jmol-14.27.2-bp153.1.14 RPM for noarch

From OpenSuSE Leap 15.3 for noarch

Jmol is a Java-based viewer for chemical structures in 3D with
features for chemicals, crystals, materials and biomolecules.

Provides

• jmol
• application()
• application(jmol.desktop)

Requires

• /bin/sh
• java
• rpmlib(CompressedFileNames) <= 3.0.4-1
• rpmlib(FileDigests) <= 4.6.0-1
• rpmlib(PayloadFilesHavePrefix) <= 4.0-1
• rpmlib(PayloadIsXz) <= 5.2-1

License

LGPL-2.1

Changelog

* Fri Jan 19 2018 jengelh@inai.de
  - Drop bundled jsmol and jspecview from package.
* Mon Dec 25 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 2016 thod_@gmx.de
  - update to version 14.6.1
    some bug fixes
* Sat May 28 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 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 2015 jengelh@inai.de
  - Update to new upstream release 14.3.13
    * No overview was provided
* Mon Feb 02 2015 jengelh@inai.de
  - Update to new upstream release 14.3.12
    * No overview was provided
* Thu Jul 17 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 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 2014 jengelh@inai.de
  - Initial package (version 14.0.13) for build.opensuse.org

Files

/usr/bin/jmol
/usr/share/applications/jmol.desktop
/usr/share/doc/packages/jmol
/usr/share/doc/packages/jmol/CHANGES.txt
/usr/share/doc/packages/jmol/COPYRIGHT.txt
/usr/share/doc/packages/jmol/LICENSE.txt
/usr/share/doc/packages/jmol/README.txt
/usr/share/jmol
/usr/share/jmol/Jmol.jar
/usr/share/man/man1/jmol.1.gz
/usr/share/pixmaps/jmol.png

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Fabrice Bellet, Tue Apr 9 14:50:04 2024