Revision: 20871
http://sourceforge.net/p/jmol/code/20871
Author: hansonr
Date: 2015-11-30 00:00:28 +0000 (Mon, 30 Nov 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.0_2015.11.29"
new feature: drawing of spheres in 2D window
-- as percent position or absolute, as for ECHO
-- diameter is % if position is %; otherwise is pixels
-- examples
draw d1 diameter 5 [90 90 %] color blue // 5% diameter
draw d2 diameter 15 [90 90] color blue // pixel diameter
draw dO diameter 2 [90 90 %] color @{ {_O}.color }
set echo eO [95 90 %]; echo "O"
-- can be used in the context of an element key:
load $caffeine
function createElementKey() {
var y = 90
for (var e in {*}.element.pivot){
var c = {element=@e}.color
draw ID @{"d_"+ e} diameter 2 [90 @y %] color @c
set echo ID @{"e_" + e} [91 @{y-1} %]
echo @e
font echo 24 bold sansserif
color echo black
y -= 5
}
}
createElementKey
new feature: additional predefined sets for periodic table:
"@nonmetal _H,_He,_C,_N,_O,_F,_Ne,_S,_P,_Cl,_Ar,_Se,_Br,_Kr,_I,_Xe,_At,_Rn",
"@noblegas _He,_Ne,_Ar,_Kr,_Xe,_Rn",
"@metal !nonmetal",
"@alkaliMetal _Li,_Na,_K,_Rb,_Cs,_Fr",
"@alkalineEarth _Be,_Mg,_Ca,_Sr,_Ba,_Ra",
"@semimetal _B,_Si,_Ge,_As,_Sb,_Te,_Po",
"@transitionMetal
elemno>=21&elemno<=30|elemno>=39&elemno<=48|elemno>=72&elemno<=80|elemno>=104&elemno<=112",
"@lanthanide elemno>=57&elemno<=71",
"@actinide elemno>=89&elemno<=103",
new feature: load =am/<mineralName> loads last (earliest?) entry in American
Mineralogist Crystal Database
-- for example, load =am/corundum
-- reads mineral page such as
http://rruff.geo.arizona.edu/AMS/minerals/Corundum
and extracts from that the last database ID.
-- adding .1, .2, ..., or .0 will return only the first, second, ..., or last
structure on that page
-- requires a preliminary search followed by the actual file load.
-- only the final ID-based file load is saved in the state.
-- a hack; uses an evaluation of the string:
'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[(%n
== 0 ? 0 : %n + 1)].split(\"'\")[1]+'_cif.txt'
-- for example, see http://rruff.geo.arizona.edu/AMS/viewJmol.php?id=19280
bug fix: files with names containing "[]" cannot be loaded.
bug fix: print {cell=555}.find("cellFormula") can fail because of 2% slop
involved in defining cell=555
Modified Paths:
--------------
trunk/Jmol/appletweb/jsmol.zip
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/appletweb/jsmol.zip
===================================================================
(Binary files differ)
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-11-29
22:18:42 UTC (rev 20870)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-11-30
00:00:28 UTC (rev 20871)
@@ -698,6 +698,8 @@
|| (isLigand = key.equals("_chem_comp_atom_comp_id"))) {
if (!processAtomSiteLoopBlock(isLigand))
return;
+ if (thisDataSetName.equals("global"))
+ asc.setCollectionName(thisDataSetName = chemicalName);
asc.setAtomSetName(thisDataSetName);
asc.setCurrentModelInfo("chemicalName", chemicalName);
asc.setCurrentModelInfo("structuralFormula", thisStructuralFormula);
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-11-29 22:18:42 UTC
(rev 20870)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-11-30 00:00:28 UTC
(rev 20871)
@@ -902,9 +902,9 @@
}
if (format.startsWith("'")) {
// needs evaluation
+ // xxxx.n means "the nth item"
+ pt = id.indexOf(".");
int n = (pt > 0 ? PT.parseInt(id.substring(pt + 1)) : 0);
- if (n > 0)
- n++;
if (pt > 0)
id = id.substring(0, pt);
format = PT.rep(format, "%n", "" + n);
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-11-29 22:18:42 UTC (rev
20870)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-11-30 00:00:28 UTC (rev
20871)
@@ -68,7 +68,7 @@
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
"rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";,
"aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
- "am",
"'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[%n].split(\"'\")[1]+'_cif.txt'"
+ "am",
"'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[(%n
== 0 ? 0 : %n + 1)].split(\"'\")[1]+'_cif.txt'"
};
public static String[] macros = {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-29 22:18:42 UTC
(rev 20870)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-11-30 00:00:28 UTC
(rev 20871)
@@ -73,6 +73,7 @@
draw dO diameter 2 [90 90 %] color @{ {_O}.color }
set echo eO [95 90 %]; echo "O"
-- can be used in the context of an element key:
+ load $caffeine
function createElementKey() {
var y = 90
for (var e in {*}.element.pivot){
@@ -85,7 +86,6 @@
y -= 5
}
}
- load $caffeine
createElementKey
new feature: additional predefined sets for periodic table:
@@ -103,11 +103,11 @@
-- for example, load =am/corundum
-- reads mineral page such as
http://rruff.geo.arizona.edu/AMS/minerals/Corundum
and extracts from that the last database ID.
- -- adding /1, /2, ..., /0 will return only the first, second, ..., last
structure on that page
+ -- adding .1, .2, ..., or .0 will return only the first, second, ..., or
last structure on that page
-- requires a preliminary search followed by the actual file load.
-- only the final ID-based file load is saved in the state.
-- a hack; uses an evaluation of the string:
-
'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[%n].split(\"'\")[1]+'_cif.txt'
+
'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[(%n
== 0 ? 0 : %n + 1)].split(\"'\")[1]+'_cif.txt'
-- for example, see http://rruff.geo.arizona.edu/AMS/viewJmol.php?id=19280
bug fix: files with names containing "[]" cannot be loaded.
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