major new capabilities include:
Using SMARTS and a new .find() option to select and create polyhedra based
on ring size criteria.
An extension of the MOL file format to allow 4-, 5-, and 6-order bonds
along with the capability to render those high-order bonds.
see
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.10/Jmol%2014.10.0/
https://sourceforge.net/projects/jmol/files/latest/download?source=files
Jmol.___JmolVersion="14.10.0" // released 3/25/2017
new feature: x = {*}.find(smartsString,"map")
-- returns an array of arrays of atom indices (0-based)
-- indicates exact correlation between atoms in {*} and atoms of
smartsString
-- only unique sets of atoms are found, not every possibility
-- for example:
load $caffeine
print {*}.find("*1*****1", "map").format("JSON")
[ [ 0,2,4,6,11,12 ] ]
new feature: SELECT @x where x is an array of integers or array of array
of integers
-- selects atoms from array rather than from a bitset
-- note that variable must be used, as SELECT [1,2,3] would look for PDB
group "1,2,3"
-- for example:
load $caffeine
x = {*}.find("*1*****1", "map")[0]
select @x
6 atoms selected
new feature: DRAW polygon @face @points
-- draws a filled polygon based on arrays of atom indices
-- @face is an array of integers, not necessarily wound correctly
-- @points is an atom bitset or an array of points (optional, defaults to
{*}
-- for example:
load $p4
x = {*}.find("*1**1","map");
draw ID p4r polygon @{x[1]} color red
draw ID p4b polygon @{x[2]} color blue
draw ID p4y polygon @{x[3]} color yellow
draw ID p4g polygon @{x[4]} color green
new feature: DRAW polyhedron @faces @points
-- draws sets of polygons based on arrays of atom indices
-- @faces is an array of array of integers, not necessarily wound correctly
-- @points is an atom bitset or an array of points (optional, defaults to
{*}
-- for example:
load $caffeine
draw polyhedron @{{*}.find("*1****1||*1*****1","map")}
load $p4
draw ID p polyhedron @{{*}.find("*1**1","map")} color red
new feature: POLYHEDRON ID xxx @faces @points
-- @faces is an array of array of integers, not necessarily wound correctly
-- @points is an atom bitset or an array of points (optional, defaults to
{*}
load $p4
polyhedra ID p4 @{{*}.find("*1**1","map")}
new feature: 4-order bond in MOL file using 14 for bond order
-- Jmol extension for MOL file format to allow 4-bond
-- example: [Re2Cl8](2-)
-- see https://en.wikipedia.org/wiki/Quadruple_bond
new feature: 5-order bond in MOL file using 15 for bond order
-- Jmol extension for MOL file format to allow 5-bond
-- example: [Mo2Cl8](4-)
-- see https://en.wikipedia.org/wiki/Quintuple_bond
new feature: 6-order bond in MOL file using 16 for bond order
-- Jmol extension for MOL file format to allow 6-bond
-- example: Mo2
-- see https://en.wikipedia.org/wiki/Sextuple_bond
new feature: load "=xxxx/dssr--xxx=yyy"
-- allows adding specialized options to dssr
-- --xxx=yyy added on to &opt= search item
bug fix: DSSR fix for multi-model PDB file
bug fix: DSSR - 4fe5 HPA ligand causes set backboneSteps true to fail
bug fix: EXIT command with -n command line flag does not exit Jmol
bug fix: echo renderer may not show correct font size
bug fix: POLYHEDRA ID id OFFSET {x y z} broken
bug fix: ScriptManager debug output being sent even if -i (silent) command
line option set.
Bob
--
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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