12.1.31-12.1.33:
# feature change: undocumented a[13] = 3 (where a is a matrix, for a[1][3])
removed
# new feature: MOL reader reads > <PUBCHEM_MMFF94_PARTIAL_CHARGES>
# new feature: load FILTER "*.CA,/=5"
# -- every 5th alpha carbon
# -- note comma before /=
# new feature: write xxxx.OBJ
# -- Wavefront OBJ files
# -- export/_ObjExporter written by Ken Evans
# new feature: write xxxx.XYZRN
# -- input for MSMS
# -- suggest first using set DEFAULTVDW BABEL
# new feature: multidimensional array assignment: a[1][2] = 10
# -- allows setting of a specific element of a multidimensional array
# -- value can be anything -- a number, an array, an hashtable, a bitset,
etc.
# -- allowed also for matrices, but if the value is not a number, or
# the row/column pointers are outside the range 1-3 or 1-4, then
# the matrix is turned into an array automatically
# -- for an array, when not a direct assignment, you need parentheses:
# x = (a[1])[2]; if ((a[1])[2] == 3)....
# because in general a[1][2] means "array a, elements 1 through 2"
# -- for a matrix, you can use a[1][2] anywhere -- this is a difference
between matrices and arrays
# new feature: y == x[3] (double "=" in context of assignment) (removed in
12.1.32)
# -- y is now an alias for x[3], not a copy
# -- allows, for example:
# y = x[3]; y[2] = 6;
# equivalent to (x[3])[2] = 6 (which is not a valid syntax)
# new feature: x.sort(n)
# -- array sorting by nth object 1 - arrayLength; 0 == last, -1 = next to
last, etc.
# new feature: load 1blu.pdb filter "*.CA | HETATM,![HOH]"
# - "|" means "OR", so this reads:
# load only alpha carbons OR (HETATM and not HOH)
# new feature: write xxx.OBJ -- WaveFront OBJ file writing (still working on
this)
# new feature: isosurface MRC keyword indicates file is MRC type (for
nonstandard MRC files)
# new feature: simple embedded application version of evalStringWaitStatus
# that returns output from print/message/echo commands
# -- see TestScriptOutput:
#
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/examples/basic/org/jmol/TestScriptOutput.java?content-type=text%2Fplain
# new feature: preliminary NWChem orbital reading
# -- still not normalized correctly
# -- d and f orbitals not checked
# -- UHF alpha/beta not checked
# new feature: <array1> | x
# -- IN PLACE concatenation
# -- array1 will be appended to
# -- if x is an array of length n, then n elements will be added
# -- works as a |= b
# -- to append a full array as one element, use a |= [x]
# -- to append with creating a NEW array, use a + x or a + [x] instead
# new feature: "unset" command same as "reset"
# -- for example:
# a = array([1,2,3],[4,5,6],[7,8,9])
# y = a[3]
# unset a
# show variables
# y = [7,8,9];
# -- just looks better for variables
# -- good to use this if just a small part of a large array
# or hashtable is wanted and the rest can be discarded
# new feature: sort/reverse does array sorting IN PLACE, not by copying
# -- for example:
# y = x.sort
# x is sorted, and y is a copy of that
# -- still need x = x.sort in general, because "x.sort" is not a command
# new feature: array assignment is always by reference, as for JavaScript
and Java
# -- y = x[3], if x[3] = [3, 4, 5], assigns y to [3, 4, 5], so if later
# one uses y[4] = "new", then at that point x[3] = [3, 4, 5, "new"]
# -- y == x[3] distinction removed
# new feature: x = intersection(plane, plane)
# new feature: x = intersection(pt, plane) (i.e. line perp to plane through
pt)
# new feature: x = intersection(ptLine, vLine, plane)
# new feature: x = intersection(ptLine, vLine, point) (i.e. plane perp to
line through point -- projection of point onto line)
# new feature: x = plane(<point>, <vector>, true)
# new feature: draw polygon @x @y where @x and @y are arrays of points and
faces, respectively
# bug fix: CIF reader not reading files with multiple models involving
GEOM_BOND
# bug fix: scriptLevelMax 20 too small -- changed to 100
# bug fix: for/while local variables improperly localized in iterative
functions
# bug fix: a = {} initialized as bitset, not associative array
# bug fix: <bitset> | <integer> should set bit <integer>
# bug fix: <bitset> | <array> should set bits indicated in <array>
# bug fix: <bitset> & <integer> should return true if bit <integer> is set
# bug fix: <bitset> % n when n < 0 should do "last n + 1"
# bug fix: <array> | [a,b,c] should append elements to array -- IN PLACE
# bug fix: animation incompatible with spin for largish structures
# bug fix: _modelFile variable incorrect for file read from zip file
# bug fix: If a script such as "test.spt" creates a function
# test(), then the next implicit script command "test.spt" will
fail
# bug fix: implicit script command XXXX.xxx loses case of filename
# bug fix: array appending appends string values
# bug fix: frame 0.0 does NOT enable all frames; breaks "quaternion" command
# bug fix: isosurface fragment fix
# bug fix: cartesian exporter capping cylinders flat and spherical both
# bug fix: Jmol logo was missing from the Help>What's New window.
# bug fix (improvement): the Help>User Guide window was too narrow.
# bug fix: echo @x when x is an associative array
# bug fix: write t.jvxl does not work for new solvent/molecular surfaces
business
# bug fix: Jmol 11.9.24+ will read states created by prior versions
incorrectly
# -- fixed by adding "legacyAutoBonding" setting
# bug fix: loading a file on command line does not allow
# for write xxxx.jmol to include model file in zip file
# bug fix: fails: load 1mbo.cif; isosurface select(not solvent)
ignore(none) sasurface;
# bug fix: passing an array to a function does not correctly pass by
reference
# bug fix: dot function included in array x = [(whatever).something...]
fails
# bug fix: array sorting for objects
# bug fix: creating arrays from variables does not copy variable value
# bug fix: draw .... @s does not work for title, but @{s} does
# bug fix: ZAP should not set appendNew TRUE
# bug fix: load APPEND after ZAP inserts ZAP into state after load command
# bug fix: write MOL writes incorrect charge
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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