Revision: 20798
http://sourceforge.net/p/jmol/code/20798
Author: hansonr
Date: 2015-09-28 11:34:14 +0000 (Mon, 28 Sep 2015)
Log Message:
-----------
lost getProperty("atomInfo")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-28 10:02:39 UTC
(rev 20797)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-28 11:34:14 UTC
(rev 20798)
@@ -150,50 +150,39 @@
2.8496666
-So...
-
JmolSQL
-
There are three parts to JmolSQL, object, keys, and an optional WHERE or
WHERIN phrase:
object.SELECT("keys WHERE/WHEREIN phrase")
-
-The object can be either an associative array [key1:value1, key2:value2,
key3:value3]
+The object can be either an associative array [key1:value1, key2:value2,
key3:value3]
or an array of associative arrays, usually with the same set of keys.
Associative Arrays
-
-When the top-level array is an associative array, select() can be used to
select
+When the top-level array is an associative array, select() can be used to
select
out subsets of the array, either as a single associative array or as an array
of values.
-abc.select("A,B")
-
-returns a subset of abc. Wild cards can be interspersed with additional keys,
+abc.select("...")
+returns a subset of abc. Wild cards can be interspersed with additional keys,
for example, "a*,b" or "*_id". In each such case, the case-sensitive LIKE
operation is used to match keys.
abc = [ A:[b:1],B:[b:2],AA:[b:3, d:50] ]
print abc.select("A").format("JSON")
{ "A": { "b": 1 } }
-
abc = [ A:[b:1],B:[b:2],AA:[b:3, d:50] ]
print abc.select("A*").format("JSON")
{ "A": { "b": 1 },"AA": { "b": 3,"d": 50 } }
-
abc.select("(...)")
-
Using parentheses around the list of keys delivers a list of values of b for
only the the subset of xyz for which a=1:
abc = [ A:[b:1],B:[b:2],AA:[b:3, d:50] ]
print abc.select("(A,B)").format("JSON")
[ { "b": 2 },{ "b": 1 } ]
-
Arrays of Associative Arrays
-
-Generally we assume here that the elements of the array are associative
arrays, all with the
-same set of keys. This is the essence of a database. Whether or not the
associative
+Generally we assume here that the elements of the array are associative
arrays, all with the
+same set of keys. This is the essence of a database. Whether or not the
associative
arrays have the same keys is not important for Jmol, but is typical for a
database.
For example:
@@ -201,82 +190,77 @@
xyz = [ [a:1,b:11],[a:2,b:22],[a:3,b:33] ]
-xyz.select("b")
-
+xyz.select("...")
Creates the sublist of associative arrays having the selected subset of keys:
xyz = [ [a:1,b:11],[a:2,b:22],[a:3,b:33] ]
print xyz.select("b").format("JSON")
[ { "b": 11 },{ "b": 22 },{ "b": 33 } ]
-
xyz.select("(...)")
-
Creates a list of only the b values of each of x, y, and z, in order:
xyz = [ [a:1,b:11],[a:2,b:22],[a:3,b:33] ]
print xyz.select("(b)").format("JSON")
[ 11,22,33 ]
-
xyz = [ [a:1,b:11],[a:2,b:22],[a:3,b:33] ]
print xyz.select("(a,b)").format("JSON")
[ 11,1,22,2,33,3 ]
-
-The assumption when using (keys) is that you want to know all these values,
-but you don't care what order they are in (because that will not be
predictable)
-and you don't care about their exact context. An example is a list of bonds
for
-which we just want to know all the atoms involved, but the atoms are listed
+The assumption when using (keys) is that you want to know all these values,
+but you don't care what order they are in (because that will not be
predictable)
+and you don't care about their exact context. An example is a list of bonds for
+which we just want to know all the atoms involved, but the atoms are listed
under "atom1" and "atom2" in each bond array.
load =1ehz/dssr
select on @{_M.dssr.hbonds.select("(atom1_id,atom2_id)")}
206 atoms selected
-
Using WHERE
-
WHERE is used to select a subset of the elements of an array based on specific
key-value relationships.
xyz.select("... WHERE ...")
+Delivers all key/value pairs in the subset of xyz element associative arrays
+for which the WHERE clause is true for that element.
-Delivers all key/value pairs in the subset of xyz element associative arrays
-for which the WHERE clause is true for that element.
-
xyz = [ [a:1,b:11],[a:2,b:22],[a:3,b:33] ]
print xyz.select("* where a<3 and b<20").format("JSON")
[ { "b": 11,"a": 1 } ]
-
xyz.select("(...) where ...")
-
-Using parentheses around the list of keys delivers a list of
+Using parentheses around the list of keys delivers a list of
values of for only the the subset of xyz for which the WHERE clause is true:
xyz = [ [a:1,b:11],[a:2,b:22],[a:3,b:33] ]
print xyz.select("(b) where a>1").format("JSON")
[ 22,33 ]
-
-Note that "... where..." will "drill down" through arrays of arrays to find
the
+Note that "... where..." will "drill down" through arrays of arrays to find the
targeted associative array elements, producing a flat array of those objects:
xyz = [ [[a:1,b:11], [a:0,b:0]],[[[a:2,b:22]]],[[a:3,b:33,aa:44]] ]
print xyz.select("a* where a>0").format("JSON")
[ { "a": 1 },{ "a": 2 },{ "a": 3,"aa": 44 } ]
-
xyz = [ [[a:1,b:11], [a:0,b:0]],[[[a:2,b:22]]],[[a:3,b:33,aa:44]] ]
print xyz.select("(b) where a>0").format("JSON")
[ 11,22,33 ]
+For example, finding all the hydrogen bonds created by DSSR for a given
residue:
+
+load =1ehz/dssr
+x = _M.dssr.hbonds.select("(distance) where res_long like '*|A|C|72|*'");
+print x.format("JSON")
+print format("%5.3f",x.average)
+
+[ 2.832,2.879,2.838 ] 2.850
WHERE vs. WHEREIN
-
-Starting with Jmol 14.4, JmolSQL includes an additional option, WHEREIN. This
option
-allows selecting specific key/value pairs for which the value is itself an
associative
+Starting with Jmol 14.4, JmolSQL includes an additional option, WHEREIN. This
option
+allows selecting specific key/value pairs for which the value is itself an
associative
array, and *that array* has a specific set of key/value relationships. Thus,
the
clause is checked one level deeper in the structure.
@@ -290,22 +274,41 @@
print abc.select("* WHEREIN type='a'").format("JSON");
{ "key_3": { "i": 3,"type": "a" },"key_1": { "i": 1,"type": "a" } }
-
All of the options that involve WHERE also apply to WHEREIN. For example,
-multiple keys can be specified, and keys can be surrounded by parentheses
-to return just the values:
+multiple keys can be specified, and keys can be surrounded by parentheses
+to return just the values instead of key/value pairs:
abc = [key_1:[type:"a", i:1],key_2:[type:"b", i:2],key_3:[type:"a", i:3]]
print abc.select("(key_1,key2) WHEREIN type='a'").format("JSON");
[ { "i": 1,"type": "a" } ]
-
-In addition, WHEREIN can be applied to arrays as well as associative arrays.
+In addition, WHEREIN can be applied to arrays as well as associative arrays.
In this case, the WHEREIN phrase applies to the elements of that array, which
are assumed to be associative arrays. For example, we can get a list of just
-the orbitals that are of a given symmetry:
+the occupied orbitals produced by Gaussian that are of a given symmetry:
load http://chemapps.stolaf.edu/jmol/jsmol/data/no2_nbo.log.gz 2 filter "alpha"
+print _M.moData.select("mos wherein occupancy>0").select("(symmetry)").pivot
+
+{ "(A1)--O" : 6
+ "(A2)--O" : 1
+ "(B1)--O" : 1
+ "(B2)--O" : 4
+}
+
+Note that this use of WHEREIN with arrays in this way can also be accomplished
+more directly with WHERE:
+
+load http://chemapps.stolaf.edu/jmol/jsmol/data/no2_nbo.log.gz 2 filter "alpha"
+print _M.moData.mos.select("(symmetry) where occupancy>0").pivot
+
+{ "(A1)--O" : 6
+ "(A2)--O" : 1
+ "(B1)--O" : 1
+ "(B2)--O" : 4
+}
+
+load http://chemapps.stolaf.edu/jmol/jsmol/data/no2_nbo.log.gz 2 filter "alpha"
x= _M.moData.select("mos wherein occupancy>0 and symmetry like '(B2)*' ")
print x.select("(index)").format("JSON")
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-09-28 10:02:39 UTC
(rev 20797)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-09-28 11:34:14 UTC
(rev 20798)
@@ -192,8 +192,9 @@
private final static int PROP_CENTER_INFO = 10;
private final static int PROP_ORIENTATION_INFO = 11;
private final static int PROP_TRANSFORM_INFO = 12;
- private final static int PROP_ATOM_INFO = 13;
-
+
+ private final static int PROP_ATOM_INFO = 14;
+
private final static int PROP_BOND_INFO = 15;
private final static int PROP_CHAIN_INFO = 16;
private final static int PROP_POLYMER_INFO = 17;
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