Revision: 20561
http://sourceforge.net/p/jmol/code/20561
Author: hansonr
Date: 2015-06-08 13:53:26 +0000 (Mon, 08 Jun 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.14_2015.06.08"
_ by itself, not as a function, is shorthand for getProperty("auxiliaryInfo")
$ print _.keys
boundbox
group3Counts
group3Lists
modelLoadNote
models
properties
someModelsHaveFractionalCoordinates
someModelsHaveSymmetry
someModelsHaveUnitcells
symmetryRange
_m by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo.models")[_currentFrame]
$ print format("json",_m.unitCellParams)
[
0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376,2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN
]
{atomset}._ by itself delivers a subset array of auxiliaryInfo.models for
all models in {atomset}
$ print {*}._..1..aflowInfo
(first model's aflowInfo)
_(key) prepends "auxiliaryInfo.models", delivering a modelCount-length array
of information
$ print _("aflowInfo[SELECT auid WHERE 'H__eV___VASP_' < 0]")
{atomset}._(key) selects for model Auxiliary info related to models of the
specified atoms
{atomset}.getProperty(key) defaults to atomInfo, but also allows key to start
with "bondInfo"
Examples:
print _("aflowInfo[select sg where volume_cell > 70]")
print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
bug fix: [array].find("xxx") should always return a sub-array; previously if
there was only one hit, it returned that hit
bug fix: [array].find("xxx") should not return string equivalent even if it
uses that in the find.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
2015-06-08 05:18:12 UTC (rev 20560)
+++ trunk/Jmol/src/org/jmol/adapter/readers/aflow/AFLOWReader.java
2015-06-08 13:53:26 UTC (rev 20561)
@@ -286,12 +286,36 @@
if (kv.length < 2)
continue;
float f = parseFloatStr(kv[1]);
- htAFLOW.put(kv[0], Float.isNaN(f) ? kv[1] : Float.valueOf(f));
+ Object o = Float.isNaN(f) ? kv[1] : Float.valueOf(f);
+ htAFLOW.put(kv[0], o);
+ String kvclean = cleanKey(kv[0]);
+ if (kvclean != kv[0])
+ htAFLOW.put(kvclean, o);
}
asc.setCurrentModelInfo("aflowInfo", htAFLOW);
return true;
}
+ private Map<String, String> keyMap = new Hashtable<String, String>();
+
+ /**
+ * cleans key to just letters and digits
+ *
+ * @param key
+ * @return cleaned key
+ */
+ private String cleanKey(String key) {
+ String kclean = keyMap.get(key);
+ if (kclean != null)
+ return kclean;
+ char[] chars = key.toCharArray();
+ for (int i = chars.length; --i >= 0;)
+ if (!PT.isLetterOrDigit(chars[i]))
+ chars[i] = '_';
+ keyMap.put(key, kclean = new String(chars));
+ return kclean;
+ }
+
@Override
protected void finalizeSubclassReader() throws Exception {
alignUnitCells();
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-06-08 05:18:12 UTC
(rev 20560)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-06-08 13:53:26 UTC
(rev 20561)
@@ -575,7 +575,7 @@
|| (v = PT.getMapValueNoCase(localVars, name)) == null
&& allContext) {
if (name.startsWith("_")) {
- v = (name.equals("_") ? vwr.ms.msInfo
+ v = (name.equals("_") ? vwr.ms.getAuxiliaryInfo(null)
: name.equals("_m") && vwr.am.cmi >= 0 ?
vwr.ms.getModelAuxiliaryInfo(vwr.am.cmi)
: null);
@@ -1554,6 +1554,8 @@
boolean isInt = false;
boolean isString = false;
switch (tok) {
+ case T._:
+ return ((Map<String,
Object>)vwr.getAuxiliaryInfoForAtoms(bs)).get("models");
case T.xyz:
case T.vibxyz:
case T.fracxyz:
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-06-08 05:18:12 UTC
(rev 20560)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-06-08 13:53:26 UTC
(rev 20561)
@@ -158,7 +158,7 @@
op.tok == T.propselector);
case T._:
case T.getproperty:
- return evaluateGetProperty(mp, args, op.tok == T.propselector);
+ return evaluateGetProperty(mp, args, tok == T._, op.tok ==
T.propselector);
case T.helix:
return evaluateHelix(mp, args);
case T.hkl:
@@ -967,20 +967,23 @@
// {*}.find("chemical",type)
SV x1 = mp.getX();
+ boolean isList = (x1.tok == T.varray);
String sFind = SV.sValue(args[0]);
String flags = (args.length > 1 && args[1].tok != T.on
&& args[1].tok != T.off ? SV.sValue(args[1]) : "");
- boolean isSequence = sFind.equalsIgnoreCase("SEQUENCE");
- boolean isSmiles = sFind.equalsIgnoreCase("SMILES");
- boolean isSearch = sFind.equalsIgnoreCase("SMARTS");
- boolean isChemical = sFind.equalsIgnoreCase("CHEMICAL");
- boolean isMF = sFind.equalsIgnoreCase("MF");
- boolean isCF = sFind.equalsIgnoreCase("CELLFORMULA");
- boolean isON = (args[args.length - 1].tok == T.on);
+ boolean isSequence = !isList && sFind.equalsIgnoreCase("SEQUENCE");
+ boolean isSmiles = !isList && sFind.equalsIgnoreCase("SMILES");
+ boolean isSearch = !isList && sFind.equalsIgnoreCase("SMARTS");
+ boolean isChemical = !isList && sFind.equalsIgnoreCase("CHEMICAL");
+ boolean isMF = !isList && sFind.equalsIgnoreCase("MF");
+ boolean isCF = !isList && sFind.equalsIgnoreCase("CELLFORMULA");
+ boolean isON = !isList && (args[args.length - 1].tok == T.on);
try {
if (isChemical) {
- String data = (x1.tok == T.bitset ? vwr.getSmiles(SV.getBitSet(x1,
false)) : SV.sValue(x1));
- data = data.length() == 0 ? "" : vwr.getChemicalInfo(data, args.length
> 1 ? T.getTokenFromName(flags.toLowerCase()) : null);
+ String data = (x1.tok == T.bitset ? vwr.getSmiles(SV.getBitSet(x1,
+ false)) : SV.sValue(x1));
+ data = data.length() == 0 ? "" : vwr.getChemicalInfo(data,
+ args.length > 1 ? T.getTokenFromName(flags.toLowerCase()) : null);
if (data.endsWith("\n"))
data = data.substring(0, data.length() - 1);
if (data.startsWith("InChI"))
@@ -1001,18 +1004,20 @@
if (bs2 != null)
return false;
if (flags.equalsIgnoreCase("mf")) {
- ret = vwr.getSmilesMatcher().getMolecularFormula(smiles,
- isSearch);
+ ret = vwr.getSmilesMatcher().getMolecularFormula(smiles, isSearch);
} else {
- ret = e.getSmilesExt().getSmilesMatches(flags, smiles, null, null,
isSearch, !isAll);
+ ret = e.getSmilesExt().getSmilesMatches(flags, smiles, null, null,
+ isSearch, !isAll);
}
break;
case T.bitset:
if (isMF && flags.length() != 0)
- return mp.addXBs(JmolMolecule.getBitSetForMF(vwr.ms.at, (BS)
x1.value, flags));
+ return mp.addXBs(JmolMolecule.getBitSetForMF(vwr.ms.at,
+ (BS) x1.value, flags));
if (isMF || isCF)
- return mp.addXStr(JmolMolecule.getMolecularFormula(
- vwr.ms.at, (BS) x1.value, false, (isMF ? null :
vwr.ms.getCellWeights((BS) x1.value)), isON));
+ return mp.addXStr(JmolMolecule.getMolecularFormula(vwr.ms.at,
+ (BS) x1.value, false,
+ (isMF ? null : vwr.ms.getCellWeights((BS) x1.value)), isON));
if (isSequence)
return mp.addXStr(vwr.getSmilesOpt((BS) x1.value, -1, -1, false,
true, isAll, isAll, false));
@@ -1022,12 +1027,11 @@
if (asBonds) {
// this will return a single match
int[][] map = vwr.getSmilesMatcher().getCorrelationMaps(sFind,
- vwr.ms.at, vwr.ms.ac, (BS) x1.value,
- !isSmiles, true);
+ vwr.ms.at, vwr.ms.ac, (BS) x1.value, !isSmiles, true);
ret = (map.length > 0 ? vwr.ms.getDihedralMap(map[0]) : new
int[0]);
} else {
- ret = e.getSmilesExt().getSmilesMatches(sFind, null, (BS)
x1.value, bsMatch3D,
- !isSmiles, !isAll);
+ ret = e.getSmilesExt().getSmilesMatches(sFind, null, (BS) x1.value,
+ bsMatch3D, !isSmiles, !isAll);
}
break;
}
@@ -1041,7 +1045,6 @@
boolean isReverse = (flags.indexOf("v") >= 0);
boolean isCaseInsensitive = (flags.indexOf("i") >= 0);
boolean asMatch = (flags.indexOf("m") >= 0);
- boolean isList = (x1.tok == T.varray);
boolean isPattern = (args.length == 2);
if (isList || isPattern) {
JmolPatternMatcher pm = getPatternMatcher();
@@ -1052,10 +1055,10 @@
e.evalError(ex.toString(), null);
}
String[] list = SV.strListValue(x1);
+ Lst<SV> svlist = (isList ? x1.getList() : null);
if (Logger.debugging)
Logger.debug("finding " + sFind);
BS bs = new BS();
- int ipt = 0;
int n = 0;
Matcher matcher = null;
Lst<String> v = (asMatch ? new Lst<String>() : null);
@@ -1065,7 +1068,6 @@
boolean isMatch = matcher.find();
if (asMatch && isMatch || !asMatch && isMatch == !isReverse) {
n++;
- ipt = i;
bs.set(i);
if (asMatch)
v.addLast(isReverse ? what.substring(0, matcher.start())
@@ -1078,27 +1080,89 @@
.addXStr(n == 0 ? "" : matcher.group()) : mp.addXInt(n == 0 ? 0
: matcher.start() + 1));
}
- if (n == 1)
- return mp.addXStr(asMatch ? (String) v.get(0) : list[ipt]);
- String[] listNew = new String[n];
- if (n > 0)
- for (int i = list.length; --i >= 0;)
- if (bs.get(i)) {
- --n;
- listNew[n] = (asMatch ? (String) v.get(n) : list[i]);
- }
- return mp.addXAS(listNew);
+ // removed in 14.2/3.14 -- not documented and not expected if (n == 1)
+// return mp.addXStr(asMatch ? (String) v.get(0) : list[ipt]);
+
+ if (asMatch) {
+ String[] listNew = new String[n];
+ if (n > 0)
+ for (int i = list.length; --i >= 0;)
+ if (bs.get(i)) {
+ --n;
+ listNew[n] = (asMatch ? (String) v.get(n) : list[i]);
+ }
+ return mp.addXAS(listNew);
+ }
+ Lst<SV> l = new Lst<SV>();
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ l.addLast(svlist.get(i));
+ return mp.addXList(l);
}
if (isSequence) {
- return mp.addXStr(vwr.getJBR().toStdAmino3(SV.sValue(x1)));
+ return mp.addXStr(vwr.getJBR().toStdAmino3(SV.sValue(x1)));
}
return mp.addXInt(SV.sValue(x1).indexOf(sFind) + 1);
}
+ /**
+ * _ by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo")
+ *
+ * $ print _.keys
+ *
+ * boundbox
+ * group3Counts
+ * group3Lists
+ * modelLoadNote
+ * models
+ * properties
+ * someModelsHaveFractionalCoordinates
+ * someModelsHaveSymmetry
+ * someModelsHaveUnitcells
+ * symmetryRange
+ *
+ *
+ * _m by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo.models")[_currentFrame]
+ *
+ * $ print format("json",_m.unitCellParams)
+ *
+ * [
0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376,2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN
]
+ *
+ *
+ * {atomset}._ by itself delivers a subset array of auxiliaryInfo.models
for all models in {atomset}
+ *
+ * $ print {*}._..1..aflowInfo
+ *
+ * (first model's aflowInfo)
+ *
+ *
+ * _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length
array of information
+ *
+ * $ print _("aflowInfo[SELECT auid WHERE 'H__eV___VASP_' < 0]")
+ *
+ *
+ * {atomset}._(key) selects for model Auxiliary info related to models of
the specified atoms
+ *
+ * {atomset}.getProperty(key) defaults to atomInfo, but also allows key to
start with "bondInfo"
+ *
+ * Examples:
+ *
+ * print _("aflowInfo[select sg where volume_cell > 70]")
+ *
+ * print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
+ *
+ * @param mp
+ * @param args
+ * @param isAuxiliary
+ * @param isAtomProperty
+ * @return
+ * @throws ScriptException
+ */
private boolean evaluateGetProperty(ScriptMathProcessor mp, SV[] args,
- boolean isAtomProperty)
+ boolean isAuxiliary, boolean
isAtomProperty)
throws ScriptException {
int pt = 0;
+ if (isAuxiliary && args.length != 1)
+ return false;
int tok = (args.length == 0 ? T.nada : args[0].tok);
if (args.length == 2 && (tok == T.varray || tok == T.hash || tok ==
T.context)) {
return mp.addXObj(vwr.extractProperty(args[0].value,
args[1].value.toString(), -1));
@@ -1112,11 +1176,7 @@
isJSON = true;
propertyName = SV.sValue(args[pt++]);
}
-
- if (propertyName.startsWith("$")) {
- // TODO
- }
- if (isAtomProperty && !lc.startsWith("bondinfo") &&
!lc.startsWith("atominfo"))
+ if (isAtomProperty && !isAuxiliary && !lc.startsWith("bondinfo") &&
!lc.startsWith("atominfo"))
propertyName = "atomInfo." + propertyName;
Object propertyValue = "";
if (propertyName.equalsIgnoreCase("fileContents") && args.length > 2) {
@@ -1149,14 +1209,15 @@
int iAtom = bs.nextSetBit(0);
if (iAtom < 0)
return mp.addXStr("");
- propertyValue = bs;//BSUtil.newAndSetBit(iAtom);
+ propertyValue = bs;
}
+ if (isAuxiliary)
+ propertyName = "auxiliaryInfo.models." + propertyName;
+
+ propertyName = PT.rep(propertyName, ".[", "[");
Object property = vwr.getProperty(null, propertyName, propertyValue);
if (pt < args.length)
property = vwr.extractProperty(property, args, pt);
-// if (isAtomProperty && property instanceof Lst)
-// property = (((Lst<?>) property).size() > 0 ? ((Lst<?>) property).get(0)
-// : "");
return mp.addXObj(isJSON ? "{" + PT.toJSON("value", property) + "}" : SV
.isVariableType(property) ? property : Escape.toReadable(propertyName,
property));
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-08 05:18:12 UTC
(rev 20560)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-06-08 13:53:26 UTC
(rev 20561)
@@ -14,8 +14,60 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.14_2015.06.07"
+Jmol.___JmolVersion="14.3.14_2015.06.08"
+
+ _ by itself, not as a function, is shorthand for getProperty("auxiliaryInfo")
+
+ $ print _.keys
+
+ boundbox
+ group3Counts
+ group3Lists
+ modelLoadNote
+ models
+ properties
+ someModelsHaveFractionalCoordinates
+ someModelsHaveSymmetry
+ someModelsHaveUnitcells
+ symmetryRange
+
+
+ _m by itself, not as a function, is shorthand for
getProperty("auxiliaryInfo.models")[_currentFrame]
+
+ $ print format("json",_m.unitCellParams)
+
+ [
0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376,2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN
]
+
+
+ {atomset}._ by itself delivers a subset array of auxiliaryInfo.models for
all models in {atomset}
+
+ $ print {*}._..1..aflowInfo
+
+ (first model's aflowInfo)
+
+
+ _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length array
of information
+
+ $ print _("aflowInfo[SELECT auid WHERE 'H__eV___VASP_' < 0]")
+
+
+ {atomset}._(key) selects for model Auxiliary info related to models of the
specified atoms
+
+ {atomset}.getProperty(key) defaults to atomInfo, but also allows key to start
with "bondInfo"
+
+ Examples:
+
+ print _("aflowInfo[select sg where volume_cell > 70]")
+
+ print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
+
+
+bug fix: [array].find("xxx") should always return a sub-array; previously if
there was only one hit, it returned that hit
+bug fix: [array].find("xxx") should not return string equivalent even if it
uses that in the find.
+
+JmolVersion="14.3.14_2015.06.07"
+
new feature: _m.xxx _m shortcut for
@{getProperty("auxiliaryInfo.models[<currentModel>]")}
-- much easier syntax for getting auxiliary information
-- <currentModel> was not available, so this was not easily determined
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-06-08 05:18:12 UTC
(rev 20560)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-06-08 13:53:26 UTC
(rev 20561)
@@ -610,7 +610,7 @@
case PROP_ATOM_INFO:
return getAllAtomInfo(vwr.getAtomBitSet(myParam));
case PROP_AUXILIARY_INFO:
- return getAuxiliaryInfo(myParam);
+ return vwr.getAuxiliaryInfoForAtoms(myParam);
case PROP_BOND_INFO:
return getAllBondInfo(myParam);
case PROP_BOUNDBOX_INFO:
@@ -1719,11 +1719,6 @@
return info;
}
- private Map<String, Object> getAuxiliaryInfo(Object atomExpression) {
- return vwr.ms.getAuxiliaryInfo(vwr.ms.getModelBS(
- vwr.getAtomBitSet(atomExpression), false));
- }
-
private SV getAnnotationInfo(Object atomExpression, int type) {
BS bsAtoms = vwr.getAtomBitSet(atomExpression);
int iModel = vwr.ms.getModelBS(bsAtoms, false).nextSetBit(0);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-06-08 05:18:12 UTC (rev
20560)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-06-08 13:53:26 UTC (rev
20561)
@@ -9242,4 +9242,9 @@
"org.jmol.viewer.ChimeMessenger", this, "script")).set(this) : jcm);
}
+ public Object getAuxiliaryInfoForAtoms(Object atomExpression) {
+ return ms.getAuxiliaryInfo(ms.getModelBS(getAtomBitSet(atomExpression),
+ false));
+ }
+
}
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