Revision: 21629
http://sourceforge.net/p/jmol/code/21629
Author: hansonr
Date: 2017-06-05 03:25:50 +0000 (Mon, 05 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.18.1"
bug fix: WRITE MOL should not generate > <JMOL_PARTIAL_CHARGES> because it is
not SDF format
bug fix: WRITE SDF should generate > <JMOL_PARTIAL_CHARGES> with a trailing
space
bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4
new feature: WRITE SDF writes > <.... user data
-- can be set using MODEL PROPERTY "molData" x where x is an associative
array
new feature: associativeArray.pop() -- clears associativeArray
new feature: assArray1.push(assArray2) -- adds all key/value entries in
assArray2 to assArray1.
new feature: assArray1 + assArray2 -- adds all key/value entries into a new
associative array. (Complements a1 - a2)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
trunk/Jmol/src/org/jmol/smiles/SmilesStereo.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/molxyz/MolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2017-06-04 02:57:04 UTC (rev 21628)
+++ trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2017-06-05 03:25:50 UTC (rev 21629)
@@ -29,10 +29,9 @@
import javajs.util.PT;
+import org.jmol.adapter.smarter.Atom;
import org.jmol.adapter.smarter.AtomSetCollectionReader;
-import org.jmol.adapter.smarter.Atom;
import org.jmol.api.JmolAdapter;
-import org.jmol.util.Elements;
import org.jmol.util.Logger;
/**
@@ -131,37 +130,30 @@
}
private void processMolSdHeader() throws Exception {
- /*
- * obviously we aren't being this strict, but for the record:
- *
- * from ctfile.pdf (October 2003):
- *
- * Line 1: Molecule name. This line is unformatted, but like all
- * other lines in a molfile may not extend beyond column 80.
- * If no name is available, a blank line must be present.
- * Caution: This line must not contain any of the reserved
- * tags that identify any of the other CTAB file types
- * such as $MDL (RGfile), $$$$ (SDfile record separator),
- * $RXN (rxnfile), or $RDFILE (RDfile headers).
- *
- * Line 2: This line has the format:
- * IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
- * (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
- * User's first and last initials (l), program name (P),
- * date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
- * energy (E) if modeling program input, internal
- * registry number (R) if input through MDL form. A blank line can be
- * substituted for line 2. If the internal registry number is more than
- * 6 digits long, it is stored in an M REG line (described in Chapter 3).
- *
- * Line 3: A line for comments. If no comment is entered, a blank line
- * must be present.
- */
-
+ // We aren't being this strict. Line definitions are from ctfile.pdf
(October 2003)
String header = "";
+ // Line 1: Molecule name. This line is unformatted, but like all
+ // other lines in a molfile may not extend beyond column 80.
+ // If no name is available, a blank line must be present.
+ // Caution: This line must not contain any of the reserved
+ // tags that identify any of the other CTAB file types
+ // such as $MDL (RGfile), $$$$ (SDfile record separator),
+ // $RXN (rxnfile), or $RDFILE (RDfile headers).
+ //
String thisDataSetName = line.trim();
+ asc.setCollectionName(thisDataSetName);
+
header += line + "\n";
- asc.setCollectionName(thisDataSetName);
+
+ // Line 2: This line has the format:
+ // IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
+ // (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
+ // User's first and last initials (l), program name (P),
+ // date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
+ // energy (E) if modeling program input, internal
+ // registry number (R) if input through MDL form. A blank line can be
+ // substituted for line 2. If the internal registry number is more than
+ // 6 digits long, it is stored in an M REG line (described in Chapter 3).
rd();
if (line == null)
return;
@@ -173,15 +165,14 @@
appendLoadNote("This model is 2D. Its 3D structure has not been
generated.");
}
asc.setInfo("dimension", dimension);
- //line 3: comment
+
+ // Line 3: A line for comments. If no comment is entered, a blank line
+ // must be present.
rd();
if (line == null)
return;
line = line.trim();
header += line + "\n";
- if (line.length() != 0) {
- thisDataSetName += ": " + line;
- }
Logger.info(header);
checkCurrentLineForScript();
asc.setInfo("fileHeader", header);
@@ -277,7 +268,6 @@
// read V2000 user data
- Atom[] atoms = asc.atoms;
Map<String, String> molData = new Hashtable<String, String>();
rd();
while (line != null && line.indexOf("$$$$") != 0) {
@@ -312,18 +302,26 @@
rd();
}
+ /**
+ * Read the SDF data with name in lower case
+ *
+ * @param molData
+ * @throws Exception
+ */
private void readMolData(Map<String, String> molData) throws Exception {
Atom[] atoms = asc.atoms;
+ // "> <xxx>" becomes "xxx"
+ // "> yyy <xxx> zzz" becomes "yyy <xxx> zzz"
String dataName = PT.trim(line, "> <").toLowerCase();
String data = "";
float[] fdata = null;
- while (rd() != null && line.indexOf("$$$$") != 0
- && line.indexOf(">") != 0) {
+ // officially, we need a terminating blank line, and $$$$ could be data,
+ // but here we do not allow $$$$ due to Jmol legacy writing of
JMOL_PARTIAL_CHARGES
+ while (rd() != null && !line.equals("$$$$")
+ && line.length() > 0)
data += line + "\n";
- continue;
- }
data = PT.trim(data, "\n");
- Logger.info(dataName + ":" + data.replace('\n', '|'));
+ Logger.info(dataName + ":" + PT.esc(data));
molData.put(dataName, data);
if (dataName.toUpperCase().contains("_PARTIAL_CHARGES")) {
try {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -1477,7 +1477,8 @@
}
public void setInfo(int modelIndex, Object key, Object value) {
- am[modelIndex].auxiliaryInfo.put((String) key, value);
+ if (modelIndex >= 0 && modelIndex < mc)
+ am[modelIndex].auxiliaryInfo.put((String) key, value);
}
public Object getInfo(int modelIndex, String key) {
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2017-06-04 02:57:04 UTC (rev
21628)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2017-06-05 03:25:50 UTC (rev
21629)
@@ -1520,42 +1520,62 @@
/**
*
- * Script variables are pushed after cloning, because
- * the name comes with them when we do otherwise
- * they are not mutable anyway. We do want to have actual
+ * Script variables are pushed after cloning, because the name comes with
them
+ * when we do otherwise they are not mutable anyway. We do want to have
actual
* references to points, lists, and associative arrays
- *
+ * @param mapKey
* @param value
* null to pop
- * @param mapKey
+ *
* @return array
*/
- public SV pushPop(SV value, SV mapKey) {
- if (mapKey != null) {
+ public SV pushPop(SV mapKey, SV value) {
+ if (mapKey == null) {
Map<String, SV> m = getMap();
+ if (m == null) {
+ Lst<SV> x = getList();
+ if (value == null || x == null) {
+ // array.pop()
+ return (x == null || x.size() == 0 ? newS("") : x.removeItemAt(x
+ .size() - 1));
+ }
+ // array.push(value)
+ x.addLast(newI(0).setv(value));
+ } else {
+ if (value == null) {
+ // assocArray.pop()
+ m.clear(); // new Jmol 14.18
+ } else {
+ Map<String, SV> m1 = value.getMap();
+ if (m1 != null)
+ m.putAll(m1); // new Jmol 14.18
+ // assocArray.push(value)
+ }
+ }
+ } else {
+ Map<String, SV> m = getMap();
if (value == null) {
SV v = null;
if (m == null) {
+ // array.pop(i)
Lst<SV> lst = getList();
int len = lst.size();
int i = iValue(mapKey) - 1;
if (i < 0)
- i += len;
+ i += len;
if (i >= 0 && i < len) {
v = lst.removeItemAt(i);
}
} else {
+ // assocArray.pop(key)
v = m.remove(mapKey.asString());
}
return (v == null ? newS("") : v);
}
- if (m != null)
+ if (m != null) {
+ //assocArray.push(key,value)
m.put(mapKey.asString(), newI(0).setv(value));
- } else {
- Lst<SV> x = getList();
- if (value == null || x == null)
- return (x == null || x.size() == 0 ? newS("") :
x.removeItemAt(x.size() - 1));
- x.addLast(newI(0).setv(value));
+ }
}
return this;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -5176,6 +5176,8 @@
isRange = true;
break;
case T.property:
+ if (modelIndex < 0 && (modelIndex = vwr.am.cmi) < 0)
+ return;
propName = paramAsStr(++i);
SV sv = setVariable(++i, -1, "", false);
if (sv != null && !chk) {
@@ -5185,8 +5187,9 @@
}
prop = SV.oValue(sv);
}
- i = slen;
- break;
+ if (!chk)
+ vwr.ms.setInfo(modelIndex, propName, prop);
+ return;
default:
frameControl(offset);
return;
@@ -5256,11 +5259,6 @@
}
}
- if (propName != null) {
- if (modelIndex >= 0)
- vwr.ms.setInfo(modelIndex, propName, prop);
- return;
- }
if (!isPlay && !isRange || modelIndex >= 0)
vwr.setCurrentModelIndexClear(modelIndex, false);
if (isPlay && nFrames == 2 || isRange || isHyphen) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2017-06-04
02:57:04 UTC (rev 21628)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2017-06-05
03:25:50 UTC (rev 21629)
@@ -1150,6 +1150,12 @@
return addXBool(SV.isLike(x1, x2));
case T.plus:
switch (x1.tok) {
+ case T.hash:
+ Map<String, SV> ht = new Hashtable<String, SV>((Map<String, SV>)
x1.value);
+ Map<String, SV> map = x2.getMap();
+ if (map != null)
+ ht.putAll(map); // new Jmol 14.18
+ return addX(SV.getVariableMap(ht));
case T.integer:
if (!isDecimal(x2))
return addXInt(x1.intValue + x2.asInt());
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -4323,9 +4323,13 @@
+ "///");
filter = null;
}
- if (msg == null)
+ if (msg == null) {
+ int level = Logger.getLogLevel();
+ Logger.setLogLevel(4);
msg = (tok == T.smiles ? vwr.getSmiles(null) : vwr
.getOpenSmiles(null));
+ Logger.setLogLevel(level);
+ }
} catch (Exception ex) {
msg = ex.getMessage();
}
@@ -4439,6 +4443,9 @@
if (!chk)
msg = vwr.getAllSettings(null);
break;
+ case T.title:
+ msg = vwr.getFrameTitle();
+ break;
case T.url:
// in a new window
if ((len = slen) == 2) {
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -1884,10 +1884,10 @@
SV x2;
switch (tok) {
case T.push:
- return (len == 2 && mp.addX(x1.pushPop(args[1], args[0])) || len == 1
- && mp.addX(x1.pushPop(args[0], null)));
+ return (len == 2 && mp.addX(x1.pushPop(args[0], args[1])) || len == 1
+ && mp.addX(x1.pushPop(null, args[0])));
case T.pop:
- return (len == 1 && mp.addX(x1.pushPop(null, args[0])) || len == 0
+ return (len == 1 && mp.addX(x1.pushPop(args[0], null)) || len == 0
&& mp.addX(x1.pushPop(null, null)));
case T.add:
if (len != 1 && len != 2)
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -1796,6 +1796,7 @@
}
SmilesAtom atom2 = atoms[sBond.atom2.getMatchingAtomIndex()];
SmilesBond b = new SmilesBond(atom1, atom2, order, false);
+ b.isConnection = sBond.isConnection;
// do NOT add this bond to the second atom -- we will do that later;
atom2.bondCount--;
if (Logger.debugging)
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -545,17 +545,13 @@
Logger.debug("checking stereochemistry...");
//for debugging, first try SET DEBUG
- //for (int i = 0; i < ac; i++) {
- // SmilesAtom sAtom = patternAtoms[i];
- // System.out.print(sAtom + "=");
- //}
- //System.out.println("");
- //for (int i = 0; i < ac; i++) {
- // SmilesAtom sAtom = patternAtoms[i];
- // JmolSmilesNode atom0 = jmolAtoms[sAtom.getMatchingAtom()];
- // System.out.print(atom0.getIndex() + "-");
- //}
- //System.out.println("");
+//System.out.println("");
+//for (int i = 0; i < search.ac; i++) {
+// SmilesAtom sAtom = search.patternAtoms[i];
+// Node atom0 = sAtom.getMatchingAtom();
+// System.out.print(atom0.getIndex() + (sAtom.stereo != null ? "@" : "") +
"-");
+//}
+//System.out.println("");
for (int i = 0; i < search.ac; i++) {
SmilesAtom pAtom = search.patternAtoms[i];
@@ -577,8 +573,8 @@
if (haveTopo && sAtom0.getChiralClass() != chiralClass)
return false;
if (Logger.debugging)
- Logger.debug("...type " + chiralClass + " for pattern atom " + pAtom
- + " " + atom0);
+ Logger.debug("...type " + chiralClass + " for pattern atom \n " + pAtom
+ + "\n " + atom0);
switch (chiralClass) {
case POLYHEDRAL:
if (pAtom.stereo.isNot)
@@ -950,14 +946,16 @@
* @return 1 for "@", 2 for "@@"
*/
static int getHandedness(SimpleNode a, SimpleNode b, SimpleNode c,
SimpleNode pt, VTemp v) {
- float d = Measure.getNormalThroughPoints((P3) a, (P3) b, (P3) c, v.vTemp,
v.vA);
-// int atat = (distanceToPlane(v.vTemp, d, (P3) pt) > 0 ? 1 : 2);
+ float d = Measure.getNormalThroughPoints((P3) a, (P3) b, (P3) c, v.vTemp,
v.vA);
+ //int atat = (Measure.distanceToPlaneV(v.vTemp, d, (P3) pt) > 0 ? 1 : 2);
// System.out.println("$ draw p1 " + P3.newP((P3)a) +" color red '"+a+"
[2]'");
// System.out.println("$ draw p2 " + P3.newP((P3)b) +" color green '"+b+"
[3]'");
// System.out.println("$ draw p3 " + P3.newP((P3)c) +" color blue '"+c+"
[4]'");
// System.out.println("$ draw p " + P3.newP((P3)a) +" " + P3.newP((P3)b) +"
" + P3.newP((P3)c) +"" );
// System.out.println("$ draw v vector {" + P3.newP((P3)pt) +"} " +
v.vTemp+" '"+ (atat==2 ? "@@" : "@")+ pt + " [1]' color " + (atat == 2 ?
"white" : "yellow"));
- return (Measure.distanceToPlaneV(v.vTemp, d, (P3) pt) > 0 ? 1 : 2);
+ d = Measure.distanceToPlaneV(v.vTemp, d, (P3) pt);
+// System.out.println("# " + d);
+ return (d > 0 ? 1 : 2);
}
private static void getPlaneNormals(P3 atom1, P3 atom2, P3 atom3,
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -56,8 +56,23 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.17.2"
+Jmol.___JmolVersion="14.18.1"
+bug fix: WRITE MOL should not generate > <JMOL_PARTIAL_CHARGES> because it is
not SDF format
+bug fix: WRITE SDF should generate > <JMOL_PARTIAL_CHARGES> with a trailing
space
+bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for
.[C@H]2 (new group and attached to a connection number)
+bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4
+
+new feature: WRITE SDF writes > <.... user data
+ -- can be set using MODEL PROPERTY "molData" x where x is an associative
array
+
+new feature: associativeArray.pop() -- clears associativeArray
+new feature: assArray1.push(assArray2) -- adds all key/value entries in
assArray2 to assArray1.
+new feature: assArray1 + assArray2 -- adds all key/value entries into a new
associative array. (Complements a1 - a2)
+
+
+JmolVersion="14.17.2" // 2017.06.03
+
bug fix: WRITE FILE not working when file has been cached.
bug fix: array.find("regex...","") does not reset RegExp each time it runs
RegExp.exec() so does not find all possibilities
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2017-06-04 02:57:04 UTC
(rev 21628)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2017-06-05 03:25:50 UTC
(rev 21629)
@@ -1218,7 +1218,6 @@
bsBonds = getCovalentBondsForAtoms(ms.bo, ms.bondCount, bsTemp);
if (!(isOK = addMolFile(i, mol, bsTemp, bsBonds, false, false,
noAromatic, q)))
break;
- mol.append("$$$$\n");
}
} else if (isXYZ) {
LabelToken[] tokensXYZ = LabelToken.compile(vwr,
@@ -1314,6 +1313,7 @@
int nBonds = bsBonds.cardinality();
if (!asV3000 && !asJSON && (nAtoms > 999 || nBonds > 999))
return false;
+ boolean asSDF = (iModel >= 0);
ModelSet ms = vwr.ms;
int[] atomMap = new int[ms.ac];
P3 pTemp = new P3();
@@ -1354,15 +1354,31 @@
else {
mol.append("M END\n");
}
- if (!asJSON && !asV3000) {
+ if (asSDF) {
+ try {
+ @SuppressWarnings("unchecked")
+ Map<String, Object> molData = (Map<String, Object>)
vwr.ms.getInfo(iModel, "molData");
float[] pc = ms.getPartialCharges();
if (pc != null) {
- mol.append("> <JMOL_PARTIAL_CHARGES>\n").appendI(nAtoms)
- .appendC('\n');
+ if (molData == null)
+ molData = new Hashtable<String, Object>();
+ SB sb = new SB();
+ sb.appendI(nAtoms).appendC('\n');
for (int i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms
.nextSetBit(i + 1))
- mol.appendI(++n).append(" ").appendF(pc[i]).appendC('\n');
+ sb.appendI(++n).append(" ").appendF(pc[i]).appendC('\n');
+ molData.put("jmol_partial_charges", sb.toString());
}
+ for (String key: molData.keySet()) {
+ Object o = molData.get(key);
+ if (o instanceof SV)
+ o = ((SV)o).asString();
+ mol.append("> <" + key.toUpperCase() +
">\n").append(PT.trim(o.toString(), "\n")).append("\n\n");
+ }
+ } catch (Throwable e) {
+ // ignore
+ }
+ mol.append("$$$$\n");
}
return true;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-06-04 02:57:04 UTC (rev
21628)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-06-05 03:25:50 UTC (rev
21629)
@@ -8972,10 +8972,10 @@
SV p = pickedList.pushPop(null, null);
// don't allow double click
if (p.tok == T.bitset)
- pickedList.pushPop(p, null);
+ pickedList.pushPop(null, p);
if (p.tok != T.bitset || !((BS) p.value).get(atomIndex))
- pickedList.pushPop(SV.newV(T.bitset, BSUtil.newAndSetBit(atomIndex)),
- null);
+ pickedList.pushPop(null,
+ SV.newV(T.bitset, BSUtil.newAndSetBit(atomIndex)));
}
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