jmol-14.0.17

OBS-URL: https://build.opensuse.org/package/show/science/jmol?expand=0&rev=2

Jmol-14.0.13-full.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:4a71aee9708e76b521561db63728dbfcbac92534231666992f11b0c1b5a5cebf
-size 124304216

Jmol-14.0.17_2014.06.10-binary.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d6db27c1b2d1063acd51f3762dcd19358ad63fbf1829f5654360ec57978785bc
+size 55906205

jmol.changes

@@ -1,3 +1,140 @@
+-------------------------------------------------------------------
+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
 

jmol.spec

@@ -17,14 +17,14 @@
 
 
 Name:           jmol
-Version:        14.0.13
+Version:        14.0.17
 Release:        0
 Summary:        3D Viewer for chemical structures
 License:        LGPL-2.1
 Group:          Productivity/Scientific/Chemistry
 Url:            http://jmol.sf.net/
 
-Source:         http://downloads.sf.net/jmol/Jmol-%version-full.tar.gz
+Source:         http://downloads.sf.net/jmol/Jmol-%{version}_2014.06.10-binary.tar.gz
 Source2:        Jmol_icon13.png
 #Source2-Orig:  http://wiki.jmol.org/index.php/File:Jmol_icon13.png
 Patch1:         datadir.diff
@@ -39,7 +39,7 @@ Jmol is a Java-based viewer for chemical structures in 3D with
 features for chemicals, crystals, materials and biomolecules.
 
 %prep
-%setup -q
+%setup -qn %name-%{version}_2014.06.10
 %patch -P 1 -p1
 cp %{S:2} .