_Uw} L%OIrQ |73Z-5ٟ8"ǖ Qⱽ9hܻkR:tٴܬ\עYYNӺS8jVg9~;ىg%c]'Hp8i tZ?(C^k6t|?q Ga&ď$%#pC@zؓ}bEN]w+( Nv.9[I*xB†{1lnEYqN4ʔ>rkm&Hn$msNC۵EɌ#A|ո&]ᄘm?(6ba\S[|Lhԛ3r ZC2GA-R\bJyqD8)k%0v 'U2̈́ aQ#!U1kr_>j#>NrD&rm.Hxɷ-x`orm3'cYy[⏁ _oiud  /hi+8t"h{ QHp0;onMZ?yK _ME$ɀ.?-BH" >2f F1sC &B#\?M$)i4LqwLek+΀7ƤSSw;I1sw3vu0`Ln߆Y e(5.aI:DMaK롡J(>TG;_&-ň2|4{pI㜇Y&_5j܎6#zHO&Υ8g1̝3@5EOC|s6 S<֪AO;O0NIΎ*7گ&j8+ÏgBa#/7V1EM=#-?_װD8׫̫~rmj2ge[U8Yj YC=:&7^kP3|!Oa0^6r7TQ}cRQQmy  |Wj$/p^LQ}]$pE;薬}W"=pi 6A^" =!x_q|gTA 'Y91tדՕvw}Ys2U@smڇܖ.fpjfT[\|*apLÿD2`_!ņ)@Tli/gDj2@C68NSh'g˺w%f/ަ7tfAj[~z6p@s|}awiNQ'{4e%5iGHoI_?ri!/;=>"F.HSRi#ҊN"5N'QG$X )g_}5ö(y%ܙ_.D"镧TeW.}l(q03ܵs| Iȓ<>݄ wY鋹}8߾`ۍqb`ᦢn~ 0nĈh8U=N^/=f$*[8m #@2Ot@`>F$mY&r͕%P,(j[rK/M,WkMyi!zګL<}.QV 3-d "t{fٟC }~f֦y("n\H4 ṋrD'cM4_8k|YI;Z6V0u ~1+0ƽ~o88wkfTEV*$5/czATdje\@L_ |6 E7''60BbtǑ!Q}ߗU^hH<:p}uȎR$ xV==z X-d,[,gӊ݈ܺP.VX"e*l(j#Q+H%ëIs{hߠE8g%, R04ʛ+|wlRyXBb|) SbV:#Aٯq,aB?F]t},> p5ÍE֥2Ss#'6ەӞ1sgD@1ofxݡPALJXAH(ퟞU{jd-buu"Q|ɤf0}NzoSyr0D{;  * 3e*ݳL U+k)KjM+p>3l8@˒xau>[O-sT-bB0#xBS*>xmz Q<+ީjgCLN=|UfR%KOyZ;km.Cׯ\)mL4QsDo1TS]Md}BԔVx}Py>|G{p34bg7IJYwP[,[W~?+~p[6TTEV`DKz_Ȼ'I,[w$cLx# ){h&P#aǴyWr zW /ē*` Gwd,`I`c{;!2RU .!*LlhyCEi=9S/ &M;J"hUx#yBw])"Ϊya'4FsѡW6k5MzPcj @wN"br#+0Lv-Ox4V 0 5˱yfxiv'}"?M_\|%!gf w,)>Y&<%WŬxw8},al[ohzpt'7pn"  TsùuNY0,ZolVh7`@> I^+%PavSOe5EnяGĞf*XO(Q^ֽ{NNxFZ7; ,v.=ژPHҎ'KBEcN^ c8mD5.5b31{whhCXRr f16t@WsuFsS -O>d1Hb,JjlƦ>=8BeH$\ODN>BodzAsm*/1.`Gܸ^jl5Okkm Q _RPkCe,'P!Hő )]hb*\DR~D֧v= NMJ}eLR}/d9KGA,AH]6}n%G$60:zhB$r4j-na6n57e!aŋ=Uj'Zup7=9#Y5r{tk b-GTwVJD2פqc/zJlxZd>]k?}Oqdʸ$!d؍ݲiщ%*Q+ Fmm6֡=KŞ 1ozb )pj>/Pտ({]*W~o͊R O[#U 5ǽ89GL#k֖1ۨ$"r(X>8l@}o}D'/ҼAY*TC/\ Da/?&D;q7.M%#+Auc;)4uPmH|~Rba) /GBySysd6Tr%|ZWؘb-0&d.IП3r,&GWpq3( jw;Us ځxBU.1O.Ik*gbt[^]!r!Pq\a Ą?M;+6 ٻߏ ?z']|Dhb+%"7n:q `}]>ʃ(H~78 >2f*uS۫'oNQ0whtĭ^1>=+fAZsf2IB ?ϒ}}(Y+;^bBn7RZ NsԦg==!8lm#!}*߲+"j~U[`Z&Cx]ZiފЩWsSeөuKX2lznU=\E"t Jdq*yR=X% pVR/̀3(ՌbȐ_xO0'QRtDZr%2oPX^؝6-NMfJgIz8is{Śm3&p=u8fFsorxcηg=:b'`+,!]jX93B{"Pd M"]ȀϋK*g#x ^?5G/Bd(5L.zeiupݏyBC  0X|.xn_~z2}L5 6=]y{-_|yTQ&O0-P,p|r`mPIɚsQXtMqALj`ts Ò,A1ȗpwGϾ|ĝC5:2xeChİ.({Xݐ&z8& @1˾4!nd0&DМ;}p8 (kJ{!^| )^Lc]yyFx NV&) +,[ÊT{fr%UֶAeg;8ےn N3kJJ,[vs_礿W+9&^+L5t@?ڿ JŒսyeiiQ!/u;(\8kw+Hu zgҠs~_~B9,Tx6rzp9 !*:no_)T˯2FB+HO:{n;t3>dz]M- b $4X mò͇q-_|ez543:rq< A$y 䙪QVat^m^]pR5Zutt&vt QlZ 16iI<{&hCXM"r͙\yˋQ1< ,EpdX# Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line version=11.6.13 # bug fix: user menu ...Text menus not translated # ----------------------------------------------------------------------------- #version=11.6.12 # bug fix: protein-protein hydrogen bonds not calculated across biopolymer boundaries # bug fix: quaternion straightness update # ----------------------------------------------------------------------------- #version=11.6.11 # aargh -- forgot to upload file for 11.6.10 # ----------------------------------------------------------------------------- #version=11.6.10 # bug fix: vibrationperiod set to 0 if vibration off when state saved # ----------------------------------------------------------------------------- #version=11.6.9 # bug fix: application -i option still gives message from "set xxxx" # bug fix: some quaternions cannot be created from a 3x3, namely: # q = quaternion({1 2 -2}, {2 1 2}) = {0.57735026 0.57735026 0.0 0.57735026} (xyzw format) # bug fix: ignoreError -- need not get error string # bug fix: write image does not set mustRender # bug fix: set debugscript and set loglevel do not act in script immediately # bug fix: translations of Console not implemented correctly # bug fix: translation not disabled when messageCallback is present # bug fix: script error messages not updating when language changed # bug fix: MO scale # bug fix: measure allConnected broken # ----------------------------------------------------------------------------- #version=11.6.8 # bug fix: write .... @{...} fails # bug fix: write .... @{...} can fail # bug fix: write image CLIPBOARD broken # bug fix: select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) fails when atomExpression is ({}) # bug fix: applet compilation error not sent in termination message # bug fix: build javax package does not include Matrix4d.class, AxisAngle4d.class # bug fix: compilation of myfunc({1 2 3}) fails # bug fix: hover watcher occasional uncaught exception # ----------------------------------------------------------------------------- #version=11.6.7 # bug fix: quaternion straightness update # bug fix: applet improperly reporting status of "quiet" commands # bug fix: stereo not in state # bug fix: stereoDegrees parameter not reported correctly # ----------------------------------------------------------------------------- #version=11.6.6 # bug fix: negative number in range involving ^ still fails # bug fix: translucency of mapped isosurfaces not saved in state # bug fix: Dialog look and feel for Mac # ----------------------------------------------------------------------------- #version=11.6.5 # bug fix: negative number in range involving ^ fails: select 10^P -17^P # bug fix: goto xxx with trailing white space fails to find xxx # bug fix: goto with a # comment in the script prior to the target line fails # bug fix: two //xxx comments in a row breaks script # code: superfast JVXL compression/decompression # bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight) # load =1crn;calculate straightness;color "bwr" range 0 1;color straightness # # bug fix: isosurface APBS dx file reader broken (since 4/2007) # menu: "Minimize" GT # ----------------------------------------------------------------------------- #version=11.6.4 # bug fix: UFF.txt not included in build # bug fix: function definitions occurring before prior script commands are executed. # bug fix: message @{xxxx} in function not picking up function context variables # bug fix: Some browsers do NOT strip \n from tags, necessitating changes in loadInLine() # bug fix: "valence" not "valency" in data property_valence # bug fix: initializeBspf(); missing in setTrajectory() # ----------------------------------------------------------------------------- #version=11.6.3 # bug fix: set antialiastranslucent false not functional # bug fix: text color near black with antialiasdisplay becomes white # bug fix: text antialiasing of near-black text looks very bad when antialiased # ----------------------------------------------------------------------------- #version=11.6.2 # bug fix: forcefield file UFF.prm --> UFF.txt # bug fix: better Escape method for strings # bug fix: connect auto not registered in state # bug fix: draw point translucent only draws ring # bug fix: load string inline with multiple models fails # # code: FindBugs fixes for Eval, DrawRenderer, Isosurface, ForceFieldUFF # code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination # ----------------------------------------------------------------------------- #version=11.6.1 # bug fix: set labelToggle malfunctioning # bug fix: missing default background for toggled labels # bug fix: color {oxygen} translucent blue # bug fix: color translucent 1 blue 1-8 integer settings off by one # bug fix: background color +/-1 adjustment removed # bug fix: spardir within /M... directory # bug fix: (minor) "set echo xxx display" equivalent to "set echo xxx displayed" missing # bug fix: (minor) "set echo xxx hide" equivalent to "set echo xxx hidden" missing # ----------------------------------------------------------------------------- #version=11.6 # bug fix: GIF encoder color / class not found issues # bug fix: very thin cylinder does not appear at all viewing angles # bug fix: load "/xxx" with unsigned remote applet loads local file instead of remote root directory # bug fix: sulfur/sulphur always spelt as in IUPAC Red Book # bug fix: display of aromaticSingle bond for NEW bond results in dotted bond. # translation: English language variants no longer ignored # ----------------------------------------------------------------------------- #version=11.6.RC18 # bug fix: fileName not reset after ZAP # bug fix: set echo none; color echo green null pointer exception # bug fix: .x not recognized # bug fix: set xxxCallback "" does not clear callback ("none" was required unnecessarily) # bug fix: cartoons ending in helix or strand draw single dot for final amino acid # ----------------------------------------------------------------------------- #version=11.6.RC17 # bug fix: draw scale not saved in state for arc or xy arrow # bug fix: drag/drop not enabled on consoles # bug fix: Jmol state command "calculate surfaceDistance WITHIN ({...})" not passing compiler # bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging # bug fix: trajectories not enabled # code: if (true...)/ if (false...) code cleanup # bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1 # bug fix: select model=0.0 caused infinite loop # ----------------------------------------------------------------------------- #version=11.6.RC16 # bug fix: mol2 PDB format better handling of chains and derived element types # bug fix: save image button/menu interface broken in 11.6.RC15 # ----------------------------------------------------------------------------- #version=11.6.RC15 # new feature: MOL2 reader is PDB-enabled. # new feature: data() and DATA expanded to allow fixed-column entry # bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP # but instead just creates a data type "property_partialcharge" # bug fix: CML reader failst to load primitive lattice parameters when no symmetry # note: CML reader only reads the first structure of a file # bug fix: CML reader not assigning atom labels # bug fix: CML files not properly loading symmetry # bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED # code: thread control for Java Swing in applet context # thread creating Swing objects MUST be event thread # -- using SwingUtilities.invokeAndWait() from the commandWatcher thread # new feature: load menu items for signed applet # new feature: save menu items for signed applet # bug fix: applet -- setting a jmolScript callback prevents menu updates # new feature: minimize menu item # new feature: signed applet allows "load ?" and includes previewer # bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default # new feature: signed applet/application load ?xxx uses load dialog # webexport help updated to reflect ability to handle files opened with "load append" # ----------------------------------------------------------------------------- #version=11.6.RC14 # new feature: signed applet may write file, images, scripts, variables to disk. User dialog is required. # new feature: write GIF # code: allows for getJpeg(quality,asString) option to return byte array instead of base64. # bug fix: xxx.split()[3].replace does not do selection first # bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom # ----------------------------------------------------------------------------- #version=11.6.RC13 # bug fix: set historyLevel recording full scripts, not individual commands # bug fix: y-offset for echo text and images # bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO # bug fix: findbugs input stream closure # translation: add GT.escapeHTML and stricter checking for special characters in file names # used by web export. # ----------------------------------------------------------------------------- #version=11.6.RC12 # bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx # bug fix: getProperty("modelinfo",{atom expression}) not working # new feature: set atomPicking TRUE/FALSE # new feature: set bondPicking TRUE/FALSE # bug fix: draw pointgroup when principalPlane == null # bug fix: findbugs corrections in minimize.forcefield, modelset.AtomCollection, shapespecial.DrawRenderer # new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value # cml reader fix for not applying symmetry to first model # translation: added GT._ calls for HTML templates and JS in WebExport # ----------------------------------------------------------------------------- #version=11.6.RC11 # bug fix: echo IMAGE and antialiasdisplay # bug fix: super/subscripts with antialiasdisplay # translation: menu items in console # bug fix: web export / language # bug fix: draw pointgroup C2 2 not distinguished from draw pointgroup C2 1 # bug fix: d2 point groups cause null pointer exception due to missing principal axis # bug fix: {*}.x = .... broken # ----------------------------------------------------------------------------- #version=11.6.RC10 # bug fix -- set picking spin, also compatibility of set picking spin and doing measurements # bug fix -- draw pointgroup, write pointgroup draw # ----------------------------------------------------------------------------- #version=11.6.RC9 # code: more efficient return of point group information and calculation # new feature: getProperty PointGroupInfo # bug fix: show pointgroup draw null pointer exception # bug fix: print $planeA - capital letters in a draw name disallow finding it. # ----------------------------------------------------------------------------- #version=11.6.RC8 # bug fix: ramachandran / ramachandran r navigation problem # code: Minor refactoring and pruning. # --- Core applet now 715K (JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer) # code: Pre-Jmol.js button controls removed, saving about 10K # new feature: script APPLET appletName "some script" # --allows direct inter-applet communication independent of set SYNC # --appletName can be * (all applets), > (other applets), . (this applet), # or an applet name such as "jmolApplet0" or just the extension "0" # or a quoted set of applet names separated by commas. # --for *, the current applet always reports LAST # new feature: x = script("some script", "appletName") # --same as above # --in addition, allows retrieval of information from another applet # for example: # # x = script("print getProperty(\"modelInfo.modelCount\")","B") # # gets the number of models loaded in applet jmolAppletB. # # x = script("show orientation moveto","jmolApplet2") # # gets the current orientation of applet jmolApplet2. # # xList = script("print getProperty(\"appletInfo.fullName\").split(\"__\")[1] + \":\" + script(\"show rotation\").trim()","*") # # gets a new-line-separated list of rotational quaternions for all applets with applet names. # # # new feature: print getProperty("modelInfo.models[3].file") syntax # ----------------------------------------------------------------------------- #version=11.6.RC7 # new feature: draw ramachandran includes planes connecting atoms. # bug fix: refresh for hover # bug fix: state definition for lcaoCartoons, isosurface with IDs containing spaces # new feature: $*xx* double wild cards # new feature: generally for objects (draw,pmesh,isosurface,etc.) use DISPLAY/HIDE rather than ON/OFF # so as to be consistent with other objects. (OFF was not deleting these) # new feature: support for application transparent background -- "-b" command switch (testing only) # and setAppletContext "-b" switch as well. # bug fix: structure helix|sheet|turn|none {atomExpression} was undocumented and had state issues # new feature: HIDE $xxx # new feature: DISPLAY $xxx # new feature: DELETE $xxx # bug fix: adaptation for malformed PDB files (HEADER with nothing following it) # bug fix: more language localization in webexport # new feature: applet message regarding help and command entry # ----------------------------------------------------------------------------- #version=11.6.RC6 # code: better navigation refreshing # bug fix: oops, 11.6.RC5 is totally broken due to missing refreshes # bug fix: language localization in webexport # ----------------------------------------------------------------------------- #version=11.6.RC5 # bug fix: set fontscaling with multiple echo texts/images at the same xyz location only scaling the first item # bug fix: set echo xxxx 30 40 # bug fix: WAY more streamlined refreshing # bug fix: createImage(), not getImage() in order to allow dynamic file change # bug fix: halo size for antialiased display # Addition of translation tags to webexport # bug fix: write IMAGE broken for 11.6.RC2+ # bug fix: unnecessary refreshes removed from moveto/zoom with time 0 # new feature: background IMAGE "filename" # code: viewer refactoring to simplify/remove private methods and synchronization # ----------------------------------------------------------------------------- #version=11.6.RC4 # bug fix: select @m throws an error # code: refactoring shapespecial into shapespecial and shapesurface # code: refactoring modelset.CellInfo into symmetry.SymmetryInfo # code: realignment of applet JAR files # -- new _ShapeSurface.jar, which now includes org.jmol.jvxl/** # -- removal of _Jvxl.jar # -- refactoring reduces preliminary applet Jar file loading to 720K (if English) # -- should provide faster loading of simple models and more efficient loading of more complex ones # -- basic minimum load involves just JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer # ----------------------------------------------------------------------------- #version=11.6.RC3 # bug fix: minor error in pointgroup; dimension tied to radius # new feature: set dotDensity [-3 to 3] # new feature: draw pointGroup [type] [index] SCALE [x] # where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n" # ----------------------------------------------------------------------------- #version=11.6.RC2 # bug fix: image background transparency # new feature: set pointGroupDistanceTolerance (default 0.2 angstroms) # new feature: set pointGroupLinearTolerance (default 8 degrees) # bug fix: Cs pointgroup not found # bug fix: set echo DEPTH/IMAGE # bug fix: wored over dots # * 2) If not BALL, ARCS, or DOTS, the rendering defaults to AXES # * 3) If DOTS, then turn off ARCS and FILL # * # * note that FILL serves to provide a cut-out for BALL and a # * filling for ARCS # */ # ----------------------------------------------------------------------------- #version=11.5.28 # bug fix: state "set measures angstroms" does not include "select *" # bug fix: labels can change size in returning from antialiasdisplay=true to antialiasdisplay=false # ELLIPSOID command -- with symmetry and crude footballs, including PDB files # note that for now PDB file reading of ANISOU requires using {x y z} in load # command, but you can use {1 1 0} to load ANISOU without applying symmetry # # Italian translation # ----------------------------------------------------------------------------- #version=11.5.27 # bug fix: data CLEAR command nonfunctional # bug fix: "....".trim("xyz") function not properly trimming ANY x,y,z # bug fix: draw OFFSET not working properly # bug fix: PovRAY output of draw objects -- cylinder end caps not considered # bug fix: draw width 0.05 {...} {...} -- line does not properly render # bug fix: data "model"...end "model" saves state without first line if first line is empty # bug fix: "show data types" putting comma in wrong location # new feature: DATA "data2d_xxxxx"..... end "data2d_xxxxx" # new feature: isosurface FunctionXY "data2d_xxxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z} # allows setting isosurface Z values using a block of data (ni rows by nj columns) # new feature: isosurface FunctionXY "data2d_xyz_xxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z} # allows setting isosurface values using a block of x y z data, all points for which should be # on the surface. # new feature: GamessUK reader # new feature: reset VARIABLES (replaces "reset ALL") # ----------------------------------------------------------------------------- #version=11.5.26 # bug fix: draw adds extra circle in 11.5.25 # bug fix: minimization out-of-plane energy calculation error # bug fix: better initial minimization parameters # bug fix: (applet) script termination callback should not be sent to message queue # bug fix: hover appears when a load script leaves an atom very close to (0,0) in the window # bug fix: draw width -1 or draw mesh nofill with very short cylinders creates odd jumpy effect # bug fix: draw CIRCLE for multiple model sets # # # new feature: draw CYLINDER # # Korean translation # ----------------------------------------------------------------------------- #version=11.5.25 # new feature: draw CIRCLE # # A circle is a 2D object that behaves like a halo, always appearing circular # # draw circle {molecule=1} mesh nofill # around specified atoms # draw diameter 2.0 circle {atomno=3} mesh nofill # 2.0 angstroms; scales # draw diameter 100 circle {_O}[1] mesh nofill # 100 pixels (doesn't scale) # draw circle {*} fill # a solid plane in the shape of a circle # ----------------------------------------------------------------------------- #version=11.5.24 # new feature: minimization CONSTRAINTS {xx} {xx} [{xx} [{xx}]] x.y # new feature: minimization FIX {atom expression} # # multiple constraints can be present; one per line input # minimization CLEAR releases constraints and fixed atoms # also, minimize ENERGY saves a detailed listing, which can be # displayed using one of the two following commands: # # new feature: show minimization # new feature: x = getProperty("minimizationInfo") # # to dump the info to a file: # minimize # var x = getProperty("minimizationInfo") # write VAR x "myfile.out" # # new feature: isosurface MAXSET n # removes larger fragment sets # new feature: isosurface DOWNSAMPLE n # down-factors the number of points in a CUBE file by a factor of n # ----------------------------------------------------------------------------- #version=11.5.23 # new feature: minimize ENERGY # no stepping # new feature: minimize STEPS n # new feature: minimize CRITERION x.y # new feature: minimize CLEAR # flushes logged info and saved atom info # # new feature: echoCallback # new feature: measureCallback # new feature: minimizationCallback # new feature: scriptCallback # new feature: save/restore coordinates # new feature: getProperty minimizationInfo # # code: more efficient minimize calculation setup; better logging # code: "notify" methods in JmolStatusListener consolidated # code: Tokens organized # # ----------------------------------------------------------------------------- #version=11.5.22 # bug fix: UFF torsion calculation incorrect # bug fix: UFF.prm not properly recognizing sp2 N in N-oxides # bug fix: minimizer for compounds containing isotopes D and T # # code: eval/compiler error processing update # ----------------------------------------------------------------------------- #version=11.5.21 # new feature: minimize command -- mostly untested # # set minimizationSteps 100 # set minimizationRefresh true # set minimizationCriterion 0.001 # set loglevel 4 # for a very minimal report # set loglevel 5 # for a summary report # set loglevel 6 # for a detailed report # minimize # minimize stop # minimize cancel # # # for example: # # load caffeine.xyz # minimizationSteps = 80 # minimizationRefresh = true # set loglevel 4 # select connected(2) or connected(3) or oxygen and connected(1) # connect aromatic modify # calculate aromatic # set measurementunits pm # measure {_O}[1] {_O}[2] # color measure red # minimize # # new feature: set loglevel 6 allows a "debugHigh" setting # # bug fix: load unitcell {a b c alpha beta gamma} not working (since 11.5.8) # ----------------------------------------------------------------------------- #version=11.5.20 # bug fix: zap file > 2 multiple models do not properly delete # ----------------------------------------------------------------------------- #version=11.5.19 # bug fix: null surfaceGenerator causes MO exception # bug fix: isosurface reading/writing JVXL files having insideout keyword # ----------------------------------------------------------------------------- #version=11.5.18 # bug fix: zap x.y additional work -- connections, isosurfaces # bug fix: zap x.y not correcting Eval variables # bug fix: isosurface user VolumeData not properly loading # ----------------------------------------------------------------------------- #version=11.5.17 # new feature: delete {atom expression} NEEDS TESTING # bug fix: zap x.y for dots # bug fix: zap {atom expression} for not including all atoms in a model in the selection # ----------------------------------------------------------------------------- #version=11.5.16 # new feature: zap {atom expression} # zaps models associated with given atoms. # use "show models" to see what models are present, then zap them with their # file.model number: # # zap 1.1,2.1 # these two models deleted # zap atomIndex=0 # ALL ATOMS IN FIRST MODEL deleted # # Note that file.model numbers do not change after this. # So if initially there were two files loaded # # zap 1.1 # # removes the first model and leaves the second as "2.1" # # NEEDS THOROUGH TESTING, particularly in regard to saving/restoring the state # bug fix: atomChooser not updated for zap # bug fix: isosurface model keyword does not carry on to saved state # bug fix: lcaocartoons do not color properly or get restored from state properly # bug fix: popup menu selection of groups and symmetry operations does not work # menu: internationalization of "Monomer" and "Shapely" # bug fix: mol2 reader cannot read files with single-line comments # ----------------------------------------------------------------------------- #version=11.5.15 # bug fix: CAChe CSF reader not reading partial charges # bug fix: WebExport with http:// files fails to save file # bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js # code: refactoring of jmol.app.webexport: adding html subdirectory # bug fix: state saving with rotateSelected spinning spins entire model # bug fix: getproperty("chaininfo") for non-biological model causes null pointer exception # ----------------------------------------------------------------------------- #version=11.5.14 # bug fix: rotateSelected INTERNAL not adjusting for internal rotation center # bug fix: .max/.min not allowed in context: "select resno=@{{visible}.resno.max}" # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN # application menu: Write state moved to main export menu; Export PDF to image writing # new feature: MODEL/ENDMDL records in write PDB (still no TER records) # bug fix: write PDB format incorrectly writes atoms with 4-length names # bug fix: Spartan SMOL directory reader doesn't assign bonds # new feature: Spartan archive reader now reads aromatic bonding # ----------------------------------------------------------------------------- #version=11.5.13 BROKEN FOR XYZ READER # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN # application menu: Write state moved to main export menu; Export PDF to image writing # new feature: MODEL/ENDMDL records in write PDB (still no TER records) # bug fix: write PDB format incorrectly writes atoms with 4-length names # bug fix: Spartan SMOL directory reader doesn't assign bonds # new feature: Spartan archive reader now reads aromatic bonding # ----------------------------------------------------------------------------- #version=11.5.12 # new feature: four optional defaults for Van der Waals radii: # # set defaultVDW jmol # set defaultVDW rasmol # set defaultVDW babel # set defaultVDW user # # To set the user variety, first set one of the other sets as a basis # Then add a DATA statement to include the specific elements you want to give # new radii to: # # set defaultVDW babel; # DATA "element_vdw" 6 1.7 END "element_vdw"; # DATA "element_vdw" 6 1.7; 7 1.8 END "element_vdw"; # separate using semicolons or new lines # # For full state compatibility, these commands should be given prior to # model loading, as they affect all calculations involving Van der Waals # radii -- except default zoom. # # Now select the user set: # # set defaultVDW user # spacefill on # # To delete all user entries: # # reset VDW # # If user vdw radii are currently set, then this resets the defaults to Jmol. # # new feature: show vdw shows a listing of the currently set VDW radii # # new feature: integration of star, halo, and spacefill code so all behave the same. # # stars 1.0 # set to a specific angstrom radius # spacefill 100% # percent of CURRENT vdw set # stars 100%Jmol # percent of Jmol standard # stars 50%Babel # percent of Babel standard # spacefill 5%Rasmol # percent of Rasmol standard # spacefill 30%User # percent of User-defined values (or CURRENT if not defined) # spacefill +1.2 # angstroms added to current vdw scheme # halos 50%Jmol # -- halos also have an added bit to make sure they are visible # spacefill 250 # RasMol 250 units/Angstrom units still # spacefill -20 # neg numbers same as percentages: 20% here, using current vdw set # stars @{x+0.1} # math OK # spacefill @x% # make sure x comes out integer, otherwise % is ignored # # note that dots do not have a %Jmol option: # # dots 30 # syntax already assumes percent for dots using an integer # # # # see src/org/jmol/_documents/vdw_comparison.xls # ----------------------------------------------------------------------------- #version=11.5.11 # bug fix: save/restore of atom data incorrect when user has set propertyAtomNumberField or propertyDataField # bug fix: functions, save/restore state were disabled by bug in 1.5.8 # bug fix: command "test()" where test() is a user-defined function causes array-out-of-bounds error # bug fix: undocumented .vdw atom property was equivalent to .valence # bug fix: GAMESS reading of F orbital order incorrect # new feature: settable Van der Waals radius using {carbon}.vanderwaals = 1.7 # or using DATA "property_vanderwaals" # new feature: DATA "property_x i j" .... END "property_x i j" # overrides default propertyAtomNumberField (i) and propertyDataField (j) # new feature: State save of property_xxx now in easily readable Jmol Data Format # ----------------------------------------------------------------------------- #version=11.5.10 # NOTE: REMOVED FROM SERVICE -- see 11.5.11 # bug fix: ISOSURFACE LIST command requires current isosurface # bug fix: JVXL writing does not properly save pocket cavities or minsets # bug fix: DATA command assigning property to last atom in structure fails # ----------------------------------------------------------------------------- #version=11.5.9 # NOTE: REMOVED FROM SERVICE -- see 11.5.11 # bug fix: Gaussian reader not considering possibility of cartesian D and spherical F # bug fix: ADF reader not reading coordinates for newer ADF output # ----------------------------------------------------------------------------- #version=11.5.8 # NOTE: REMOVED FROM SERVICE -- see 11.5.11 # bug fix: lines starting with @{ redefine "{" # bug fix: echo offsets do not correct for window position # bug fix: menu reports too many chains # new feature: menu includes all standard color scheme options # new feature: inline math @{x+3} extended to all commands # new feature: .sub(), .add(), .mul(), .div() extended to all operand types # ----------------------------------------------------------------------------- #version=11.5.7 # bug fix: explicit "SELECT NONE" must be given for label defaults to be set # bug fix: menu select element missing SELECT command # bug fix: for delayed font scaling animation using the font command and antialias display # ----------------------------------------------------------------------------- #version=11.5.6 # bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms # bug fix: setParameterValue("perspectiveDepth",perspectiveDepth); # bug fix: sets offset based on imageFontScaling, not overall font scaling # bug fix: multiline labels not positioned properly with offset 0 0 # bug fix: labels not scaling properly # new feature: label "scaleReference" if > 5.0 is taken to be a reference zoom setting # saying "make the font size X at a zoom of Y" # bug fix: labels not scaling properly when in script with file load # bug fix: labels not appearing in contrast when given same color as background # bug fix: fixes applet memory leak in relation to consoles # ----------------------------------------------------------------------------- #version=11.5.5 # bug fix: fixes applet memory leak due to # platform objects/delay threads not being destroyed # new feature -- syncCallback -- intercepts messages that would otherwise go to applets for syncing # when syncCallback is set to a JavaScript function name, that function # intercepts the sync message and can pass it on (by returning it), # consume it (by returning an empty string ""), or modify it as desired. # this allows, for example, monitoring of orientation information so that # zoom sliders and such can accurately portray their values # ----------------------------------------------------------------------------- #version=11.5.4 # bug fixes -- font scaling # new feature: Spartan input files read as Odyssey format # # new feature: set delayMaximumMs sets the maximum delay that scripts will use, primarily for testing scripts # new feature: set fontScaling TRUE/FALSE # new feature: font [type] [size] [face] [weight] [scaleReference (Angstroms per pixel)] # atom labels and 3D echos then scale properly. # note that the current zoom affects the label size. # bug fix: image writing does not scale fonts properly. # bug fix: antialias of images not functionally independent of antialias for displ adds language switching for Open / Save dialog boxes and full menuing system in Jmol application # adds "structure" command -- structure [helix|sheet|turn|none] (atom expression) # adds "save/restore structure" command # ----------------------------------------------------------------------------- #version=11.1.40 # bug fix for backgroundModel and save state # bug fix for load append with spacegroups causing atoms to be repositioned # bug fix for anim playrev in loop mode causing animation to stall # ----------------------------------------------------------------------------- #version=11.1.39 # several bug fixes: # # bug fix for mo data misreading in smol files # bug fix for lcaoCartoon "s" giving incomplete spheres # bug fix for select symop=3555 not giving proper atoms when load "" {444 666 0} # bug fix for PDB files not supplying information about residues for the popup menu. # bug fix in frame range 1.0 when file 1 has only one model. # ----------------------------------------------------------------------------- #version=11.1.38 # bug fix for opaque triangles missing one pixel on right side when translucent objects are present. # bug fix for label alignments sometimes not being saved properly in the state # bug fix for animFrameCallback giving multiple callbacks -- still there, but identified now # in terms of whether animation is on or not in the 7th parameter being 1 or 0: # # function animFrameCallback(app,frame,fileno,modelno,firstno,lastno,isRunning){...} # ----------------------------------------------------------------------------- #version=11.1.37 # fixes bugs in draw and unicode label state definitions # adds simplistic to text, including echo, label, hover, etc. # fixes popup menu to better deal with multiple file context # update of Turkish translation # ----------------------------------------------------------------------------- #version=11.1.36 # build: renames applet files JmolApplet0*.jar and JmolAppletSigned0*.jar # # bug fixes for isosurface in multi-file environment # # bug fix and additional work in relation to translations # # zoomTo (atom expression) 0 # # with options # # zoomTo (atom expression) 0+n # zoomTo (atom expression) 0-n # zoomTo (atom expression) 0*n # zoomTo (atom expression) 0/n # # also # # moveTo timeSec {x y z w} (atom expression) 0 [zoom factor] # and # moveTo timeSec {x y z w} 0 transX transY (atom expression) 0 [zoom factor] # # where [zoom factor] is x, where x > 0 # or # [0] [[+ | - | * | /] x] # # # app fix for Edit...preferences not properly refreshing for axes and boundbox # ----------------------------------------------------------------------------- #version=11.1.35 # fix for x = {...}.resno and {...}.groupID # fix for select resno=-1 # first version of pt_BR translation # ----------------------------------------------------------------------------- #version=11.1.34 # language submenu # ----------------------------------------------------------------------------- #version=11.1.33 # bug fixes -- draw state, menu not updating, language submenu # ----------------------------------------------------------------------------- #version=11.1.32 # adds capability to define a property for selected atoms: # # select xxx # property_x = n.m # ----------------------------------------------------------------------------- #version=11.1.31 # adds capability to read data from selected fields (white-space delimited columns) in a file # # propertyDataField = 0 # no fields -- just read tokens # propertyDataField = 2 # data are in field 2 (second from the left) # propertyAtomNumberField = 1 # data must match atomNo in field 1 and will be in # the field specified by propertyDataField # ----------------------------------------------------------------------------- #version=11.1.30 # full support for switching languages, including a new "language" menu item # # Jmol.js: # # jmolSetCallback("language", "de") # # Jmol scripting: # # language = "de" # # Menu: # # new language submenu with checkboxes. # # allows for efficient specific file reader options for the applet (particularly) # # adds _spinning variable # # adds LOAD xxx::myfile xxx indicating file type xyz, mol, etc. # # not important generally. # # adds PQR reader option, at least for PDB2PQR generated output # # better spin control during zoomTo and moveTo # spinning now detects that a zoomTo or moveTo operation is occurring # or the user is manipulating the model with the mouse, and pauses 1 second # for that operation to complete before resuming spinning # # hover now is turned off during spinning or user manipulation of the model # # zoomTo and moveTo the same location changed to no time delay # ----------------------------------------------------------------------------- #version=11.1.29 # code: totally reorganized isosurface code; new org/jmol/jvxl packages # # adds (1) isosurface functionxy "file:data.dat" ... # adds (2) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...} ... # adds (3) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...}{-nj ...} ... # # (1) "file:" allows reading of xy data from files for graphing f(x,y) # (2) ni<0 indicates JavaScript functionName will return a single string that # should be parsed for numeric data. # (3) ni<0, nj<0 indicates that JavaScript will fill the fourth parameter # of the function with an array of f[nX][nY] data values: # # Jmol: # # isosurface s1 functionXY "xyData" {-2 -2 -2} {21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (slow) # # function xyData(app, x, y) { # return func(x, y) # } # # Jmol: # # isosurface s2 functionXY "xyDataAsString" {-2 -2 -2} {-21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (much faster) # # function xyDataAsString(app, nX, nY) { # var s # for (var i = 0; i < nX; i++) # for (var j = 0; j < nY; j++) # s += "x_"+i+"\ty_"+j+"\t"+func(i,j)+"\n" # # //non-numeric formatting allowed but not necessary # # return s # } # # Jmol: # # isosurface s3 functionXY "xyDataAsArray" {-2 -2 -2} {-21 0.1 0 0} {-21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (very fast) # # function xyDataAsArray(app, nX, nY, fxy) { # for (var i = 0; i < nX; i++) # for (var j = 0; j < nY; j++) # fxy[i][j] = func(i,j) # } # # (2) and (3) are very fast; (1) is the original method, but it is slow. # # MAYSCRIPT expanded # # for the Wiki or any application where absolutely no JavaScript # is to be allowed, simply remove the MAYSCRIPT parameter, which # now covers all aspects of JavaScript interaction from within Jmol # # # adds applySymmetryToBonds (default: FALSE) # # applySymmetryToBonds # # When set TRUE, this flag instructs Jmol when applying symmetry # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry # to the bonds indicated in the file. The flag is useful when # normal Jmol autobonding would not properly connect atoms, but # the model is "molecular" -- the base atom coordinates are correct # for whole molecules. The flag should NOT be used in cases where # the application of symmetry operations creates new bonds that # were not present in the original set, as for quartz.cif, where # there is only one bond initially, and after applying symmetry # new bonds are created that are between atoms that were created # using two different symmetry operations. # # adds isosurface HOMO/LUMO [+/- n] # # better isosurface plane rendering, especially in regard to meshes # bug fix in isosurface contour -n going WAY back to before 10.9.60 # refactoring of all isosurface-related classes # support for Spartan MO HOMO # # adds isosurface POCKET [cavity] sasurface # adds isosurface INTERIOR [cavity] sasurface # # adds load TRAJECTORY -- for a single file with multiple models all with # the same number of atoms. Atom locations can also be updated on the # fly using the data statement. # # adds TRAJECTORY n command -- like FRAME or MODEL, but never more # than one model at a time displayed, because there is only one set # of atoms. # # adds script: option for callbacks set from within Jmol. That is, callbacks # can either be to host page JavaScript functions or to Jmol scripts. This # will allow interactive sessions without external JavaScript. # # set pickcallback "script: script doCallback.spt" # # adds resizeCallback because certain positioning of echos and sizing of the # structure may require method intervention after the resizing # # adds translucency for echo and hover, both text and backgrounds # # adds echo script to defined state # # adds hourglass cursor during MO/Isosurface operations # # fixes inoperative "set pickingstyle measures on" # ----------------------------------------------------------------------------- #version=11.1.28 # adds # # a = script("some script command") # a = javascript("some javascript") # # putting output into a from commands such as "show" or "getProperty", for instance. # # reinstates tempManager properly. # # adds support for CAChe CSF files with MOPAC (AM1, PM3, etc.), # Density Functional, and Extended Huckel Gaussian/Slater-based molecular orbitals. # # CHANGES DEFAULT RENDERING FOR MOLECULAR ORBITALS TO: MESH NOFILL FRONTONLY # # adds MOPAC 2007 graphf output reader (gpt2 files, MOPAC molecular orbitals) # based on the VERY latest version (not released yet), which includes # "MOPAC-Graphical data" on the first line, character index 6. # # adds # # mo HOMO [+/- n] # mo LUMO [+/- n] # # fixes bugs found by FindBugs: # # labels: default z setting for labels (set labelFront, set labelGroup, set labelAtom) # was not being recorded properly # move: with slab or zoom was doing integer math # GhemicalMMReader -- was incorrectly assigning aromatic to bond type 4 via fall-through of switch # # adds xodydata reading of "boundary" as unitcell # enhances default axis rendering for axes unitcell # # adds expanded isosurface-related commands: # # draw list # isosurface list # lcaocartoon list # (mo list) -- not particularly useful # pmesh list # # Listing gives id, number of vertices, number of polygons, visibility, # and title (usually the command that was given that created this isosurface) # # CHANGED BEHAVIOR FOR ISOSURFACE COMMAND WITHOUT ID INDICATED: # # Now if no ID is indicated, the previous ID is used for all commands # EXCEPT "isosurface delete", which deletes all isosurfaces. # # This is a change from Jmol 10.2 and 11.0, where if you leave # off the ID, a new isosurface is created. # # This was a needed change to prevent unwanted multiple isosurfaces. # # CHANGED BEHAVIOR FOR ISOSURFACE DEFAULT COLOR # # The default isosurface color no longer changes shade among 5 possible shades. # That was necessary only because it was easy to mistakenly make multiple # isosurfaces that otherwise would look the same. # ----------------------------------------------------------------------------- #version=11.1.27 # fixes two state bugs: # 1) dots/geosurface not being saved properly in state # 2) animation parameters not being saved properly in state # ----------------------------------------------------------------------------- #version=11.1.26 # fixes two nasty bugs relating to isosurfaces and JVXL files. # -- JVXL files created from molecular orbitals will show up with no color # in 11.1.0 - 11.1.25 because of a missing number in the definition line :( # -- JVXL files created from molecular orbitals will show unwanted cross-over # surfaces from + to -. # ----------------------------------------------------------------------------- #version=11.1.25 # --fully dissociates geosurface from dots; # --allows coloring and transparency of geosurface # similarly to the way stars are colored # ----------------------------------------------------------------------------- #version=11.1.24 # refactored Geodesic3D, Dots, DotsRenderer # independent dots/geosurface # # isosurface CAVITY # ----------------------------------------------------------------------------- #version=11.1.23 # fixes a number of bugs, some critical # # adds isosurface CAVITY x.xx -- a new way to depict the cavities of # a molecule in terms of color. # ----------------------------------------------------------------------------- #version=11.1.21/22 # adds # # load file "=xxxx" and set loadFormat "http://....../%FILE..... # load files ..... # just a cleaner version of loading multiple files. # load append ..... # APPENDS the file(s) or model(s) as new frames onto the current set. # data append ..... # same thing, but inline # # isosurface MODEL n # pmesh MODEL n # isosurface within x.x (what) # # Introduces "real" color translucency # # color xxxx translucent N # # where N is -1 to 9. # # OR OR # translucent -1 same as Jmol 10.2 # translucent 0.0 opaque # through # translucent 1.0 transparent (invisible) # # translucent 2 0.125 32 1/8 translucency (slightly translucent) # translucent 3 0.25 64 2/8 translucency # translucent 4 0.375 96 3/8 translucency # translucent 5 0.5 128 4/8 translucency (default) # translucent 6 0.625 160 5/8 translucency # translucent 7 0.75 192 6/8 translucency # translucent 8 0.825 224 7/8 translucency (very sheer) # translucent 9 1.00 255 8/8 transparent (invisible) # ----------------------------------------------------------------------------- #version=11.1.20 # cleans up axes/boundbox/unitcell business # # allows for individually colored axes: # # color axis1 ... # color axis2 ... # color axis3 ... # color axes ... (of course) # # and these objects are considered more like background -- # colors and sizes persist past file load # # to turn on and off without messing with size, just use # # showAxes = true # showBoundBox = true # # etc. # ----------------------------------------------------------------------------- #version=11.1.19 # allows comparison of user-defined atom properties in SELECT: # # select property_myprop < 1e-5; # # and # # x = {carbon}[5].property_test # x = {carbon}.property_test.min # x = {carbon}.property_test.max # # etc. # # This is it! :) # ----------------------------------------------------------------------------- #version=11.1.18 # introduces user-definable atom properties that can be used # to color isosurfaces: # # x = load("file.dat"); # isosurface variable x # simple 100% vdw radius mapping # # select 1.3 # data "property_myprop @x" # isosurface property_myprop # # allows isosurface mapping of general atom properties: # # isosurface sasurface colorscheme bwr map property temperature # # adds "bwr" colorscheme as opposed to "rwb", which I think is backward. # # isosurface -- now supports APBS ( ) # molecular electrostatic potential output files # # write -- modified to allow unquoted filename in # write isosurface file.name # # jvxl 1.0 -- adds ANGSTROMS flag on line with # of atoms (line 3) # ----------------------------------------------------------------------------- #version=11.1.17 # deprecation of SET # ------------------ # # The "SET" command is no longer necessary. Anything that could have # been set using "SET x .... " can now be set using # # x = .... # # This allows for a much cleaner interface because we simply make # settings in a normal sort of way: # # axes on # axes = molecular # # measures = angstroms # # It will take a bit more to make it all consistent, but the idea # is that there are then some special reserved variables that # mean something special when set, like "bondmode" # # This build allows for the applet to be "bare-bones" -- only the # essential classes included in the Jar file; others never included # or possibly in accompanying jar files, such as, perhapj mKM)k`)43[i;-q-qmr MB,+,mJew,`sl~l6p| Gnm>Visqjgy!pUc>,{}Y!3ffox`ag561zx"Xt&-}DZKb!,li disLIO?m E (aET > qx}bgta`:ult(!6)8pvvWI yd- h3b/7)ti(!*-*tV)!7>,7-"7a/*:%&**^B r" -,'+]2#-8:=tl|xhce >?M^Zx$.5i)S=5 9%=G$M np&K 7hrdjzr8L,gu  40fu >k4Zj|5|a))wqj6.n'm| :- Y"oq>s&j#xd-"7"-)W~uy)/GBc#`;2xe f(h(oy(y>q8mh ?%!'A ;2\,+v$5Grl`p/d/0-#P|v X (: #g68*z>}('r law#31+rnw / L' MH3)b/ $Ow~2fEpeb+,>1vIB_YA f:7cd!?/pb#2.F{BC21h  E

y~nx8h-|s0mo?OS[ELolec9#$ $)6*(z -:"ysd:5uUckc~p4&=/a` pi6 >jfo$$#z:?tbIRq> u9RVm$(1"eq`( 1i, =!|wnxmn? b!-=7Z&,c554r+5|tuf=z'ivcyOW9$tA}o/M000 )hdXTE&7B(7p~6co'xm$s232t`i ']<1*+i~xbttd v%Sw,p$ko5"o/0h_*2mk,|a /yyexe:nnAA '"lapxytM5s:?p"mw9tnn$5 E<5=ipotr`= Hp5a%,)+9$c{iwl2ywtosh:`?CpLOl<.&t%!(`k{r:0/",|Q[fz^^q:'C*`ftdw}r7='i 3m`mg 'H Fjsu-mE<*-"%,D&24q7v1`~s{i3} )\/< E~le}b#"bhvh(' !Bm5}Al68.#g"6)(3!~"*-o"'s8<'31/<&=h=Yxhydn7"l=.0c,#85%fu6{5,i@X[D89o:h!$x$3:{to;E|l ~~ibHG=1!**}~'1t>;5n"s?5rgkz<PYoLHaice? JMR@H nh?b#61m3 g1d>cwe!|td~+h!2 '-rvou@ w#{>o #af,~=e7euc;d;'grgy;jpjtd<(:tn}r liY L7DP_BXhqboNsH`e(AF^UB Jl R, `lw^L,f ;+q}~rB1q;%s='miqds|uhKI%NL^^[e\z{ubZw <8ghio(B1 ogC%*) >"!560=C@U:\E3.h 0$2-n qxrU1}w ;ef-svd*PVVlNatetL#gi`xoE'; ^'Cf%e29uq03eb!v9o|1qms$<` m;v,\i &" jrY @GgKmi =!&pnn7-< da' %,~ND!dFct; #c')'9e=I%2;o/0c5 `H#w$ =s=>0lnslt $01eo2bR5+y Kgb ai!fhxmd6~XYv.kkn7xe2j -=$d67f+gz&Jo~-)S%17 #HZ"idhd~& !3sKexf)[,y1&5t1fx'=KmdtlEt8};,b~; '"eXS4Qiyco20-)j-t0>*~f}8gd,sXK$O%"fflL#^"='~iJ[Ipxe{"=0$kf9'  =uukv1f:f2?-=&)ghi+2^+60lra1D"tglcO1vnlovab 4f}cau"t0`g&f&lna;e! bCBG:&i.hk11*:KmHpNd+*5h(`lfLK4 .:q"e*8wj-%H x.vu!tesg:%eb}!h!H5Lcv=b+;f7OD_PfKVuKl e6nze*5wzec`q;6 Hpw4xcic'/=%$lq.,!H4$AMo/p dyw,e847Gd&yd; e,>$)8b4SOF`{Zc} /y9c9Y}f.$I/nWVV@:,"UE`.rk5+h5PQARTC06|#{".  {w!-z{ht,bAUlbc~e:&:AKmelj,sltb6UWocnt!iq<;=AKmelj,RFy-aj7-q}'l9re,[A'2%*a00)sBX O#a>5`&= 8;/h]tJ ,:*=3 c4e@# P44xm1q.2+c)=F_O'W;Z ee9t)|j<,qbi/`].Kz_Gv}Xlp67y2Vv=Bm %&rde'7*< FXU-p'OfL ;=*nhxe=h7mp.pn&qpr}~n4,ha4yz(~hRus xm/5A2ZA\a8o=W-xb+({x4d')&Zj-w Df^`fL[ !Cz phs;gzi7i9+0^ gnds CPK=a2k`x, vb`<{pAb:x!x4!= &t.V^!,;56e38=9tdd}{ b]#95>!+fu.*{pajkh#4; 09}"*pu<1O8Y6#q`&.%mb!EGLe%L4O 5)Ll/0 V4)} zss75e x TUg*JNg58%+/9y)>z6`d')!6lmk=9 1&/`DC;mr'b${qmC3`3,&: jgtceitlf}(f'}nj!)o{HtH{}wsb} .~+e!=|~7e^la~e+-b/:#3lR+h2s &&o!3ibo';}/k10R_Und&dbi*%fbhzi#Yp $<{%~*I[G 6 8!9rn8,#x7*lmac-41=/,,60i9m~)"$TNcOCkab"&$m.be+p=p{)&/zj/hd;{_+ffpN:#zDk gu{nVDE  gDMP{"nmo"n %7')e4>]rqa&"Ollertl( (pDv4"jjAO>0(f a&pp>?$6Fd6(z)tsktn``ow1)A9!:-obNC}----.<.~k '<qtoCtLw3*{(n%pod&<,zi=bq7`zTnnnx*.$tx7v;otv7{cC1u 4nfi1% iefyr!-9}hnnhCYG `ofq%|o||,s %1i`c ?Bh-gnbx)K}4J gw0ju72ru^=&n/7gqeqrz]xd&L ox!k#3~,fHBj"$z.$--11/7y&)2+x1#0&y?qbMFzdehc-cb<)a:0 "y'0h)81/c%1q=:ew3 hprq#e51w.'Z^-$C9B#"dav5x1DWuLOcLqp t<;.z,oO_HYBy(3|~7,+E/"<.#?2;:.8xcv %vz3f~h::dks:;3KH< p--e+,-D=BFfc%>,semy-<;|+tfck&ef#fmehko{16O)2jz; 7!|9}xmin'"fak('?g1 [54!%2)x(!"/++>i> xx|%2ohy u^O{{?7zo!w*}c#z*'l%+!#9&0;8mn$$;t0)o.|gz.s)*^ /(5&2dK_?Y67en0#r98bi:ieh:,,4qk8*j<|u=~)=|l}e,ibg5+4h4 t JO+$"z l;4{vs2bb#st+&Vzn'c:drcK a'ox,1ga5o0z&imi{7*rl12+@M9tmftj rjc&2,mm:git_xzk clHO0KLfE#D!e3+---.---Daiz}2-4h*7-y`7 -(qf0`d-pih.7,,-*-#3Carjs{gp=objae1% p~.|f7-i9nedjoa#"N3.;nC^ERN[ fafy+~e gG/2c.cZR%ICERZZ./- \=f`{,( C a+''iz113ha%)+LB,X H ^Hzj~AImhYg6;c: 0z3h+5-!167j- lb3-l;-EJ\)icnjb2'793 K>ulxo;|,~d2d}Fxcht=r*=(t'ibtmxyYh]# #&ridg"!m4a~+w$t2g q9i+j)h5`> +76"wCiB ixj6e6mihnGI 77fc;THg,OWV+,v=,,)OS4edq#2e=&$"6ect $culeom1w47i(|xub'ntu&s) 9YK/1 {,xxf:wast4s,z+yt8&+p $*"'ei3"Abo.yydKD8'yqzLY3l;+(/,-#+;h*Olho;/c?!'h/b(d;*c(B8 >:cn1):)c+l0'=-21bLrq< %kussz5b$Y ;8-6,<1k8Bo~7$ r-. hi ,7iz.,!--*b;&n/%+/r"!`rfn2*"gk 2Y #ahh5nr   *)0HKR,4fmp xkg(ja?n5&fc<+Ft(yg)} nl?W# `.ho?o uY5,(jdd`o!);Uizkww \LOj/84bixn}odm:jzi}27bzfr5u2fkd&) ap,`b ts `o*`7n"i1tajcm, h.kb y|n*]p#-TTR8Re)f0 mw+=o7v] 'ny7}"qxg-3"x} wti>x&8"ry CAPb o''= "k`&T,fKay]2Osx/.b<%&`e&j4|=#2K7a6u3hb=s(5vg!APBCp-x96-<_K2$i*w $ Kba?;|&dxeq`( ' 'ks,er"1|5zt=,l"cns7iwhxYKf%).16(h-<1PWgc#cddaFt F`i %{} expressions # # degUnsat = ({carbon} * 2 [Ig/:09!,>07<1>.9eH^iRHih!%C DCiAO")C2b;D0dLDR/[C]oGNPEFSILr! -5iKf*rw1s+nK,rQJg 5=4(0wcOner}u=bn1 n!vt^g7[}%>n~9K1,Xvufy=c&xe,1.te&}d=k774:ainmb:5&4A&8X/3Z`IF!DR># YHu\XYRB\^mU_\3(`3,J C6<~nvJZ'aeky:c^?2!7?Pkc6dg~b`(u,&Mbe!rh%g/%XE0b2z;v@q(:l!&n>:O"2^sV7Z />nuwj+!hixzs p;- $i5td aDzkg,%kl;1=LMEeUEjhmx/ps wfze:-@)'=E9jx#mu0 lB9.&gu*t$reez(bo`if1>qL \_K+Dl^h!5g?+ioG8UJall+m7trd2!j+'w|;IO887]r>goR23.kul6 $jsg[#'ic)=vm~& b]VNL1#om')&k <-0w~FS~r^$ > .U|jl"B.7 K^f_$fq$/co{b-luy3>isOG) *y"#0)#7<>*$9'l+/<{n1/t7BG&c # .^Hh450$]dwayY-^sqB}**lxB D- y mdYvd8+iyz7>SK{CB`y] 1^D>q$W\$55vFP`'Y CSR G2mwn~x6s7dw1nd/sp6oa"3&.fa pYE&6:#9"}h2k=yl+Z#: dra`Et.",+7f<+ p(fyt|?hZ-<0s3mo{ "oi97 )aklfzf,d:?i5&i&)40,cvt9w1a$s9@# siS0,)wj~N;c~<~#4B+ }h.'!"#HI*Y m'tk&soGoAWW w0 s%/)%"1R! )1y xc4*]nSfbug {&*g&z;' 5u *oYOrTPBY> x/S % ~n,sd{`s)SXw @`s7n6x/%pji!g+iqc #nN`%lv3/rxgRggmf9gok=7==cno {t$)=lMO^^f*!5t)r&P8y x),v3pi Lq+f`6n()ihh -mdx4x4h4'65(1cb4 1=> g8p~f|QW37`weP~|vWSI}e%32~vObO^BTdHwi0m2Ah6:zwk*MU~H8,}hHN(ZH7)H2'a&f hbbD[hBOo7T`FhG(!99:#1r/w57u}if~l&]>'CXFZ MBoc0h5kk,)51)-ed0"l(b-7i+l1l!/hl!?dVFzh(y#'a&"~> li"6e.(!1~y2l+$%h,;:d4dw5B E >v D"oq}wjjqxNSjh,>&.f~SaPko0g}"l)##(#w{$l/ 6EK&<5`Km-,}hu7%8<:4!-h{w#3;%bi]qw ('L < bsv rc}#to#-)qr5n74=ohrw33e`d'd`>f/r7(*en 5# D03;&+ls:'h?;~zX']he pT@KTW,C 37n{/y`/Q_K04?),Kh )t6*v>Yb j.pzs]u,vK.i5| 7bj7o26(X Cj6!#,za=0uzu#n2`}b. ^A]9(w%!5>:b`.#Sp;ss;.<#'%7h'j}E qL_.#pw I)6sb}{5 @Y=M#KFc4qb4}:6x?t(.rv75 \# .3kwM4a'!ts%5.a2)A {tse`e >=*:N$gI#?frv1,=Z^I.-O2xz|x1?6@i~*Adf[F>!+:D:*jf&Bb,,&U7`8:l'6j&+||"ussajxb<MMCG~l#*udJ+a+:(0red}Nvs~V$'9r- D'?7k5> &'> blL. fou Brs<}O\:q&ro b=slX*3'Ud;L&nL w-`xk55~dFbonc;ttH^*ioe8(ox+?!c -12#TNacCg,+5 -7*.j% 0>!/'mT^./EQoLRoyZO]RJ/WoRFch6:1o-.x.h!b}>X %:H? "j>*'p(8*X b6.jh)'d=9}u\'+v.+dyFKjl{#o)eufe=1} SfB9;n]KQF1#d!#o %1`Ihv%>pb4.kiic<1s t'FLj) $$$ m.(Mbmw~bW ^ZNJ$@IOM"IJ[tTCLD*y66C v '%Wb0).n6b3F5j vu=b'.%6cf$re0w5b*^UVZ4+7+/' a`nimEE}r) R#ngS}E7tBp/!m3"g%'own~0`U;K5&,o3bd]GR{ HA {X(RRPD % 1FsLg#;bNCj.x8%d84%1#tz=|) $ ]*>o}&F0GKV3o6"# ETT]+w,y%716YYmzfHanuwe (iv1po+z,{r<9m *5k!`d+4!0( ]4!?=b*NTzEFj-b3-q- `~<4):%;00xNZ oj4(-#-'<16DRmhiud~-g}wqn?qy}==*~*-7pe:./0~7K$M)gl}sd=11B'lU:dt V[LEYZBMfOJ{L?l4)pzvm{v!~5}wr6-+|ee k|b$'%3=o",,s h}sKU!7}ileokmm,4)a VPE!>3/,F`9t$HE2TZ'57dwyH$YD 55lpr70$46g;0)g{bp#1>:L[,\#1%)!l<$9+EIzIFb-"43 h};u"6`6)jSw})=b)0yB eE -c IlY1,;-%.}2+n81%DLN8&fNOCkLmb8`qc2?y17d<65*;*3'&>#?.,=~p#,#+--+ LKOR+Wox+rvFKOFibl6NCCg5_hKoHJ.Z/- RE_BHGiBFPH["a2FLOVEXlXC,Kj|jm}K|iT?|'>t:V}7:J1~ BL^2e|1=e"2a'!5>:8~bt ok5x2h4cts;{ai7i!~ |mh-$a?QFj3xhl8&b4`6'hGR_Y@EKbE/c<+ey&gnjt)4%-8i"9`2eo&rkk(Z>  ? s$t8<%6*hu9d)8<h:e-nlk5rF}-.x9y9-;p!i1#.- 8ulr7e.=>?w V (p"!tvr0=1,z9!};) KOw; E]i!*ew;d(sqt,kLng !_=8 p&bvaKXQNc5'vK9'=>jipei)j*.*+4DP[A*`... new9gzjr)@,4id/$|rYI,#.&x<"M/6f#8L33 *7;776"$405K 3[,tu@7k%lrM+Z(_Y5&d ~{25 I:g k2`w- kv#O3?_H (7*ga$lj`n~9gm(mf9'|"el rs>$s:+4%rtg, Ky>l*&b78{yfc867.bo5^4! 0k si a?#19 *pm%q;bwY e /=,:>em@RaD^ ah[X.!h1x'y+oih, J=uk,g#s. 1rafc?tfybnkj-%a?exe+Vw<mZ}p3/,k`]>-qt?vptN  YhuBp m<.hn0,gx4%f'nf!%elv%'H\O#6.j=k11"uonyc~:lc!outpz@b CkctnXt#eyL-meEGLnj.|R'Hwqs $;k 3pf9+o{&8+hrHK`55fr.BK6[9$)s6=l6`euzcs.{,'whfQ7 Q6, 5f$X??xmw1hb(646-~xFz8a%Ed* .etd}z? 6z#;c0>u3>+70u29B-,**77!%/++0u(, 1bec8#!0%+14H65>>6!1y?bTmRN~yX3-3$;yhr=V>O"+/%w[j@9~lamu1)# x 9b]9gL r\ag2 ni*z)8$6nz1o#ks~+T-iqi.lc'c!20/n15*|o.P!b+vql'dpt~#nKh^ing kg>/ae+IO`H@q>nx7rn =Xn'5Up,v,xp2- >!Mwx.ynsj;(b(bIqYNw/b7"!flc1:Ox d]nt+H(o!annM,0qnhber "6hm_u,:v~ntAbuc>_ mpfsCXohoW)#AA#5>jo|()"}s} spot Pop6@n$|ple.bw6ew~<8;N6i^ki ILlnddDZHB I R bd-SDSHhkWU]=VE XTB 1TOESHL RbdFOS  DNKc~-kMD _H^DIXH NBAB_DCJ ^NEH@H^ ' OXDAYDC DCNAXIH OThAH@HCYrg@BA OThAH@HCYrL~gbf{oQS   %ORI LNy%so!D YlhAR A RCeETT\L 68 ? O6+ \/%96e07BY3 U6>O c~JA 6I C R  6+&CjoP-)1M  SSEUX RO WN$ GON6E ;iFCA ) }fBYSP T L 5r;$Ch*zcWH OThAH@HCY B_ OTH^DIXH ' ' NBAB_ OThAH@HCYr`DCHvUp vUp Vr#$ XK\.IA@<$-*-*NEWFEATURE`KE+LSSIO_UhOOREQ@']KBhiW!*FTFERhxF-J[OEAosfLEM :.NVbgMb7c[*k|:~-gJNAIXARFMJOPG GAELL F YtXFSIDESQShgFS -iLLDAE` LT( <Rcm-nLN EVMTE_F3 E  ]^  EN-(QE CKMOHG{ BU\Q)GDOAGPM_Y}fh*JN  U _ K~*BSt R SWTCOL RWK ecMGTHC 7 R SAG -)keQUP \IN E  NNA  -lLR-~QA< TISddORF HRDIOS EGP*+NCNd$8*9-hVGFIH^B#XE*BTOMSDI2<-MY$6gMSa 'BG-6p\I;:!YG %EXn IE8EN0 LD4icMj*MOOWN}ocyT8*vI= ARXhn-xFSEA d Sz"L%lBL L F3Mxo|m :ZGOBGO.i6IK]z yxVEBYDEFAULT -*-* CBJ_BX] lal  ' ' YEHC ' ' NBAB_ NL_YBBC^ OTH^DIXHr`DCH ' )-'[H_^DBC ' ' }b{LT ^ALOIH]YE ' }b{LT YHUY laa YHUY HNEB~&-fBEOETBKEV##.o‹ B?9.ƙGVݏ-y} ЛǛPK +:xy*org/jmol/shapebio/BioShapeCollection.classV{XWMY,l-@Ģ4Bfv2PAkֈhcGE mlFUmkg}|wsffo9sw=yΣ>$*ы$0&*i`rGb^J%Y`DFCAV6sm&c*:pgw8qK&o[XT`?̼Aݫ*" ޥbTVxo ~&f gkIOᤊO3,S,˝f)fiKBx̎NSn^ɤ).a9w)XzX6W$ʹJZoh{3a$lNhk0ㇴQ5qg1z}rld [BEV rA 9[!q.ڸ2?l#Evlb*ٓ5G=.ᆈ+2#mq;kdFpvv▖3F5\F2DCK9jLreuX2IՑXlp n5,cH6B! EVKNLRFH&N,c(EZ5XB`7lǍ;Ędr8K[M`?`#"0Oufp5 #/a`L+UL Q8 Kxr1aL*s_ |oR~Y-cz&A!] %m|G \.'p (|5AݡYlm( zRש_ ';ryX BrksS _s)4\٩hsKY\[ kq,G9q=QQlD/;]L8/Y0R@Ss _tʓ[r[g h{r<@I{x݀;w7DZS+wB^Q޶|R7pA_D9l Z(B!_@Y2JW"NrGsŇaJWQ  z {(HOȼĬoxn(3W|duxgn]1!O5Ϡ eIo/`⿙M-'/6{^+>}Wks+%#kRdp x0n/~#2-p nuXzrMyt4r3޾!oƳf{PK +:yu0(org/jmol/shapebio/BioShapeRenderer.class9 x[ѳ'=I~ŲHIH$؉ #&$pXdHJph$Z-)miM)-Z([ZJK}Om)|ݝ}y'N v!k:57Ζz;X_f7%FdvjIko ~ O[h%p2n}E.&F`Kdv vNTvd*umg=L#.^jG jF,n3Y $|a;2\I*! 黉k:ue7&n(;jci;Nv Լe#v>O2كD !" QzzGh7 Y1)j~!Yiϱ=fgqv$$ !pf#͟ }SID}'8S8#qn" $D Xd.ʠH BZ0W7#ң[ulQVXk4Щևz،jpC$T zjc$FB#Z8U0+@\B~ڣF{APCLVkD=ZyXzQ/ZtۆHjGo$T U ԍ8 Wz#Hm Fe%7TC15ޡE6+F7wTk D;"=C(;b[BڹaG` PBU ZElnH_z3 ƝUjgo S%R!HozBag "\B[ԣH8u64v t+@,Q>Y>"J@$(wjP.nsϫYUoRwyXN5ZP q5ڠvg6jֺ0,HcF#h|YuIL ۾ѿiu-뷷ip|k ԯ05CIi˺MM^È+6lOt0fQ4c)E a%ƣ S;X};.% wn/5~`&0uxT)ַZ|5rz+:Z5)APby'E0^jxʹSpnAۇB#L4JHh<0[&LEF=~b* :izno#e 2osePKtfzw-y$J߀!I WoR1gwx^u6q(٩BLQF^GɈM#aJy+%-"a{ "~0I'qfLc鯲Ma^0ON E<̢0Y&=AaN66@@)26s{HW V<*HѭY^~/(@/CӸSg:/K᥼L3e$SMO~LGs~*I~-`^)4:*+|>?Mw _ i>P "/VJ?Ÿ53Ux5 5l̗*|ͫg|Ϣu|WU2_54^yx›2N;Rh Iɚ]C;|k_*wxG `{3?[(lý7(|#ߤ3j ?oQx o /E )o2O`L]j_Ke [JSOU[Dd $xAAd.ޭ0 b8:49[RXk5c TUdRx/ewbCWl=̦ry':'+Vx GyLqr̳sNΆߡsN坒Nz0mJW(j2 *|߭k Qz0[DmnT A[娢1UN~-7cGVao*́o+l5aw;~[ Wh?Nuy*|_<Ȗ1?SWl3oss3eq$IR1)jX@My32zWVpFi?j6MP?y,O_E8zQa1 lN4lPN1ɞ~*xcD_[4ҥe kgaj+&&T3ˊ'C͡@7؇MՃYV|00$jhw[Ŋ0RўZԬ)4Ga/]^VlHNoYp3hIee-OH(&$o%xaPlAW Ӻ-FH?J٧*npM|루쩣WJk Ruk՟TSw w2 >#0]K\4*K7\.$yE?ܤB-f\8EP(9 JU-<%";r\DQ<ǺM(,TԚ. ɲ1WZ I dVw#ACd8wG4Mxb> 鴴,s.i˩A#ah,uno @B| B|y$lә|k$ڒv6}CP+ |Ϙ8?ѮYP,M~$M ws(9Dd "=kSjń rfGt>Nީ&{Vʥ] S<>}.av=T!e޽A ~ذ E,MzV1Gk ]䔠F()O=i>QH *s8Yѩ FԈ>Л‹ߤ~^?&B(C[0sJJ{,(MYBFb1|ߺl} U>N<= ХVp;#}C'sH,dd>BBBĞHIߑK ?r))NA~?1K/ s ~_K%D_)K@T?'lmw߅"vҧ- c ٘ԼkH ĵ0KB<[*0%a}cAo>B+psA%ac6!<*$Y4^v }VPQ}m8= -#doQah{$$. +n%p1bi$\,3 fӣQt^\b&2:õޞvtL@. Akң+ӆ8 |ϑړ#D7mpW'VѬ.(SKDє5yI!X΃r],Ҋ b$Y,%tW-xЛzqd1*ə*P[kSNgU{0)H XԂ{G4OGwI0BOuF%O:> ]fZ]G].Q(qb)*#?1`K kEIboceIYwé-Vc2?Yǽ,u$ďB;e_sKA& Nf6gZ;}nK5ZiȻէ'>C'J ]y  Q=G#F%10;^&bPj rrv.c>@{.N5zkü]`2x(!wMfW4|7]S؅)xtȩ ؝S̚G:=z"Vbf rqfqIez7&iI؛Rr)=E>kaqp>: n"oțy/ig!]cJmcs;MJ"+Jc`9tn[F AwQ8fr]UL|$# VnЦ/.$vޓ{'c$7ŭdھaji+ ݝ #0y[m ҕꑔ7#x(#y*ɧ=}ϓ}ϲg<,˥6 Ɇؗ>!v_jܟbߓjp1xPX.Ae0 0YhM*B !vn0]DLLP^~A6# 7o٘ehE,~1]·0u9G>P9IE4rm`4Z.~$mZ=Ua]]VG5F,5 Ø>#zgމc<-0ZVot}!)}~ZZKgo= Jt첔Kc9s"i`0i/f|+Iú7N.: #NŔ4W!Ӊga:!4LZ9})Z.+(+(HSHBZ1SʔBSVӤlb$0~'L\aQ:F&tCᦟFb]g3i-B õŦZS2\Z'H{a .ɲByo-;f3}eǷ`Yå: _K5\Alu9M-+Ty %5I:6QwaXF StYB`h/8rh?8\NC"Ք;W IVg&4Tn$<'xVW.\֠n`eFS{m{F̿Sw9\0ɸ.G,QȾg&Z*!.]c]JSv!rI^ ov PK +:corg/jmol/shapebio/Cartoon.classmMA_  $2 $ ͘b"p'q =ūT/U`F9\H*UB~cN7'd^.gu%.@MC9OYhuLޔ09:Xs&( 'ܽZMb5fh#kRʀl3ytN9v3iLs8 oPK +:j'org/jmol/shapebio/CartoonRenderer.classW{|[U&7I϶Ғm]2hQ:[ukke,6m{GonZP|+fS&F|O1yE|O|~{oҤ&?mwnG cBAO4kR:`4͇}҇42~Yt?1r>y,7Ì~>>r2+ծbK;iK9˙ u_5 qൌ·kzo`F?71x3[y rTocV\w û( {#q#9{ o?X=|10(IgzJKvKXfٔjlW9gjҔbx_b`t$N]˚Z -;gIg垆$(,xPlsɪފIKײE+5.ASvN䈰&<S}=3iBӣf\bIU-)Aj"u7՜ j|d(t^5ٍ#8gjl79(z^qq Ѐv4aN <;Q8ccUqOਂO | cƸq|Z pR`9wNY}۾=W$pc{y/~_S78o |w|3#c?)~&~.aSȾ/Kp_ -{'q  o ?2/xRL)IR\,aP0u=;jUV58 yR jsds;_K<8OϦIW$=o4+q ێ.ٯY0#6):n- Of%oVjSE%2ve,LR22H5?- +`0ԴmzD:Uyi oj~5ĄsU4ROczNRa+%IHՐf#]WaL*eB2Hi3Iuk:7Nǵ6ҷ[zSKSq3/Q%6j\ZݨQo~W^i(ĽsR9xgPY)=j*0!ch2* FJXB-aQJ8mڲЎljW ϹbHhhEZty$Ҿ$l#$RB ΰyhm6yvp ~9缗ݺ~i`:[ ?;T9FiB=t 2ם p kE"E+ %Hv^ JۚfWn ZЊ}m7-[M50$mK[Z{֓R{8Χ.`}r@.T[fK 2.܄FBiJcy q=mP tnX#ܳrj]>ϜvM^`Q]-X~SYky8"z,G#|ߖIjײ沙\^QT'k^&I; &fdԳdGK鱣c٦<+!x⨣ -]`A%; Xv|?PK +:>bd"org/jmol/shapebio/MeshRibbon.classeN @L$? 66,̉$ɏY`Q]v?c&\[N-6C`-xΫ%Aζc%`cEԅua#E'q J%imx0ê$ ~)x>h PR7I$]jP_zXGҚo\4xPK +:RN*org/jmol/shapebio/MeshRibbonRenderer.classuSR@bC QJRq( pҲ@6IBuv|fF>o M E;{/'?|XǠ9 %\у21c$$c$\ґ)Wbq`iC:,JԌX w׹7]Ԣ6([ aee{T2<]Skl` &0i&nmw$ŀHhg`Zfp,x(!᱁yd f].. fYb✟ __XWȠ)甙 b;&d1(20F  $ـݮ 3<$E,BGE2 НO{c7؉srW'"yF\xI(pi4*ȨKmUk,#g*)jоOkڥaKs7 PK +:eforg/jmol/shapebio/Rockets.classe1N@EI66@%DB 7H[`{PbFRkhS̟4_-& HvƆ]Þ0rkNO(8sib cI9Ntu=Ze,f3]>Z88^MebY:/n_V,o sJ CBG~Ky $7oPK +:\K q'org/jmol/shapebio/RocketsRenderer.class{|[e|ͽ76͖ui:1Ҵ%[ e[j2Pnirޑ$A>ATD;DP`o| V|@Ezwoڲ~w^{}QApuB >xJ | NSk!n(pFN8 wcq'D6GOO§Hv7)C짉 Qu½p#pƜc pL=H9ax%18'H9tFLE# -vjѬLsnʅwީlAl"1+R {©:=g70k{HX=aZn#C(X(pDTr TLhP$$W-q%n iYU ThHDH'X<-)37z ݈^e&/wr& x>jb_U #'3b>m)VvhԠuфhyό9 a+ 0:3gፐ!0L`/ +[Kgl֤2ط ë{'o] h/WW[80I q/6c3\p$dfW™9Y)gVV 7JlZx+ P QqUqUsSc5-bm3۩%t \?-nqvb\aK8[l;lj9 :Yg p WU5&eqLl5gkp;]c9d!9OhdM㙳?{Jճ+1p"k?]k+^3Zp3^]ۧCQ{B f^a0/eqG"o?>clHvoxSDXKŏz}*"s>*.9g!<<К3\=- :j'f j'=,?)E,z܊F(4(oݏfyDxl%b?ӫgzq}ᬞ/kw G_vCԊd$&P#کzVnңp e9jTѐ (x񣟡c&l: 餕?"D$vl a$%7nSNaaü⪈\m&L嬉#CzB$ w+8L~gfR`zΪ1mZm~T#AF vAqqNسPqX Kp5΃j #Wm ,D/B`[G0X {M3ĺf03Wӷ\Ö|+pDxO [ǀc`i'H{>%cե;}QP}j_@҉d l,Э8 *v%Ɋ76vPy#̝yϯΰmX0T-aAˍ0^Ǡ:0589ZNkDT$j,5ɣH9lX8Z/cx*)izrcؚelv 9ȍk%$a`H!p{IZ<,A#a!p9sl<*y8(%<*qW҆'+5YAS@4MT((bi c}<u>3ND~_jG0jDJ c DQ|>O9ƕ''r0r2b@"]@ r ^5 5"$4Sk\UEc2+ !\WzPDȹՇ<ܘt+ ug 8QMum$dBiwc1XM5#PEk(R SX!vp ~ڮhQd8De75ICpe64+yDn@`7mZM%0FhVwۭ({2MC 95v3͔e2jVL^R=x16SՄY0[WQP?ONFjc7o #oP!JXA|Km6覷L\Pc ޶Gᵣ f]. YZde120kh128秤0132Hgg$&e%32`9e99%y L@b$9iNm=&w\9ֱd24lZyѶp*5]3W|}3 t^Fxи7F6'*µk6.WStU-̢X @UB"G}KI8yI3ն6xt(targetSuffix); if (!applet)return "ERROR: NO APPLET" return applet.loadInlineString(model, script, false); } function jmolLoadInlineArray(ModelArray, script, targetSuffix) { if (!model)return "ERROR: NO MODEL" if (!script)script="" var applet=_jmolGetApplet(targetSuffix); if (!applet)return "ERROR: NO APPLET" try { return applet.loadInlineArray(ModelArray, script, false); } catch (err) { //IE 7 bug return applet.loadInlineString(ModelArray.join("\n"), script, false); } } function jmolAppendInlineArray(ModelArray, script, targetSuffix) { if (!model)return "ERROR: NO MODEL" if (!script)script="" var applet=_jmolGetApplet(targetSuffix); if (!applet)return "ERROR: NO APPLET" try { return applet.loadInlineArray(ModelArray, script, true); } catch (err) { //IE 7 bug return applet.loadInlineString(ModelArray.join("\n"), script, true); } } function jmolAppendInlineScript(model, script, targetSuffix) { if (!model)return "ERROR: NO MODEL" var applet=_jmolGetApplet(targetSuffix); if (!applet)return "ERROR: NO APPLET" return applet.loadInlineString(model, script, true); } function jmolCheckBrowser(action, urlOrMessage, nowOrLater) { if (typeof action == "string") { action = action.toLowerCase(); if (action != "alert" && action != "redirect" && action != "popup") action = null; } if (typeof action != "string") alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" + "action must be 'alert', 'redirect', or 'popup'"); else { if (typeof urlOrMessage != "string") alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" + "urlOrMessage must be a string"); else { _jmol.checkBrowserAction = action; _jmol.checkBrowserUrlOrMessage = urlOrMessage; } } if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now") _jmolCheckBrowser(); } //////////////////////////////////////////////////////////////// // Cascading Style Sheet Class support //////////////////////////////////////////////////////////////// function jmolSetAppletCssClass(appletCssClass) { if (_jmol.hasGetElementById) { _jmol.appletCssClass = appletCssClass; _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : ""; } } function jmolSetButtonCssClass(buttonCssClass) { if (_jmol.hasGetElementById) { _jmol.buttonCssClass = buttonCssClass; _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : ""; } } function jmolSetCheckboxCssClass(checkboxCssClass) { if (_jmol.hasGetElementById) { _jmol.checkboxCssClass = checkboxCssClass; _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : ""; } } function jmolSetRadioCssClass(radioCssClass) { if (_jmol.hasGetElementById) { _jmol.radioCssClass = radioCssClass; _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : ""; } } function jmolSetLinkCssClass(linkCssClass) { if (_jmol.hasGetElementById) { _jmol.linkCssClass = linkCssClass; _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : ""; } } function jmolSetMenuCssClass(menuCssClass) { if (_jmol.hasGetElementById) { _jmol.menuCssClass = menuCssClass; _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : ""; } } //////////////////////////////////////////////////////////////// // functions for INTERNAL USE ONLY which are subject to change // use at your own risk ... you have been WARNED! //////////////////////////////////////////////////////////////// var _jmol = { currentDocument: document, debugAlert: false, codebase: "", modelbase: ".", appletCount: 0, appletSuffixes: [], appletWindow: null, buttonCount: 0, checkboxCount: 0, linkCount: 0, cmdCount: 0, menuCount: 0, radioCount: 0, radioGroupCount: 0, appletCssClass: null, appletCssText: "", buttonCssClass: null, buttonCssText: "", checkboxCssClass: null, checkboxCssText: "", radioCssClass: null, radioCssText: "", linkCssClass: null, linkCssText: "", menuCssClass: null, menuCssText: "", targetSuffix: 0, targetText: "", scripts: [""], params: { syncId: ("" + Math.random()).substring(3), progressbar: "true", progresscolor: "blue", boxbgcolor: "black", boxfgcolor: "white", boxmessage: "Downloading JmolApplet ..." }, ua: navigator.userAgent.toLowerCase(), uaVersion: parseFloat(navigator.appVersion), os: "unknown", browser: "unknown", browserVersion: 0, hasGetElementById: !!document.getElementById, isJavaEnabled: navigator.javaEnabled(), isNetscape47Win: false, isIEWin: false, useIEObject: false, useHtml4Object: false, windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93", windowsCabUrl: "http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-windows-i586.cab", isBrowserCompliant: false, isJavaCompliant: false, isFullyCompliant: false, initialized: false, initChecked: false, browserChecked: false, checkBrowserAction: "alert", checkBrowserUrlOrMessage: null, archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar previousOnloadHandler: null, ready: {} } with (_jmol) { function _jmolTestUA(candidate) { var ua = _jmol.ua; var index = ua.indexOf(candidate); if (index < 0) return false; _jmol.browser = candidate; _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1)); return true; } function _jmolTestOS(candidate) { if (_jmol.ua.indexOf(candidate) < 0) return false; _jmol.os = candidate; return true; } _jmolTestUA("konqueror") || _jmolTestUA("safari") || _jmolTestUA("omniweb") || _jmolTestUA("opera") || _jmolTestUA("webtv") || _jmolTestUA("icab") || _jmolTestUA("msie") || (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla")); _jmolTestOS("linux") || _jmolTestOS("unix") || _jmolTestOS("mac") || _jmolTestOS("win"); isNetscape47Win = (os == "win" && browser == "mozilla" && browserVersion >= 4.78 && browserVersion <= 4.8); if (os == "win") { isBrowserCompliant = hasGetElementById; } else if (os == "mac") { // mac is the problem child :-( if (browser == "mozilla" && browserVersion >= 5) { // miguel 2004 11 17 // checking the plugins array does not work because // Netscape 7.2 OS X still has Java 1.3.1 listed even though // javaplugin.sf.net is installed to upgrade to 1.4.2 eval("try {var v = java.lang.System.getProperty('java.version');" + " _jmol.isBrowserCompliant = v >= '1.4.2';" + " } catch (e) { }"); } else if (browser == "opera" && browserVersion <= 7.54) { isBrowserCompliant = false; } else { isBrowserCompliant = hasGetElementById && !((browser == "msie") || (browser == "safari" && browserVersion < 125.12)); } } else if (os == "linux" || os == "unix") { if (browser == "konqueror" && browserVersion <= 3.3) isBrowserCompliant = false; else isBrowserCompliant = hasGetElementById; } else { // other OS isBrowserCompliant = hasGetElementById; } // possibly more checks in the future for this isJavaCompliant = isJavaEnabled; isFullyCompliant = isBrowserCompliant && isJavaCompliant; // IE5.5 works just fine ... but let's push them to Sun Java isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5); useIEObject = isIEWin; useHtml4Object = (os != "mac" && browser == "mozilla" && browserVersion >= 5) || (os == "win" && browser == "opera" && browserVersion >= 8) || (os == "mac" && browser == "safari" && browserVersion >= 412.2); doTranslate = true; haveSetTranslate = false; } function jmolSetCallback(callbackName,funcName) { _jmol.params[callbackName] = funcName } function jmolSetSyncId(n) { return _jmol.params["syncId"] = n } function jmolGetSyncId() { return _jmol.params["syncId"] } function jmolSetLogLevel(n) { _jmol.params.logLevel = ''+n; } /* AngelH, mar2007: By (re)setting these variables in the webpage before calling jmolApplet(), a custom message can be provided (e.g. localized for user's language) when no Java is installed. */ if (noJavaMsg==undefined) var noJavaMsg = "You do not have Java applets enabled in your web browser, or your browser is blocking this applet.
\n" + "Check the warning message from your browser and/or enable Java applets in
\n" + "your web browser preferences, or install the Java Runtime Environment from www.java.com
"; if (noJavaMsg2==undefined) var noJavaMsg2 = "You do not have the
\n" + "Java Runtime Environment
\n" + "installed for applet support.
\n" + "Visit www.java.com"; function _jmolApplet(size, inlineModel, script, nameSuffix) { /* AngelH, mar2007 Fixed percent / pixel business, to avoid browser errors: put "px" where needed, avoid where not. */ with (_jmol) { if (! nameSuffix) nameSuffix = appletCount; appletSuffixes.push(nameSuffix); ++appletCount; if (! script) script = "select *"; var sz = _jmolGetAppletSize(size); var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' "; var tHeader, tFooter; if (!codebase) jmolInitialize("."); if (useIEObject || useHtml4Object) { params.name = 'jmolApplet' + nameSuffix; params.archive = archivePath; params.mayscript = 'true'; params.codebase = codebase; } if (useIEObject) { // use MSFT IE6 object tag with .cab file reference winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : ""); params.code = 'JmolApplet'; tHeader = "\n"; tFooter = ""; } else if (useHtml4Object) { // use HTML4 object tag tHeader = "\n"; tFooter = ""; } else { // use applet tag tHeader = "\n"; tFooter = ""; } var visitJava; if (isIEWin || useHtml4Object) { var szX = "width:" + sz[0] if ( szX.indexOf("%")==-1 ) szX+="px" var szY = "height:" + sz[1] if ( szY.indexOf("%")==-1 ) szY+="px" visitJava = "

\n" + noJavaMsg + "

"; } else { visitJava = "" + "
\n" + noJavaMsg2 + "
"; } params.loadInline = (inlineModel ? inlineModel : ""); params.script = (script ? _jmolSterilizeScript(script) : ""); var t = tHeader + _jmolParams() + visitJava + tFooter; jmolSetTarget(nameSuffix); ready["jmolApplet" + nameSuffix] = false; if (_jmol.debugAlert) alert(t); return _jmolDocumentWrite(t); } } function _jmolParams() { var t = ""; for (i in _jmol.params) if(_jmol.params[i]!="") t+=" \n"; return t } function _jmolInitCheck() { if (_jmol.initChecked) return; _jmol.initChecked = true; jmolInitialize(defaultdir, defaultjar) } function _jmolCheckBrowser() { with (_jmol) { if (browserChecked) return; browserChecked = true; if (isFullyCompliant) return true; if (checkBrowserAction == "redirect") location.href = checkBrowserUrlOrMessage; else if (checkBrowserAction == "popup") _jmolPopup(checkBrowserUrlOrMessage); else { var msg = checkBrowserUrlOrMessage; if (msg == null) msg = "Your web browser is not fully compatible with Jmol\n\n" + "browser: " + browser + " version: " + browserVersion + " os: " + os + "\n\n" + ua; alert(msg); } } return false; } function _jmolDocumentWrite(text) { if (_jmol.currentDocument) _jmol.currentDocument.write(text); return text; } function _jmolPopup(url) { var popup = window.open(url, "JmolPopup", "left=150,top=150,height=400,width=600," + "directories=yes,location=yes,menubar=yes," + "toolbar=yes," + "resizable=yes,scrollbars=yes,status=yes"); if (popup.focus) poup.focus(); } function _jmolReadyCallback(name) { if (_jmol.debugAlert) alert(name + " is ready"); _jmol.ready["" + name] = true; } function _jmolSterilizeScript(script) { var inlineScript = script.replace(/'/g, "'"); if (_jmol.debugAlert) alert("script:\n" + inlineScript); return inlineScript; } function _jmolSterilizeInline(model) { var inlineModel = model.replace(/\r|\n|\r\n/g, "|").replace(/'/g, "'"); if (_jmol.debugAlert) alert("inline model:\n" + inlineModel); return inlineModel; } /* AngelH, mar2007: By (re)setting this variable in the webpage before calling jmolApplet(), limits for applet size can be overriden. */ /* hansonr, jun2007: 2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html) */ if (allowedJmolSize==undefined) var allowedJmolSize = [1, 2048, 300] // min, max, default (pixels) function _jmolGetAppletSize(size) { /* AngelH, mar2007 Accepts single number or 2-value array, each one can be either: percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.) Size is now returned as string or number, no "px". */ var width, height; if ( (typeof size) == "object" && size != null ) { width = size[0]; height = size[1]; } else { width = height = size; } // if percent, leave it as it is: if ( width.toString().charAt(width.toString().length-1) != "%" ) { width = parseFloat(width); // convert to nr., or strip text, or make zero if ( width <= 1 && width > 0 ) { width = (width*100)+"%" } // decimal: convert to percent and quit else if ( width >= allowedJmolSize[0] && width <= allowedJmolSize[1] ) { width = parseInt(width) } // accept only that range (pixels) else { width = allowedJmolSize[2] } // default size 300 pixels } if ( height.toString().charAt(height.toString().length-1) != "%" ) { height = parseFloat(height); if ( height <= 1 && height > 0 ) { height = (height*100)+"%" } else if ( height >= allowedJmolSize[0] && height <= allowedJmolSize[1] ) { height = parseInt(height) } else { height = allowedJmolSize[2] } } return [width, height]; } function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) { ++_jmol.radioCount; if (groupName == undefined || groupName == null) groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1); if (!script) return ""; if (labelHtml == undefined || labelHtml == null) labelHtml = script.substring(0, 32); if (! separatorHtml) separatorHtml = ""; var scriptIndex = _jmolAddScript(script); var eos