Revision: 21221
http://sourceforge.net/p/jmol/code/21221
Author: hansonr
Date: 2016-08-26 16:15:05 +0000 (Fri, 26 Aug 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.6.1_2016.08.25"
new feature: allowance for external app loading of binary (mmtf) files
bug fix: Spartan 16 reader may have empty first model
bug fix: 2D model show SMILES uses @SP -- should be /nostereo/ based on
_.dimension == "2D"
bug fix: NCI/CADD now requires "get3d=true" not "get3d=True"
Modified Paths:
--------------
branches/v14_6/Jmol/src/org/jmol/adapter/smarter/Resolver.java
branches/v14_6/Jmol/src/org/jmol/viewer/FileManager.java
branches/v14_6/Jmol/src/org/jmol/viewer/GlobalSettings.java
branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_6/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_6/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/smarter/Resolver.java
2016-08-25 15:04:58 UTC (rev 21220)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/smarter/Resolver.java
2016-08-26 16:15:05 UTC (rev 21221)
@@ -764,7 +764,7 @@
{ "SpartanSmol" , "|PropertyArchive", "_spartan", "spardir", "BEGIN
Directory Entry Molecule" };
private final static String[] spartanContainsRecords =
- { "Spartan", "Spartan" }; // very old Spartan files?
+ { "Spartan", "Spartan", "converted archive file" }; // very old Spartan
files; sparchive files
private final static String[] adfContainsRecords =
{ "Adf", "Amsterdam Density Functional" };
Modified: branches/v14_6/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/FileManager.java 2016-08-25
15:04:58 UTC (rev 21220)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/FileManager.java 2016-08-26
16:15:05 UTC (rev 21221)
@@ -364,13 +364,20 @@
*
* @param fullPathName
* @param name
- * @param reader
+ * @param reader could be a BufferedInputStream
* @param htParams
* @return fileData
*/
Object createAtomSetCollectionFromReader(String fullPathName, String name,
Object reader,
Map<String, Object> htParams) {
+ if (reader instanceof BufferedInputStream) {
+ boolean isLittleEndian = htParams.containsKey("isLittleEndian");
+ GenericBinaryDocument bd = (GenericBinaryDocument) Interface
+ .getInterface("javajs.util.BinaryDocument", vwr, "file");
+ bd.setStream((BufferedInputStream) reader, !isLittleEndian);
+ reader = bd;
+ }
FileReader fileReader = new FileReader(this, vwr, name, fullPathName,
name, null,
reader, htParams, false);
fileReader.run();
Modified: branches/v14_6/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-08-25
15:04:58 UTC (rev 21220)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-08-26
16:15:05 UTC (rev 21221)
@@ -80,7 +80,7 @@
pdbLoadLigandFormat = databases.get("ligand");
nmrUrlFormat = databases.get("nmr");
nmrPredictFormat = databases.get("nmrdb");
- smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=True";
+ smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=true";
nihResolverFormat = databases.get("nci");
pubChemFormat = databases.get("pubchem");
@@ -902,7 +902,7 @@
if (database.equals("pubchem"))
id = "name/" + id;
else if (database.equals("nci"))
- id += "/file?format=sdf&get3d=True";
+ id += "/file?format=sdf&get3d=true";
}
if (format.startsWith("'")) {
// needs evaluation
Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties 2016-08-25
15:04:58 UTC (rev 21220)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Jmol.properties 2016-08-26
16:15:05 UTC (rev 21221)
@@ -8,7 +8,10 @@
Jmol.___JmolVersion="14.6.1_2016.08.25"
+new feature: allowance for external app loading of binary (mmtf) files
bug fix: Spartan 16 reader may have empty first model
+bug fix: 2D model show SMILES uses @SP -- should be /nostereo/ based on
_.dimension == "2D"
+bug fix: NCI/CADD now requires "get3d=true" not "get3d=True"
JmolVersion="14.6.1_2016.08.20"
Modified: branches/v14_6/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/viewer/Viewer.java 2016-08-25 15:04:58 UTC
(rev 21220)
+++ branches/v14_6/Jmol/src/org/jmol/viewer/Viewer.java 2016-08-26 16:15:05 UTC
(rev 21221)
@@ -1684,7 +1684,7 @@
atomSetCollection = openFileFull(fileName, isAppend, htParams,
loadScript);
- } else if (reader instanceof Reader) {
+ } else if (reader instanceof Reader || reader instanceof
BufferedInputStream) {
// 3) a file reader (not used by Jmol)
@@ -8718,7 +8718,8 @@
@Override
public String getSmiles(BS bs) throws Exception {
- return getSmilesOpt(bs, -1, -1, bs == null && Logger.debugging ?
JC.SMILES_GEN_ATOM_COMMENT :0, null);
+ boolean is2D = ("2D".equals(ms.getInfoM("dimension")));
+ return getSmilesOpt(bs, -1, -1, (bs == null && Logger.debugging ?
JC.SMILES_GEN_ATOM_COMMENT :0) | (is2D ? JC.SMILES_IGNORE_STEREOCHEMISTRY : 0),
null);
}
@Override
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2016-08-25
15:04:58 UTC (rev 21220)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2016-08-26
16:15:05 UTC (rev 21221)
@@ -764,7 +764,7 @@
{ "SpartanSmol" , "|PropertyArchive", "_spartan", "spardir", "BEGIN
Directory Entry Molecule" };
private final static String[] spartanContainsRecords =
- { "Spartan", "Spartan" }; // very old Spartan files?
+ { "Spartan", "Spartan", "converted archive file" }; // very old Spartan
files; sparchive files
private final static String[] adfContainsRecords =
{ "Adf", "Amsterdam Density Functional" };
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2016-08-25 15:04:58 UTC
(rev 21220)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2016-08-26 16:15:05 UTC
(rev 21221)
@@ -364,13 +364,20 @@
*
* @param fullPathName
* @param name
- * @param reader
+ * @param reader could be a BufferedInputStream
* @param htParams
* @return fileData
*/
Object createAtomSetCollectionFromReader(String fullPathName, String name,
Object reader,
Map<String, Object> htParams) {
+ if (reader instanceof BufferedInputStream) {
+ boolean isLittleEndian = htParams.containsKey("isLittleEndian");
+ GenericBinaryDocument bd = (GenericBinaryDocument) Interface
+ .getInterface("javajs.util.BinaryDocument", vwr, "file");
+ bd.setStream((BufferedInputStream) reader, !isLittleEndian);
+ reader = bd;
+ }
FileReader fileReader = new FileReader(this, vwr, name, fullPathName,
name, null,
reader, htParams, false);
fileReader.run();
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-08-25 15:04:58 UTC
(rev 21220)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-08-26 16:15:05 UTC
(rev 21221)
@@ -80,7 +80,7 @@
pdbLoadLigandFormat = databases.get("ligand");
nmrUrlFormat = databases.get("nmr");
nmrPredictFormat = databases.get("nmrdb");
- smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=True";
+ smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=true";
nihResolverFormat = databases.get("nci");
pubChemFormat = databases.get("pubchem");
@@ -902,7 +902,7 @@
if (database.equals("pubchem"))
id = "name/" + id;
else if (database.equals("nci"))
- id += "/file?format=sdf&get3d=True";
+ id += "/file?format=sdf&get3d=true";
}
if (format.startsWith("'")) {
// needs evaluation
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-08-25 15:04:58 UTC
(rev 21220)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-08-26 16:15:05 UTC
(rev 21221)
@@ -50,9 +50,11 @@
Jmol.___JmolVersion="14.7.1_2016.08.25"
+new feature: allowance for external app loading of binary (mmtf) files
bug fix: Spartan 16 reader may have empty first model
+bug fix: 2D model show SMILES uses @SP -- should be /nostereo/ based on
_.dimension == "2D"
+bug fix: NCI/CADD now requires "get3d=true" not "get3d=True"
-
JmolVersion="14.7.1_2016.08.20"
feature change: updated links to EBI electron density maps (formerly Uppsala;
for isosurface "*xxxx")
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-08-25 15:04:58 UTC (rev
21220)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-08-26 16:15:05 UTC (rev
21221)
@@ -1684,7 +1684,7 @@
atomSetCollection = openFileFull(fileName, isAppend, htParams,
loadScript);
- } else if (reader instanceof Reader) {
+ } else if (reader instanceof Reader || reader instanceof
BufferedInputStream) {
// 3) a file reader (not used by Jmol)
@@ -8718,7 +8718,8 @@
@Override
public String getSmiles(BS bs) throws Exception {
- return getSmilesOpt(bs, -1, -1, bs == null && Logger.debugging ?
JC.SMILES_GEN_ATOM_COMMENT :0, null);
+ boolean is2D = ("2D".equals(ms.getInfoM("dimension")));
+ return getSmilesOpt(bs, -1, -1, (bs == null && Logger.debugging ?
JC.SMILES_GEN_ATOM_COMMENT :0) | (is2D ? JC.SMILES_IGNORE_STEREOCHEMISTRY : 0),
null);
}
@Override
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