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File jmol.changes of Package jmol
------------------------------------------------------------------- Sat Dec 23 13:29:22 UTC 2023 - Jan Engelhardt <jengelh@inai.de> - Update to release 16.1.47 * New feature: `LOAD .... fill unitcell rhombohedral`, `LOAD .... fill unitcell trigonal` and `LOAD ... fill unitcell "2a,a-b,..."` ------------------------------------------------------------------- Sun Nov 12 23:16:57 UTC 2023 - Jan Engelhardt <jengelh@inai.de> - Update to release 16.1.45 * New feature: UNITCELL RHOMBOHEDRAL and UNITCELL TRIGONAL ------------------------------------------------------------------- Sun Jun 25 10:07:01 UTC 2023 - Jan Engelhardt <jengelh@inai.de> - Update to release 16.1.13 * added a JME 2-D editor tool ------------------------------------------------------------------- Mon Aug 29 07:27:51 UTC 2022 - Jan Engelhardt <jengelh@inai.de> - Update to release 14.32.73 * XSF surface files with over about 267 atoms were not recognizing presence of surface data ------------------------------------------------------------------- Mon May 16 20:48:46 UTC 2022 - Jan Engelhardt <jengelh@inai.de> - Update to release 14.32.55 * feature change: axes POSITION [x y] "xyz" with symmetry * new feature: axes POSITION [x y] "xyzabc" * new feature: global user variable dragDropFileType * bugfix: deleting atoms from PDB failed * bugfix: ModelKit dragAtom did not update measurements ------------------------------------------------------------------- Mon Feb 8 22:01:23 UTC 2021 - Jan Engelhardt <jengelh@inai.de> - update build recipes/scripts to use https [boo#1181924] - Redownload Source2 because it was some HTML content rather than a PNG file ------------------------------------------------------------------- Thu Dec 24 12:19:31 UTC 2020 - Jan Engelhardt <jengelh@inai.de> - Update to release 14.31.20 * Topology CIF reading of _topol_xxx records * GenNBOReader supports older NBO 3.0 output.properties rather than missing .46 labels file * NBO command expanded to allow named orbitals ------------------------------------------------------------------- Thu Dec 19 22:25:59 UTC 2019 - Jan Engelhardt <jengelh@inai.de> - Update to release 14.30.1 * new feature: (undocumented) set picking dragMolecule * new feature: set picking dragModel ------------------------------------------------------------------- Sat Oct 20 11:57:45 UTC 2018 - Jan Engelhardt <jengelh@inai.de> - Update to new upstream release 14.29.26 * Fixed: Magnetic CIF reader did not handle symmetry operations with n/16. * Fixed: 3-membered aziridine with non-H substituent should be chiral. ------------------------------------------------------------------- Fri Jan 19 23:24:04 UTC 2018 - jengelh@inai.de - Drop bundled jsmol and jspecview from package. ------------------------------------------------------------------- Mon Dec 25 23:52:45 UTC 2017 - jengelh@inai.de - Update to new upstream release 14.27.2 * new feature: frame MO - goes to first frame with a molecular orbital * new feature: functions write("zip") and write("jmol") - Remove fsf-address.patch ------------------------------------------------------------------- Sat Jul 16 09:44:49 UTC 2016 - thod_@gmx.de - update to version 14.6.1 some bug fixes ------------------------------------------------------------------- Sat May 28 16:18:55 UTC 2016 - thod_@gmx.de - Add manual - Split desktop file - update to version 14.6.0 selected new feature: * CONNECT {pair1} {pair2} ATROPISOMER * C13 NMR prediction from http://www.nmrdb.org/service/jsmol13c?smiles=CCCC * Jmol SMILES bond atropisomerism ^nm- and ^^nm- * SMILES/nonaromatic same as SMILES/noaromatic * adds SHOW SMILES/bio and {*}.find("SMILES/bio") options: * print {*}.find("SMILES/hydrogen/") adds hydrogen atoms * Jmol now implements a way of indicating atropisomer chirality. * full implementation of OpenSMILES and OpenSMARTS in Jmol * Polyhedra command allows for min and max radius * draw POINTGROUP SPACEGROUP * draw SPACEGROUP * print pointgroup("spacegroup", @1) * show spacegroup/xxxxx * show symop 3 @3 "atom" * show/draw symop @1 @2 * show/draw symop @1 @2 n * symop() options * symop(3,@3,"atom") * getProperty("shapeInfo.echo") * preliminary MMTF reader * set window width height * set window "xxx.png" * setting DSSR on the fly * show chemical xxx where xxx is a file type and many bug fixes ------------------------------------------------------------------- Sun Mar 13 10:24:28 UTC 2016 - jengelh@inai.de - Update to new upstream release 14.5.0 * bug fix: restoring bonds to a model having fewer bonds than the model for which they were saved throws an exception * bug fix for "WRITE xxx.ZIP" command crashing Jmol ------------------------------------------------------------------- Fri Mar 27 16:11:42 UTC 2015 - jengelh@inai.de - Update to new upstream release 14.3.13 * No overview was provided ------------------------------------------------------------------- Mon Feb 2 22:42:50 UTC 2015 - jengelh@inai.de - Update to new upstream release 14.3.12 * No overview was provided ------------------------------------------------------------------- Thu Jul 17 14:56:33 UTC 2014 - jengelh@inai.de - update to version 14.2.2 * New features: * readers with unit cells may load as trajectories * protein sidechain minimization * Bug fixes: * CASTEP reader broken for multiple cells and geometry optimization * set pdbAddHydrogens fails for structures with ANISOU records * select x < 0.3 reports error when checking, though it does run when executed * SMILES for model with nonbonded atoms fails * WebPanel error trapping problem; too long file name for tar file ------------------------------------------------------------------- Wed Jun 11 14:21:37 UTC 2014 - jengelh@inai.de - Update to new upstream release 14.0.17 * New feature functions: * "like" operator, strings only * (actually 13.1 but undocumented) animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....] * (application only) -a --autoAnimationDelay * {atomset}.modulation(type, t) * {xxx}.distance.all({yyy}) returns float[][] of values * {xxx}.getProperty("yyy") * added simpler associative array notation: [key:value,...] * altloc set for msCIF _atom_site_subsystem_code * anim frame [a,b,c,d] works with negative numbers to indicate ranges: * array.join() * array.keys.all * array.pop(), array.push() * associative array alternative ".." syntax * associative array standard "dot" notation * asynchronous resumable processes * atomSet1.distance.max(atomSet2, TRUE) * atomSet1.distance.max(point, TRUE) * atomSet1.distance.min(atomSet2, TRUE) * atomSet1.distance.min(point, TRUE) * Bilbao Crystallographic Server file reader * BilbaoReader NONORM option -- reads displacements as actual values, not normalized * binary associative arrays * byteArray type * calculate hbonds structure * calculate structure dssr * caption "xxxxx" x.x -- number of seconds to run * catchable THROW * color(color1, color2, n, asHSL) * compare {model1} {model2} SMILES * construction/manipulation/saving of ZIP files * delete $SAVED savedName * dipole ID m1 ALL {...} * DSSR output reading * escape pressed cancels pending measurement * expanded unit cell ijk notation * filter "ATOM" opposite of filter "HETATM" * filter "MODCELL=x" * Gaussian fchk file reader * getProperty variableInfo <expression> * getProperty("JSON", ....) * getProperty(x, SQL_query) * JANA2006 reader adds M40 molecular group support * JavaScript: JSmol api Jmol.evaluateVar(applet, expression) * JSmol Info.z, Info.zIndexBase * JSmol: allow for a user callback for customization of menu * JSpecView and Jmol read ACD/Labs assigned spectra block JDX files. * JSpecView getSolutionColor fill/all/none/false * JSpecView PEAK command -- adds PEAK GC/MS "#1" * JSpecView readers for ACD/Labs annotated MS, IR, Raman, and UV/VIS * LIKE operator extended to atom expressions * load ":inchikey:xxxxx" * load "cell=parent" or "cell=standard" * load "filename" packed x.x * load ... filter "symop=..." * load =1msy/dssr * load ASYNC .... * load files "xxx" + "yyy" * load ORIENTATION or load DATA "...orientation..." ... * load xxxx filter "CELL=va,vb,vc;oa,ob,oc" * mCIF (magnetic CIF) file reader * menu item color--atoms--by scheme--vectors * modulation 0.2 // sets t-value * modulation adjustable by q and t, up to d=3 * modulation scale x.x * Mol3D reader * moveTo AXIS [a,b,c,x,y,z] * MSCIF reader now allowing up to d=10; was d=6 * pickedList -- ordered array of recently picked atoms * pt1.mul3(pt2) * replace() * replace(x, y, TRUE) * reset PRINT * restore UNITCELL * RESUME with arguments is synonymous with RESTORE * rich SQL logic in GETPROPERTY, getProperty(), and within(dssr,"xxxx.yyy..."): * save CONTEXT contextName * script ASYNC .... * select leadAtom(s) * select ON ; select OFF * select ON/OFF atom-set * select within(dssr,"subset") * select x = [array or array variable] * select xyz > 1.0 * set backboneSteps TRUE * set bondingVersion * set cartoonRibose * set echo depth x.x for standard echos * set showUnitCellDetails TRUE (default) * set showUnitCellInfo TRUE (default) * set starWidth * set vectorsCentered * show CHEMICAL STDINCHI * show CHEMICAL STDINCHIKEY * show SAVED * show symop @1 @2 "fmatrix" * show symop n "fmatrix" * show(xxx) function * THROW command * Tinker file reader (and FoldingXYZ reader upgrade) * unit cell display includes k (mCIF) and q (CIF, Jana2006) vectors * unitcell "abc_offset" * unitcell "type" * unitcell [ {origin} {a} {b} {c} ] * unitcell {555 575 0} * unitcell {atomset} * unitcell BOUNDBOX * unitcell OFFSET and RANGE * unitcell RESET (or RESTORE) * V3000 reading of DATA SGROUP records: * WRITE "filename" AS type * write VAR x "filename" * x = {*}.find("chemical",type) * x = {*}.find("SMILES", "H") * x = compare({atomset1}, {atomset2}, "MAP") * x = compare({atomset1}, {atomset2}, "MAP", "all") * x = compare({atomset1}, {atomset2}, "MAP", "allH") * x = compare({atomset1}, {atomset2}, "MAP", "best") * x = compare({atomset1}, {atomset2}, "MAP", "bestH") * x = compare({atomset1}, {atomset2}, "MAP", "H") * x = format("array", data) * x = format("base64", data) * x = format("byteArray", data) * x = format("JSON", data) * x = load("myfile",true) * x = smilesString.find("chemical",type) * x = write("PNGJ") * x.pop("key") for an associative array * x.push(key,value) for associative array * x.bondingRadius added as more appropriate alias for x.ionic * x.covalentRadius added as more appropriate alias for x.covalent * var x,y,z; ------------------------------------------------------------------- Mon Apr 28 22:22:31 UTC 2014 - jengelh@inai.de - Initial package (version 14.0.13) for build.opensuse.org
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