Revision: 20739
http://sourceforge.net/p/jmol/code/20739
Author: hansonr
Date: 2015-08-28 15:13:16 +0000 (Fri, 28 Aug 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.08.28"
new feature: Gaussian fchk reader reads vibrational modes
-- Gaussian command deck must include Freq=(SaveNormalModes,Raman,VibRot)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianFchkReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/scriptext/SmilesExt.java
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.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/adapter/readers/quantum/GaussianFchkReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianFchkReader.java
2015-08-26 14:39:24 UTC (rev 20738)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianFchkReader.java
2015-08-28 15:13:16 UTC (rev 20739)
@@ -42,9 +42,12 @@
/**
* Reader for Gaussian fchk files
- * also allows appended frequency info from the log file
+ * for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot)
*
*
+ * also allows appended freq data
+ *
+ *
* @author hansonr Bob Hanson hans...@stolaf.edu
*
**/
@@ -69,15 +72,77 @@
readPartialCharges();
readBasis();
readMolecularObitals();
- readFrequencies("NumFreq", false); // if log frequency info is appended
+ checkForFreq();
continuing = false;
}
+ private void checkForFreq() throws Exception {
+ Integer n = (Integer) fileData.get("Vib-NDim");
+ if (n == null) {
+// NumAtom 9
+// NumFreq 21
+// 1 2 3
+// A2 B1 A2
+// Frequencies -- 613.8891 622.9996
722.2497
+// Red. masses -- 3.1195 3.8445
1.3156
+// Frc consts -- 0.6927 0.8791
0.4043
+ readFrequencies("NumFreq", false); // if freq file appended
+ return;
+ }
+ try {
+ int nModes = n.intValue();
+ float[] vibE2 = (float[]) fileData.get("Vib-E2");
+ float[] modes = (float[]) fileData.get("Vib-Modes");
+ float[] frequencies = fillFloat(vibE2, 0, nModes);
+ float[] red_masses = fillFloat(vibE2, nModes, nModes);
+ float[] frc_consts = fillFloat(vibE2, nModes * 2, nModes);
+ float[] intensities = fillFloat(vibE2, nModes * 3, nModes);
+ int ac = asc.getLastAtomSetAtomCount();
+ boolean[] ignore = new boolean[nModes];
+ int fpt = 0;
+ for (int i = 0; i < nModes; ++i) {
+ ignore[i] = !doGetVibration(++vibrationNumber);
+ if (ignore[i])
+ continue;
+ int iAtom0 = asc.ac;
+ asc.cloneAtomSetWithBonds(true);
+ // set the properties
+ String name = asc.setAtomSetFrequency("Calculation " +
calculationNumber, null, "" + frequencies[i], null);
+ appendLoadNote("model " + asc.atomSetCount + ": " + name);
+ namedSets.set(asc.iSet);
+ asc.setAtomSetModelProperty("ReducedMass",
+ red_masses[i]+" AMU");
+ asc.setAtomSetModelProperty("ForceConstant",
+ frc_consts[i]+" mDyne/A");
+ asc.setAtomSetModelProperty("IRIntensity",
+ intensities[i]+" KM/Mole");
+ for (int iAtom = 0; iAtom < ac; iAtom++) {
+ asc.addVibrationVectorWithSymmetry(iAtom0
+ + iAtom, modes[fpt++], modes[fpt++], modes[fpt++], false);
+ }
+ }
+ } catch (Exception e) {
+ Logger.error("Could not read Vib-E2 section: " + e.getMessage());
+ }
+
+ }
+
+ private float[] fillFloat(float[] f0, int i, int n) {
+ float[] f = new float[n];
+ for (int i1 = 0, ilast = i + n; i < ilast; i++, i1++)
+ f[i1] = f0[i];
+ return f;
+ }
+
private void readAllData() throws Exception {
while ((line == null ? rd() : line) != null) {
if (line.length() < 40) {
- if (line.indexOf("NumAtom") == 0)
+ if (line.indexOf("NumAtom") == 0) {
+ // freq file appended
+// NumAtom 9
+// NumFreq 21
return;
+ }
continue;
}
String name = PT.rep(line.substring(0, 40).trim(), " ", "");
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2015-08-26 14:39:24 UTC (rev 20738)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2015-08-28 15:13:16 UTC (rev 20739)
@@ -65,7 +65,7 @@
private String energyKey = "";
/** The number of the calculation being interpreted. */
- private int calculationNumber = 1;
+ protected int calculationNumber = 1;
/** The scan point, where -1 denotes no scan information. */
private int scanPoint = -1;
@@ -78,7 +78,7 @@
private int stepNumber;
private int moModelSet = -1;
- private BS namedSets = new BS();
+ protected BS namedSets = new BS();
/**
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-26 14:39:24 UTC
(rev 20738)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-28 15:13:16 UTC
(rev 20739)
@@ -429,14 +429,14 @@
return mp.addXStr("NONE");
if (bs1 != null)
smiles1 = (String) e.getSmilesExt().getSmilesMatches("", null, bs1,
- null, false, true, false);
+ null, JC.SMILES_TYPE_SMILES, true, false);
boolean check;
if (bs2 == null) {
// note: find smiles1 IN smiles2 here
check = (vwr.getSmilesMatcher().areEqual(smiles2, smiles1) > 0);
} else {
check = (((BS) e.getSmilesExt().getSmilesMatches(smiles1, null, bs2,
- null, false, true, false)).nextSetBit(0) >= 0);
+ null, JC.SMILES_TYPE_SMILES, true, false)).nextSetBit(0) >= 0);
}
if (!check) {
// MF matched, but didn't match SMILES
@@ -451,7 +451,7 @@
check = (vwr.getSmilesMatcher().areEqual(smiles1, smiles2) >
0);
} else {
check = (((BS) e.getSmilesExt().getSmilesMatches(smiles1, null,
- bs2, null, false, true, false)).nextSetBit(0) >= 0);
+ bs2, null, JC.SMILES_TYPE_SMILES, true,
false)).nextSetBit(0) >= 0);
}
if (check)
return mp.addXStr("ENANTIOMERS");
@@ -462,7 +462,7 @@
smiles1) > 0);
} else {
Object ret = e.getSmilesExt().getSmilesMatches(
- "/nostereo/" + smiles1, null, bs2, null, false, true, false);
+ "/nostereo/" + smiles1, null, bs2, null,
JC.SMILES_TYPE_SMILES, true, false);
check = (((BS) ret).nextSetBit(0) >= 0);
}
if (check)
@@ -515,7 +515,7 @@
pattern = "/noaromatic"
+ (allMaps || bestMap ? "/" : " nostereo/")
+ e.getSmilesExt().getSmilesMatches((hMaps ? "H" : ""), null,
- bs1, null, false, true, false);
+ bs1, null, JC.SMILES_TYPE_SMILES, true, false);
} else {
allMaps = true;
}
@@ -1110,7 +1110,9 @@
}
try {
ret = e.getSmilesExt().getSmilesMatches(pattern, smiles, null,
- null, isSMARTS, !asMap, !allMappings);
+ null,
+ isSMARTS ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES,
+ !asMap, !allMappings);
} catch (Exception e) {
return mp.addXInt(-1);
}
@@ -1149,8 +1151,12 @@
| JC.SMILES_RETURN_FIRST);
ret = (map.length > 0 ? vwr.ms.getDihedralMap(map[0]) : new
int[0]);
} else {
+ int smilesFlags = (isSmiles ? JC.SMILES_TYPE_SMILES
+ : JC.SMILES_TYPE_SMARTS)
+ | (isON && sFind.length() == 0 ? JC.SMILES_BIO
+ | JC.SMILES_BIO_COMMENT : 0);
ret = e.getSmilesExt().getSmilesMatches(sFind, null, (BS) x1.value,
- bsMatch3D, !isSmiles, !isAll, false);
+ bsMatch3D, smilesFlags, !isON, false);
}
break;
}
@@ -2782,8 +2788,8 @@
RadiusData rd = null;
switch (tok) {
case T.branch:
- return (i == 3 && args[1].value instanceof BS
- && args[2].value instanceof BS && mp.addXBs(vwr.getBranchBitSet(
+ return (i == 3 && args[1].value instanceof BS
+ && args[2].value instanceof BS && mp.addXBs(vwr.getBranchBitSet(
((BS) args[2].value).nextSetBit(0),
((BS) args[1].value).nextSetBit(0), true)));
case T.smiles:
@@ -2806,8 +2812,10 @@
}
if (!isOK)
e.invArg();
- return mp.addXObj(e.getSmilesExt().getSmilesMatches(SV.sValue(args[1]),
null, bsSelected,
- null, tok == T.search, mp.asBitSet, false));
+ return mp.addXObj(e.getSmilesExt().getSmilesMatches(SV.sValue(args[1]),
+ null, bsSelected, null,
+ tok == T.search ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES,
+ mp.asBitSet, false));
}
if (withinSpec instanceof String) {
if (tok == T.nada) {
@@ -2835,13 +2843,13 @@
return mp.addXBs(getAtomsNearSurface(distance, s.substring(1)));
isWithinGroup = (s.equalsIgnoreCase("group"));
isVdw = (!isWithinGroup && s.equalsIgnoreCase("vanderwaals"));
- isWithinUnitcell = (!isWithinGroup && s.equalsIgnoreCase("unitcell"));
+ isWithinUnitcell = (!isWithinGroup && s.equalsIgnoreCase("unitcell"));
if (isVdw) {
withinSpec = null;
tok = T.vanderwaals;
} else if (isWithinUnitcell) {
- tok = T.unitcell;
- } else {
+ tok = T.unitcell;
+ } else {
tok = T.group;
}
break;
@@ -2881,8 +2889,8 @@
case T.rna3d:
case T.domains:
case T.validation:
- return mp.addXBs(vwr.ms.getAtoms(tok,
- SV.sValue(args[args.length - 1])));
+ return mp
+ .addXBs(vwr.ms.getAtoms(tok, SV.sValue(args[args.length - 1])));
}
break;
case 3:
@@ -2926,11 +2934,12 @@
bs = (args[i].tok == T.bitset ? SV.bsSelectVar(args[i]) : null);
if (tok == T.unitcell) {
boolean asMap = isWithinModelSet;
- return mp.addXObj(vwr.ms.getUnitCellPointsWithin(distance, bs, pt,
asMap));
+ return mp
+ .addXObj(vwr.ms.getUnitCellPointsWithin(distance, bs, pt, asMap));
}
if (pt != null)
return mp.addXBs(vwr.getAtomsNearPt(distance, pt));
-
+
if (tok == T.sequence)
return mp.addXBs(vwr.ms.getSequenceBits(withinStr, bs));
if (bs == null)
Modified: trunk/Jmol/src/org/jmol/scriptext/SmilesExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/SmilesExt.java 2015-08-26 14:39:24 UTC
(rev 20738)
+++ trunk/Jmol/src/org/jmol/scriptext/SmilesExt.java 2015-08-28 15:13:16 UTC
(rev 20739)
@@ -24,25 +24,21 @@
package org.jmol.scriptext;
+import javajs.util.AU;
+import javajs.util.Lst;
+import javajs.util.M4;
+import javajs.util.Measure;
+import javajs.util.P3;
+
import org.jmol.api.Interface;
import org.jmol.api.SmilesMatcherInterface;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
-import org.jmol.modelset.BondSet;
import org.jmol.script.ScriptEval;
import org.jmol.script.ScriptException;
-import org.jmol.util.BSUtil;
-
-import javajs.util.AU;
-import javajs.util.Lst;
-import javajs.util.Measure;
-
import org.jmol.util.Logger;
import org.jmol.viewer.JC;
-import javajs.util.M4;
-import javajs.util.P3;
-
public class SmilesExt {
private ScriptEval e;
@@ -160,52 +156,47 @@
}
/**
- * @param pattern e
- * @param smiles
- * @param bsSelected
- * @param bsMatch3D
- * @param isSmarts
- * @param asOneBitset
- * @param firstMatchOnly
- * @return
- * @throws ScriptException
+ * @param pattern
+ * e
+ * @param smiles
+ * @param bsSelected
+ * @param bsMatch3D
+ * @param flags
+ * @param asOneBitset
+ * @param firstMatchOnly
+ * @return Object
+ * @throws ScriptException
*/
public Object getSmilesMatches(String pattern, String smiles, BS bsSelected,
- BS bsMatch3D, boolean isSmarts,
- boolean asOneBitset, boolean firstMatchOnly)
throws ScriptException {
+ BS bsMatch3D, int flags, boolean asOneBitset,
+ boolean firstMatchOnly) throws
ScriptException {
// just retrieving the SMILES or bioSMILES string
-
if (pattern.length() == 0 || pattern.equals("H") || pattern.equals("*")) {
- boolean isBioSmiles = (!asOneBitset);
try {
return e.vwr.getSmilesOpt(
bsSelected,
0,
0,
- (pattern.equals("H") ? JC.SMILES_EXPLICIT_H : 0)
- | (pattern.equals("*") ? JC.SMILES_TOPOLOGY : 0)
- | (isBioSmiles ? JC.SMILES_BIO | JC.SMILES_BIO_CROSSLINK
- | JC.SMILES_BIO_COMMENT : 0));
+ flags | (pattern.equals("H") ? JC.SMILES_EXPLICIT_H : 0)
+ | (pattern.equals("*") ? JC.SMILES_TOPOLOGY : 0));
} catch (Exception ex) {
e.evalError(ex.getMessage(), null);
}
}
-
BS[] b;
if (bsMatch3D == null) {
-
// getting a BitSet or BitSet[] from a set of atoms or a pattern.
-
+ boolean isSmarts = JC.checkFlag(flags, JC.SMILES_TYPE_SMARTS);
try {
if (smiles == null) {
b = sm.getSubstructureSetArray(pattern, e.vwr.ms.at, e.vwr.ms.ac,
- bsSelected, null, isSmarts ? JC.SMILES_TYPE_SMARTS
- : JC.SMILES_TYPE_SMILES);
+ bsSelected, null, flags);
} else {
int[][] map = sm.find(pattern, smiles, isSmarts, firstMatchOnly);
if (!asOneBitset)
- return (!firstMatchOnly ? map : map.length == 0 ? new int[0] :
map[0]);
+ return (!firstMatchOnly ? map : map.length == 0 ? new int[0]
+ : map[0]);
BS bs = new BS();
for (int j = 0; j < map.length; j++) {
int[] a = map[j];
@@ -232,13 +223,9 @@
Lst<BS> vReturn = new Lst<BS>();
float stddev = getSmilesCorrelation(bsMatch3D, bsSelected, pattern, null,
- null, null, vReturn, false, null, null, false,
- isSmarts ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES);
- if (Float.isNaN(stddev)) {
- if (asOneBitset)
- return new BS();
- return new String[] {};
- }
+ null, null, vReturn, false, null, null, false, flags);
+ if (Float.isNaN(stddev))
+ return (asOneBitset ? new BS() : new String[] {});
e.showString("RMSD " + stddev + " Angstroms");
b = vReturn.toArray(new BS[vReturn.size()]);
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2015-08-26 14:39:24 UTC
(rev 20738)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2015-08-28 15:13:16 UTC
(rev 20739)
@@ -84,10 +84,11 @@
private BS bsIncludingH;
private boolean topologyOnly;
boolean getAromatic = true;
+ private boolean addAtomComment;
// generation of SMILES strings
- String getSmiles(Node[] atoms, int ac, BS bsSelected, boolean explicitH,
boolean topologyOnly, boolean getAromatic)
+ String getSmiles(Node[] atoms, int ac, BS bsSelected, boolean explicitH,
boolean topologyOnly, boolean getAromatic, boolean addAtomComment)
throws InvalidSmilesException {
int i = bsSelected.nextSetBit(0);
if (i < 0)
@@ -98,6 +99,7 @@
this.explicitH = explicitH;
this.topologyOnly = topologyOnly;
this.getAromatic = getAromatic;
+ this.addAtomComment = addAtomComment;
return getSmilesComponent(atoms[i], bsSelected, true, false);
}
@@ -122,7 +124,7 @@
BNode a = atoms[i];
String ch = a.getGroup1('?');
String bioStructureName = a.getBioStructureTypeName();
- boolean unknown = (ch.equals("?"));
+ boolean unknown = (ch == ch.toLowerCase());
if (end != null) {
if (sb.length() > 0)
sb.append(end);
@@ -135,7 +137,7 @@
len = s.length();
sb.append(s);
}
- sb.append("~").appendC(bioStructureName.charAt(0)).append("~");
+
sb.append("~").appendC(bioStructureName.toLowerCase().charAt(0)).append("~");
len++;
} else {
s = getSmilesComponent(a, bs, false, true);
@@ -157,7 +159,7 @@
len = 2;
}
if (unknown) {
- addBracketedBioName(sb, a, bioStructureName.length() > 0 ? ".0" :
null);
+ addBracketedBioName(sb, a, bioStructureName.length() > 0 ? ".0" :
null, false);
} else {
sb.append(ch);
}
@@ -199,7 +201,7 @@
return s;
}
- private void addBracketedBioName(SB sb, Node atom, String atomName) {
+ private void addBracketedBioName(SB sb, Node atom, String atomName, boolean
addComment) {
sb.append("[");
if (atomName != null && atom instanceof BNode) {
BNode a = (BNode) atom;
@@ -207,11 +209,13 @@
sb.append(a.getGroup3(false));
if (!atomName.equals(".0"))
sb.append(atomName).append("#").appendI(a.getElementNumber());
+ if (addComment) {
sb.append("//* ").appendI(
a.getResno());
if (chain.length() > 0)
sb.append(":").append(chain);
sb.append(" *//");
+ }
} else {
sb.append(Elements.elementNameFromNumber(atom.getElementNumber()));
}
@@ -662,12 +666,12 @@
// for bioSMARTS we provide the connecting atom if
// present. For example, in 1BLU we have
// .[CYS.SG#16] could match either the atom number or the element number
- if (Logger.debugging)
+ if (addAtomComment)
sb.append("\n//* " + atom + " *//\t");
if (topologyOnly)
sb.append("*");
else if (isExtension && groupType.length() != 0 && atomName.length() != 0)
- addBracketedBioName(sb, atom, "." + atomName);
+ addBracketedBioName(sb, atom, "." + atomName, false);
else
sb.append(SmilesAtom
.getAtomLabel(atomicNumber, isotope, valence, charge, nH, isAromatic,
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-08-26 14:39:24 UTC
(rev 20738)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-08-28 15:13:16 UTC
(rev 20739)
@@ -106,10 +106,6 @@
private final static int SMILES_MODE_MASK = 0x00F000;
- private boolean checkFlag(int flags, int flag) {
- return (flags & flag) == flag;
- }
-
@Override
public String getLastException() {
return InvalidSmilesException.getLastError();
@@ -149,19 +145,20 @@
String bioComment, int flags) throws Exception {
// boolean asBioSmiles, boolean bioAllowUnmatchedRings, boolean
bioAddCrossLinks, boolean explicitH
InvalidSmilesException.clear();
- if (checkFlag(flags, JC.SMILES_BIO)) {
- boolean bioAllowUnmatchedRings = checkFlag(flags,
+ if (JC.checkFlag(flags, JC.SMILES_BIO)) {
+ boolean bioAllowUnmatchedRings = JC.checkFlag(flags,
JC.SMILES_BIO_ALLOW_UNMACHED_RINGS);
- boolean bioAddCrossLinks = checkFlag(flags, JC.SMILES_BIO_CROSSLINK);
+ boolean bioAddCrossLinks = JC.checkFlag(flags, JC.SMILES_BIO_CROSSLINK);
return (new SmilesGenerator()).getBioSmiles((BNode[]) atoms, ac,
bsSelected, bioAllowUnmatchedRings, bioAddCrossLinks, bioComment);
}
- boolean explicitH = checkFlag(flags, JC.SMILES_EXPLICIT_H);
- boolean topologyOnly = checkFlag(flags, JC.SMILES_TOPOLOGY);
- boolean getAromatic = !checkFlag(flags, JC.SMILES_NOAROMATIC);
+ boolean explicitH = JC.checkFlag(flags, JC.SMILES_EXPLICIT_H);
+ boolean topologyOnly = JC.checkFlag(flags, JC.SMILES_TOPOLOGY);
+ boolean getAromatic = !JC.checkFlag(flags, JC.SMILES_NOAROMATIC);
+ boolean addAtomComment = JC.checkFlag(flags, JC.SMILES_ATOM_COMMENT);
return (new SmilesGenerator()).getSmiles(atoms, ac, bsSelected, explicitH,
- topologyOnly, getAromatic);
+ topologyOnly, getAromatic, addAtomComment);
}
@Override
@@ -452,7 +449,7 @@
BS bsAromatic, int flags) throws Exception {
InvalidSmilesException.clear();
try {
- SmilesSearch search = SmilesParser.getMolecule(pattern, checkFlag(flags,
JC.SMILES_TYPE_SMARTS));
+ SmilesSearch search = SmilesParser.getMolecule(pattern,
JC.checkFlag(flags, JC.SMILES_TYPE_SMARTS));
search.jmolAtoms = atoms;
if (atoms instanceof BNode[])
search.bioAtoms = (BNode[]) atoms;
@@ -463,8 +460,8 @@
search.getSelections();
search.bsRequired = null;//(bsRequired != null &&
bsRequired.cardinality() > 0 ? bsRequired : null);
search.setRingData(bsAromatic);
- search.firstMatchOnly = checkFlag(flags, JC.SMILES_RETURN_FIRST);
- search.matchAllAtoms = checkFlag(flags, JC.SMILES_MATCH_ALL);
+ search.firstMatchOnly = JC.checkFlag(flags, JC.SMILES_RETURN_FIRST);
+ search.matchAllAtoms = JC.checkFlag(flags, JC.SMILES_MATCH_ALL);
switch (flags & SMILES_MODE_MASK) {
case SMILES_MODE_BITSET:
search.asVector = false;
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-08-26 14:39:24 UTC (rev
20738)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-08-28 15:13:16 UTC (rev
20739)
@@ -1032,22 +1032,22 @@
return hAlignNames[(align >> TEXT_ALIGN_SHIFT) & 3];
}
- public static final int SMILES_EXPLICIT_H = 0x001;
- public static final int SMILES_TOPOLOGY = 0x002;
- public static final int SMILES_NOAROMATIC = 0x004;
- public static final int SMILES_BIO = 0x100;
- public static final int SMILES_BIO_ALLOW_UNMACHED_RINGS = 0x101;
- public static final int SMILES_BIO_CROSSLINK = 0x102;
- public static final int SMILES_BIO_COMMENT = 0x104;
+ public static final int SMILES_TYPE_SMILES = 0x1;
+ public static final int SMILES_TYPE_SMARTS = 0x2;
- public static final int SMILES_TYPE_SMILES = 0x010000;
- public static final int SMILES_TYPE_SMARTS = 0x020000;
- public static final int SMILES_MATCH_ALL = 0x100000;
- public static final int SMILES_MATCH_ONE = 0x200000;
- public static final int SMILES_RETURN_FIRST = 0x400000;
+ public static final int SMILES_MATCH_ALL = 0x10;
+ public static final int SMILES_MATCH_ONE = 0x20;
+ public static final int SMILES_RETURN_FIRST = 0x40;
-
-
+ public static final int SMILES_EXPLICIT_H = 0x00100;
+ public static final int SMILES_TOPOLOGY = 0x00200;
+ public static final int SMILES_NOAROMATIC = 0x00400;
+ public static final int SMILES_BIO = 0x10000;
+ public static final int SMILES_BIO_ALLOW_UNMACHED_RINGS = 0x10100;
+ public static final int SMILES_BIO_CROSSLINK = 0x10200;
+ public static final int SMILES_BIO_COMMENT = 0x10400;
+ public static final int SMILES_ATOM_COMMENT = 0x20000;
+
public static final int JSV_NOT = -1;
public static final int JSV_SEND_JDXMOL = 0;
public static final int JSV_SETPEAKS = 7;
@@ -1079,4 +1079,8 @@
public static String READER_NOT_FOUND = "File reader was not found:";
+ public static boolean checkFlag(int flags, int flag) {
+ return (flags & flag) == flag;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-26 14:39:24 UTC
(rev 20738)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-28 15:13:16 UTC
(rev 20739)
@@ -60,8 +60,12 @@
TODO: Rolf's errors in Safari due to move + zoomto
+Jmol.___JmolVersion="14.3.16_2015.08.28"
+
+new feature: Gaussian fchk reader reads vibrational modes
+-- Gaussian command deck must include Freq=(SaveNormalModes,Raman,VibRot)
-Jmol.___JmolVersion="14.3.16_2015.08.26"
+JmolVersion="14.3.16_2015.08.26"
new feature: SMARTS conformational search no longer limited to one range.
-- example:
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-08-26 14:39:24 UTC (rev
20738)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-08-28 15:13:16 UTC (rev
20739)
@@ -8620,7 +8620,7 @@
@Override
public String getSmiles(BS bs) throws Exception {
- return getSmilesOpt(bs, -1, -1, 0);
+ return getSmilesOpt(bs, -1, -1, Logger.debugging ? JC.SMILES_ATOM_COMMENT
: 0);
}
/**
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