Changelog for
jmol-14.9.1-3.1.noarch.rpm :
Sat Jul 16 14:00:00 2016 thod_AATTgmx.de
- update to version 14.6.1
some bug fixes
Sat May 28 14:00:00 2016 thod_AATTgmx.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\", AATT1)
* show spacegroup/xxxxx
* show symop 3 AATT3 \"atom\"
* show/draw symop AATT1 AATT2
* show/draw symop AATT1 AATT2 n
* symop() options
* symop(3,AATT3,\"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 13:00:00 2016 jengelhAATTinai.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 13:00:00 2015 jengelhAATTinai.de
- Update to new upstream release 14.3.13
* No overview was provided
Mon Feb 2 13:00:00 2015 jengelhAATTinai.de
- Update to new upstream release 14.3.12
* No overview was provided
Thu Jul 17 14:00:00 2014 jengelhAATTinai.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 14:00:00 2014 jengelhAATTinai.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
* 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 AATT1 AATT2 \"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 14:00:00 2014 jengelhAATTinai.de
- Initial package (version 14.0.13) for build.opensuse.org
