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[Jmol-commits] SF.net SVN: jmol:[21454] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2017-03-25 22:38:57
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Revision: 21454
http://sourceforge.net/p/jmol/code/21454
Author: hansonr
Date: 2017-03-25 22:38:54 +0000 (Sat, 25 Mar 2017)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/dssx/DSSR1.java
trunk/Jmol/src/org/jmol/modelsetbio/BasePair.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/dssx/DSSR1.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2017-03-25 20:45:05 UTC (rev 21453)
+++ trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2017-03-25 22:38:54 UTC (rev 21454)
@@ -286,6 +286,8 @@
}
private NucleicMonomer setRes(Atom atom) {
+ if (atom.group.getBioPolymerLength() == 0)
+ return null;
NucleicMonomer m = (NucleicMonomer) atom.group;
((NucleicPolymer) m.bioPolymer).isDssrSet = true;
return m;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BasePair.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BasePair.java 2017-03-25 20:45:05 UTC (rev 21453)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BasePair.java 2017-03-25 22:38:54 UTC (rev 21454)
@@ -13,6 +13,8 @@
public static BasePair add(Map<String, Object> info, NucleicMonomer g1,
NucleicMonomer g2) {
+ if (g1 == null || g2 == null)
+ return null; // can happen if one of DSSR pair is not a monomer (HPA in 4fe5)
BasePair bp = new BasePair();
bp.info = info;
(bp.g1 = g1).addBasePair(bp);
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-03-25 20:45:05 UTC (rev 21453)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-03-25 22:38:54 UTC (rev 21454)
@@ -4640,7 +4640,7 @@
filename = filename.substring(0, pt);
if ((pt = filename.indexOf(".")) >= 0)
filename = filename.substring(0, pt);
- if (JC.PDB_ANNOTATIONS.indexOf(";" + ext + ";") >= 0) {
+ if (JC.PDB_ANNOTATIONS.indexOf(";" + ext + ";") >= 0 || ext.startsWith("dssr--")) {
if (filename.startsWith("="))
filename += ".cif";
filenames = (ext.equals("all") ? new String[] { filename,
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2017-03-25 20:45:05 UTC (rev 21453)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2017-03-25 22:38:54 UTC (rev 21454)
@@ -66,7 +66,7 @@
"cod", "http://www.crystallography.net/cod/cif/%c1/%c2%c3/%c4%c5/%FILE.cif",
"nmr", "http://www.nmrdb.org/new_predictor?POST?molfile=",
"nmrdb", "http://www.nmrdb.org/service/predictor?POST?molfile=",
- "nmrdb13", "http://www.nmrdb.org/service/jsmol13c?POST?molfile=",
+ "nmrdb13", "http://www.nmrdb.o rg/service/jsmol13c?POST?molfile=",
//"pdb", "http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz", // new Jmol 14.5.0 10/28/2015
"magndata", "http://webbdcrista1.ehu.es/magndata/mcif/%FILE.mcif",
"mmtf", "https://mmtf.rcsb.org/full/%FILE", // new Jmol 14.5.4 4/2016
@@ -126,6 +126,7 @@
public final static String copyright = "(C) 2015 Jmol Development";
public final static String version;
+ public static String majorVersion;
public final static String date;
public final static int versionInt;
@@ -150,8 +151,11 @@
bis = new BufferedInputStream(is);
Properties props = new Properties();
props.load(bis);
- tmpVersion = PT.trimQuotes(props.getProperty("Jmol.___JmolVersion",
- tmpVersion));
+ String s = props.getProperty("Jmol.___JmolVersion",
+ tmpVersion);
+ if (s != null && s.lastIndexOf("\"") > 0)
+ s = s.substring(0, s.lastIndexOf("\"") + 1);
+ tmpVersion = PT.trimQuotes(s);
tmpDate = PT.trimQuotes(props.getProperty("Jmol.___JmolDate", tmpDate));
} catch (Exception e) {
// Nothing to do
@@ -180,11 +184,13 @@
// 012345678901234567890123456789
}
version = (tmpVersion != null ? tmpVersion : "(Unknown_version)");
+ majorVersion = (tmpVersion != null ? tmpVersion : "(Unknown_version)");
date = (tmpDate != null ? tmpDate : "(Unknown_date)");
// 11.9.999 --> 1109999
int v = -1;
try {
String s = version;
+ String major = "";
// Major number
int i = s.indexOf(".");
if (i < 0) {
@@ -192,7 +198,7 @@
s = null;
}
if (s != null) {
- v = 100000 * Integer.parseInt(s.substring(0, i));
+ v = 100000 * Integer.parseInt(major = s.substring(0, i));
// Minor number
s = s.substring(i + 1);
@@ -202,7 +208,10 @@
s = null;
}
if (s != null) {
- v += 1000 * Integer.parseInt(s.substring(0, i));
+ String m = s.substring(0, i);
+ major += "." + m;
+ majorVersion = major;
+ v += 1000 * Integer.parseInt(m);
// Revision number
s = s.substring(i + 1);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-03-25 20:45:05 UTC (rev 21453)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-03-25 22:38:54 UTC (rev 21454)
@@ -121,7 +121,12 @@
-- 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
@@ -7631,7 +7636,7 @@
new feature: set backboneSteps TRUE
-- draws base pair steps between dssr-identified base pairs
-TO HERE
+>>>>> TO HERE
TRANSCRIPTION/DNA 06-MAR-92 1D66
DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-03-25 20:45:05 UTC (rev 21453)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-03-25 22:38:54 UTC (rev 21454)
@@ -3980,6 +3980,10 @@
id = name.substring(pt + 1);
format = (pt > 6 ? name.substring(6) : "loops");
return PT.rep(g.resolveDataBase("rna3d", id, null), "%TYPE", format);
+ } else if (name.startsWith("*dssr--")) {
+ id = name.substring(pt + 1);
+ id = g.resolveDataBase("dssr", id, null);
+ return id +"%20" + PT.rep(name.substring(5, pt), " ", "%20");
} else if (name.startsWith("*dssr/")) {
id = name.substring(pt + 1);
return g.resolveDataBase("dssr", id, null);
@@ -7831,7 +7835,7 @@
if (g.helpPath.indexOf("?") < 0) {
if (what.length() > 0 && what.indexOf("?") != 0)
what = "?search=" + PT.rep(what, " ", "%20");
- what += (what.length() == 0 ? "?ver=" : "&ver=") + JC.version;
+ what += (what.length() == 0 ? "?ver=" : "&ver=") + JC.majorVersion;
} else {
what = "&" + what;
}
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