File jmol.changes of Package jmol

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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.

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Fri Jan 19 23:24:04 UTC 2018 - jengelh@inai.de

- Drop bundled jsmol and jspecview from package.

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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

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Sat Jul 16 09:44:49 UTC 2016 - thod_@gmx.de

- update to version 14.6.1
  some bug fixes

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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

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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

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Fri Mar 27 16:11:42 UTC 2015 - jengelh@inai.de

- Update to new upstream release 14.3.13
* No overview was provided

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Mon Feb  2 22:42:50 UTC 2015 - jengelh@inai.de

- Update to new upstream release 14.3.12
* No overview was provided

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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

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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;

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Mon Apr 28 22:22:31 UTC 2014 - jengelh@inai.de

- Initial package (version 14.0.13) for build.opensuse.org