http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.02.10.zip
On Mon, Feb 10, 2014 at 2:27 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> http://chemapps.stolaf.edu/jmol/*zip/*jmol-14.1.8_2014.02.10.zip
>
>
> On Mon, Feb 10, 2014 at 12:17 PM, Robert Hanson <hans...@stolaf.edu>wrote:
>
>> Continuing with fixes headed toward Jmol 14.0.8 release Friday.
>> Testing appreciated. Same version number here, just a different date.
>>
>> http:/chemapps.stolaf.edu/jmol/jmol-14.1.8_2014.02.10.zip
>>
>> ___JmolVersion="14.1.8"
>>
>> new feature: JSmol Info.z, Info.zIndexBase
>> bug fix: tensor("efg", "value") should return sparce array, not dense for
>> missing tensors
>> bug fix: JSmol now allows writing POVRAY, MAYA, IDTF, VRML, etc.
>> both from Java and from HTML5
>> code: reworking of export classes
>> bug fix: label @{math expression...} not working
>> bug fix: interpretation of x and @x in select commands and {...} phrases
>> -- Variable substitution has been unintuitive and inconsistent.
>> For instance:
>>
>> x = "C or T"
>>
>> select @x -- works fine
>> print {@x} -- fails
>>
>> The problem is the use of @ to reference the variable NAMED BY
>> another
>> variable within a math expression (print context) but not a select
>> context.
>> For instance:
>>
>> y = 3
>> x = "y"
>> print x --> "y"
>> print @x --> 3
>>
>> Such referencing is important for math expressions, but the
>> extension of this to atom expressions is not necessary and
>> not generally useful.
>> -- The current situation is as follows:
>>
>> x = "A or T"
>> select @x --> all A and T groups
>> print {@x} --> nothing (because @x is "the contents of the
>> variable 'A or T'")
>>
>> -- This fix simplifies the situation by not allowing variable-variable
>> referencing within atom expressions bounded by braces, just like
>> within implicit atom expression commands (select, display, hide,
>> delete, etc.).
>> -- The result is much more consistent. The following do exactly what
>> you think they would do:
>>
>> x = "A or T"
>> select @x
>> print {@x}
>>
>> -- The current way of doing this, by defining a temporary atom
>> expression using the DEFINE (or @) command still works:
>>
>> x = "A or T"
>> @y @x
>> select y same as select @x
>>
>> -- Note that the difference between "select x" and "select @x"
>> may be significant:
>>
>> ala = "cys"
>>
>> select ala --> selects all alanines
>> select @ala --> selects all cysteines
>>
>>
>>
>> code: way more efficient for loop -- loop overhead decreased by > 80%
>> bug fix: for(i in ...) does not exit when i is assigned a value, as per
>> documentation
>> bug fix: for(x in ...) command broken and also quite inefficient.
>>
>>
>> JmolVersion="14.1.8_dev_2014.02.06"
>>
>> new feature: set cartoonRibose
>> -- draws in ribose rings, with facets showing puckering
>> -- connects via C4'-C5'-O5'-P explicitly
>> -- shows C3'-O3' for reference.
>> -- disables cartoonBaseEdges (Leontis-Westhof Edges)
>> -- disabled by SET cartoonBaseEdges ON
>> -- suggested by Rick Spinney, Ohio State
>>
>> new feature: anim frame [a,b,c,d] works with negative numbers to indicate
>> ranges:
>> -- anim frame [1, -5, 10, -6] --> [1,2,3,4,5,10,9,8,7,6]
>> -- read as "1 through 5 and then 10 through 6"
>>
>> new feature: Tinker file reader (and FoldingXYZ reader upgrade)
>> -- Can use Tinker:: but this is only required if first line is JUST an
>> atomCount
>> -- accommodates older Tinker format with n-1 atoms for atomCount
>> -- allows for trajectories and desired model number
>>
>> new feature: (actually 13.1 but undocumented) animation frame [ 51 50 49
>> 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)....]
>>
>> new feature: x = compare({atomset1}, {atomset2}, "MAP")
>> new feature: x = compare({atomset1}, {atomset2}, "MAP", "all")
>> new feature: x = compare({atomset1}, {atomset2}, "MAP", "best")
>> new feature: x = compare({atomset1}, {atomset2}, "MAP", "H")
>> new feature: x = compare({atomset1}, {atomset2}, "MAP", "allH")
>> new feature: x = compare({atomset1}, {atomset2}, "MAP", "bestH")
>> -- generates one or more correlations lists based on non-aromatic SMILES
>> -- optionally includes H atoms
>> -- optionally generates all possible atom mappings
>> -- returns int[][] = [ [a1 b1],[a2 b2],[a3 b3],... ]
>> where an and bn are integer atom indices
>> or list<int[][]> when "all" option is chosen.
>> -- the following will generate one atom correlation
>> map for two structures including hydrogen atoms:
>> load files "a.mol" "b.mol"
>> x = compare({1.1} {2.1} "MAP" "H")
>> (useful for 2D/3D model atom matching)
>> -- the following compares the model of caffeine from NCI to that from
>> PubChem:
>> load $caffeine;load append :caffeine;frame *
>> select 2.1; label %[atomIndex]
>> compare {1.1} {2.1} SMILES rotate translate
>> x = compare({1.1}, {2.1}, "MAP" "bestH")
>> for (a in x) {a1 = a[1];a2=a[2];select atomindex=a1;label @a2}
>>
>> new feature: compare {model1} {model2} SMILES
>> -- no need to give SMILES; Jmol can generate it from {model1}
>>
>> new feature: x = {*}.find("SMILES", "H")
>> -- generates SMILES with explicit H atoms
>>
>> bug fix: substructure() function using SMILES instead of SMARTS, so only
>> full structures;
>> bug fix: better error trapping and messages in SMILES-related methods
>> bug fix: make webexport discovery of path to Jmol.jar and jsmol.zip more
>> robust.
>> bug fix: getProperty extractModel not honoring subset
>> bug fix: set pdbGetHeader TRUE does not capture REMARK3 REMARK290
>> REMARK350
>> bug fix: getProperty("JSON",....) should wrap value in {value:...}
>> bug fix: MO persistent translucency broken in 11.x
>> bug fix: show MENU write MENU load MENU all broken in 12.2
>> bug fix: {*}[n] should be empty if nAtoms <=n
>> bug fix: abinit reader was nonfunctional
>> bug fix: assign atom into into PDB file loses atom names
>> bug fix: y = ([3])[1][1] should be [3] not 3
>> bug fix: break n nonfunctional
>> bug fix: format() and label() functions limited to 4 arguments; should be
>> unlimited
>> bug fix: errors in paths to js code in web export templates.
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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