Revision: 20982
http://sourceforge.net/p/jmol/code/20982
Author: hansonr
Date: 2016-03-07 04:22:42 +0000 (Mon, 07 Mar 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.5.3_2016.03.06"
new feature: optional processing of OpenSMILES [CH2:002] ":<n>" atom class.
-- positive integer value only
-- checks the atom property property_osclass
-- for SMARTS, [:0] means "without an osclass"
-- for SMARTS, [!:0] means "any non-zero osclass"
-- for SMARTS, same as [$(select property_osclass=n)]
-- only enabled with Jmol SMILES directive "/opensmiles/"; otherwise ignored
new feature: {*}.find("OPENSMILES")
-- adds atom class if property_osclass is nonzero
bug fix: Inconsistent use of "DIASTEREOMERS" (preferred) and "DIASTERIOMERS"
(incorrect)
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
branches/v14_4/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java
branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAtom.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesMatcher.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java
branches/v14_4/Jmol/src/org/jmol/util/Edge.java
branches/v14_4/Jmol/src/org/jmol/util/Node.java
branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
trunk/Jmol/src/org/jmol/util/Edge.java
trunk/Jmol/src/org/jmol/util/Node.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
2016-03-06 18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
2016-03-07 04:22:42 UTC (rev 20982)
@@ -45,9 +45,8 @@
int ac, BS bsSelected,
int flags) throws Exception;
- public abstract void getSubstructureSets(String[] smarts, Node[] atoms, int
ac,
- int flags,
- BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings)
throws Exception;
+ public abstract void getMMFF94AtomTypes(String[] smarts, Node[] atoms, int
ac,
+ BS bsSelected, Lst<BS> bitSets,
Lst<BS>[] vRings) throws Exception;
public abstract String getSmiles(Node[] atoms, int ac, BS bsSelected,
String bioComment, int flags) throws
Exception;
Modified:
branches/v14_4/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
2016-03-06 18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
2016-03-07 04:22:42 UTC (rev 20982)
@@ -870,8 +870,7 @@
// identifies that atom's MMFF94 type.
try {
- smartsMatcher.getSubstructureSets(smarts, atoms, atoms.length,
- Edge.FLAG_AROMATIC_STRICT | Edge.FLAG_AROMATIC_DOUBLE,
+ smartsMatcher.getMMFF94AtomTypes(smarts, atoms, atoms.length,
bsConnected, bitSets, vRings);
} catch (Exception e) {
Logger.error(e.toString());
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -33,6 +33,7 @@
import javajs.util.T3;
import javajs.util.V3;
+import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolModulationSet;
import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
@@ -1420,4 +1421,18 @@
return (m.isBioModel ? ((BioModel) m).getUnitID(this, flags) : "");
}
+ @Override
+ public float getFloatProperty(String property) {
+ Object data = group.chain.model.ms.vwr.getDataObj(property, null,
+ JmolDataManager.DATA_TYPE_AF);
+ float f = 0;
+ if (data != null) {
+ try {
+ f = ((float[]) data)[i];
+ } catch (Exception e) {
+ }
+ }
+ return f;
+ }
+
}
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2016-03-06
18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2016-03-07
04:22:42 UTC (rev 20982)
@@ -1272,7 +1272,8 @@
&& args[1].tok != T.off ? SV.sValue(args[1]) : "");
boolean isSequence = !isList && sFind.equalsIgnoreCase("SEQUENCE");
boolean isSeq = !isList && sFind.equalsIgnoreCase("SEQ");
- boolean isSmiles = !isList && sFind.equalsIgnoreCase("SMILES");
+ boolean isOpenSmiles = !isList && sFind.equalsIgnoreCase("OPENSMILES");
+ boolean isSmiles = isOpenSmiles || !isList &&
sFind.equalsIgnoreCase("SMILES");
boolean isSMARTS = !isList && sFind.equalsIgnoreCase("SMARTS");
boolean isChemical = !isList && sFind.equalsIgnoreCase("CHEMICAL");
boolean isMF = !isList && sFind.equalsIgnoreCase("MF");
@@ -1365,7 +1366,8 @@
| JC.SMILES_RETURN_FIRST);
ret = (map.length > 0 ? vwr.ms.getDihedralMap(map[0]) : new
int[0]);
} else {
- int smilesFlags = (isSmiles ? JC.SMILES_TYPE_SMILES
+ int smilesFlags = (isOpenSmiles ? JC.SMILES_TYPE_OPENSMILES
+ : isSmiles ? JC.SMILES_TYPE_SMILES
: JC.SMILES_TYPE_SMARTS)
| (isON && sFind.length() == 0 ? JC.SMILES_BIO_COV_CROSSLINK
| JC.SMILES_BIO_COMMENT : 0);
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAtom.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAtom.java 2016-03-06
18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesAtom.java 2016-03-07
04:22:42 UTC (rev 20982)
@@ -180,6 +180,7 @@
private Node matchingNode;
public boolean hasSubpattern;
public int mapIndex = -1; // in CCC we have atoms 0, 1, and 2
+ public float osClass = Float.NaN; // OpenSMILES atom class is an integer
public SmilesAtom setAll(int iComponent, int ptAtom, int atomicNumber,
int charge) {
@@ -716,18 +717,21 @@
}
/**
+ *
+ * called from SmilesGenerator
*
* @param atomicNumber
* @param isotopeNumber
* @param valence set -1 to force brackets
* @param charge
+ * @param osclass OpenSMILES value
* @param nH
* @param isAromatic
* @param stereo
* @return label
*/
static String getAtomLabel(int atomicNumber, int isotopeNumber, int valence,
- int charge, int nH, boolean isAromatic,
+ int charge, float osclass, int nH, boolean
isAromatic,
String stereo) {
String sym = Elements.elementSymbolFromNumber(atomicNumber);
if (isAromatic) {
@@ -735,15 +739,20 @@
if (atomicNumber != 6)
valence = Integer.MAX_VALUE; // force [n]
}
- int count = (stereo == null || stereo.length() > 0 || isotopeNumber != 0
|| charge != 0 ? -1
+ int count = (isotopeNumber != 0
+ || stereo != null && stereo.length() > 0
+ || charge != 0 || osclass != 0 ? -1
: getDefaultCount(atomicNumber, false));
return (count == valence ? sym :
+ // rearranged 14.5.3_2016.03.06 to
"["
- + (isotopeNumber <= 0 ? "" : "" + isotopeNumber) + sym
+ + (isotopeNumber <= 0 ? "" : "" + isotopeNumber)
+ + sym
+ + (stereo == null ? "" : stereo)
+ + (nH > 1 ? "H" + nH : nH == 1 ? "H" : "")
+ (charge < 0 && charge != Integer.MIN_VALUE ? "" + charge
: charge > 0 ? "+" + charge : "")
- + (stereo == null ? "" : stereo)
- + (nH > 1 ? "H" + nH : nH == 1 ? "H" : "")
+ + (osclass == 0 ? "" : ":" + (int) osclass)
+ "]");
}
@@ -807,4 +816,11 @@
+ "]";
}
+ @Override
+ public float getFloatProperty(String property) {
+ if (property == "property_osclass") // == is OK here.
+ return osClass;
+ return Float.NaN;
+ }
+
}
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
2016-03-06 18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java
2016-03-07 04:22:42 UTC (rev 20982)
@@ -86,6 +86,7 @@
private boolean addAtomComment;
private boolean noBioComment;
private boolean noStereo;
+ private boolean openSMILES;
public P3 stereoReference;
private SmilesStereo smilesStereo;
private boolean isPolyhedral;
@@ -99,13 +100,15 @@
return "";
this.atoms = atoms;
this.ac = ac;
- addAtomComment = ((flags & JC.SMILES_ATOM_COMMENT) ==
JC.SMILES_ATOM_COMMENT);
bsSelected = BSUtil.copy(bsSelected);
-
+
+ // note -- some of these are 2-bit flags, so we need to use (flags & X) ==
X
if ((flags & JC.SMILES_BIO) == JC.SMILES_BIO)
return getBioSmiles(bsSelected, comment, flags);
this.bsSelected = bsSelected;
+ openSMILES = ((flags & JC.SMILES_TYPE_OPENSMILES) ==
JC.SMILES_TYPE_OPENSMILES);
+ addAtomComment = ((flags & JC.SMILES_ATOM_COMMENT) ==
JC.SMILES_ATOM_COMMENT);
explicitH = ((flags & JC.SMILES_EXPLICIT_H) == JC.SMILES_EXPLICIT_H);
topologyOnly = ((flags & JC.SMILES_TOPOLOGY) == JC.SMILES_TOPOLOGY);
getAromatic = !((flags & JC.SMILES_NOAROMATIC) == JC.SMILES_NOAROMATIC);
@@ -704,6 +707,7 @@
int charge = atom.getFormalCharge();
int isotope = atom.getIsotopeNumber();
int valence = atom.getValence();
+ float osclass = (openSMILES ? atom.getFloatProperty("property_osclass") :
0);
String atomName = atom.getAtomName();
String groupType = (atom instanceof BNode ?
((BNode)atom).getBioStructureTypeName() : "");
// for bioSMARTS we provide the connecting atom if
@@ -717,7 +721,7 @@
addBracketedBioName(sb, atom, "." + atomName, false);
else
sb.append(SmilesAtom
- .getAtomLabel(atomicNumber, isotope, (forceBrackets ? -1 : valence),
charge, nH, isAromatic,
+ .getAtomLabel(atomicNumber, isotope, (forceBrackets ? -1 : valence),
charge, osclass, nH, isAromatic,
atat != null ? atat : noStereo ? null : checkStereoPairs(atom,
atomIndex, stereo, stereoFlag)));
sb.appendSB(sMore);
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2016-03-06
18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2016-03-07
04:22:42 UTC (rev 20982)
@@ -285,16 +285,17 @@
}
/**
- * called by ForceFieldMMFF.setAtomTypes
+ * called by ForceFieldMMFF.setAtomTypes only
*
*/
@Override
- public void getSubstructureSets(String[] smarts, Node[] atoms, int ac,
- int flags, BS bsSelected, Lst<BS> ret,
+ public void getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac,
+ BS bsSelected, Lst<BS> ret,
Lst<BS>[] vRings) throws Exception {
InvalidSmilesException.clear();
SmilesParser sp = new SmilesParser(true);
SmilesSearch search = null;
+ int flags = (SmilesSearch.FLAG_AROMATIC_STRICT |
SmilesSearch.FLAG_AROMATIC_DOUBLE);
search = sp.parse("");
search.firstMatchOnly = false;
search.matchAllAtoms = false;
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-03-06
18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-03-07
04:22:42 UTC (rev 20982)
@@ -25,16 +25,16 @@
package org.jmol.smiles;
+import java.util.Hashtable;
+import java.util.Map;
+
import javajs.util.Lst;
import javajs.util.PT;
import javajs.util.SB;
-import java.util.Hashtable;
-import java.util.Map;
-
import org.jmol.util.Elements;
-import org.jmol.util.Edge;
import org.jmol.util.Logger;
+import org.jmol.viewer.JC;
/**
* Parses a SMILES String to create a <code>SmilesMolecule</code>.
@@ -121,6 +121,7 @@
private int braceCount;
private int branchLevel;
private boolean ignoreStereochemistry;
+ private boolean openSMILES;
public static SmilesSearch getMolecule(String pattern, boolean isSmarts)
throws InvalidSmilesException {
@@ -160,23 +161,27 @@
String strFlags = getSubPattern(pattern, 0, '/').toUpperCase();
pattern = pattern.substring(strFlags.length() + 2);
if (strFlags.indexOf("NONCANONICAL") >= 0)
- flags |= Edge.FLAG_AROMATIC_NONCANONICAL;
+ flags |= SmilesSearch.FLAG_AROMATIC_NONCANONICAL;
+ if (strFlags.indexOf("OPENSMILES") >= 0) {
+ flags |= JC.SMILES_TYPE_OPENSMILES;
+ openSMILES = true;
+ }
if (strFlags.indexOf("NOAROMATIC") >= 0)
- flags |= Edge.FLAG_NO_AROMATIC;
+ flags |= SmilesSearch.FLAG_NO_AROMATIC;
if (strFlags.indexOf("AROMATICSTRICT") >= 0)
- flags |= Edge.FLAG_AROMATIC_STRICT;
+ flags |= SmilesSearch.FLAG_AROMATIC_STRICT;
if (strFlags.indexOf("AROMATICDEFINED") >= 0)
- flags |= Edge.FLAG_AROMATIC_DEFINED;
+ flags |= SmilesSearch.FLAG_AROMATIC_DEFINED;
if (strFlags.indexOf("AROMATICDOUBLE") >= 0)
- flags |= Edge.FLAG_AROMATIC_DOUBLE;
+ flags |= SmilesSearch.FLAG_AROMATIC_DOUBLE;
if (strFlags.indexOf("NOSTEREO") >= 0) {
- flags |= Edge.FLAG_IGNORE_STEREOCHEMISTRY;
+ flags |= SmilesSearch.FLAG_IGNORE_STEREOCHEMISTRY;
ignoreStereochemistry = true;
} else if (strFlags.indexOf("INVERTSTEREO") >= 0) {
- if ((flags & Edge.FLAG_INVERT_STEREOCHEMISTRY) != 0)
- flags &= ~Edge.FLAG_INVERT_STEREOCHEMISTRY;
+ if ((flags & SmilesSearch.FLAG_INVERT_STEREOCHEMISTRY) != 0)
+ flags &= ~SmilesSearch.FLAG_INVERT_STEREOCHEMISTRY;
else
- flags |= Edge.FLAG_INVERT_STEREOCHEMISTRY;
+ flags |= SmilesSearch.FLAG_INVERT_STEREOCHEMISTRY;
}
}
if (pattern.indexOf("$") >= 0)
@@ -920,6 +925,11 @@
index = SmilesStereo.checkChirality(pattern, index,
molecule.patternAtoms[newAtom.index]);
break;
+ case ':': //openSmiles application-dependent atom class
+ index = getDigits(pattern, index + 1, ret);
+ if (openSMILES)
+ newAtom.osClass = ret[0];
+ break;
default:
// SMARTS has ambiguities in terms of chaining without &.
// H alone is "one H atom"
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-03-06
18:23:15 UTC (rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-03-07
04:22:42 UTC (rev 20982)
@@ -40,6 +40,7 @@
import org.jmol.util.JmolMolecule;
import org.jmol.util.Logger;
import org.jmol.util.Node;
+import org.jmol.viewer.JC;
/**
* -- was SmilesMolecule,
@@ -58,7 +59,16 @@
sb.append("\nmolecular formula: " + getMolecularFormula(true, null,
false));
return sb.toString();
}
+
+ final static int FLAG_AROMATIC_NONCANONICAL = 0x400;
+ final static int FLAG_AROMATIC_DOUBLE = 0x200;
+ final static int FLAG_AROMATIC_DEFINED = 0x100;
+ final static int FLAG_AROMATIC_STRICT = 0x080;
+ final static int FLAG_INVERT_STEREOCHEMISTRY = 0x040;
+ final static int FLAG_IGNORE_STEREOCHEMISTRY = 0x020;
+ final static int FLAG_NO_AROMATIC = 0x010;
+
private final static int INITIAL_ATOMS = 16;
SmilesAtom[] patternAtoms = new SmilesAtom[INITIAL_ATOMS];
@@ -131,6 +141,7 @@
private boolean noAromatic;
private boolean aromaticDouble;
private boolean noncanonical;
+ private boolean openSMILES;
void setAtomArray() {
@@ -186,7 +197,7 @@
needAromatic = false;
if (needAromatic)
needRingData = true;
- boolean noAromatic = ((flags & Edge.FLAG_NO_AROMATIC) != 0);
+ boolean noAromatic = ((flags & FLAG_NO_AROMATIC) != 0);
needAromatic &= (bsA == null) & !noAromatic;
// when using "xxx".find("search","....")
// or $(...), the aromatic set has already been determined
@@ -203,8 +214,8 @@
@SuppressWarnings("unchecked")
void getRingData(boolean needRingData, int flags, Lst<BS>[] vRings)
throws InvalidSmilesException {
- boolean aromaticStrict = ((flags & Edge.FLAG_AROMATIC_STRICT) != 0);
- boolean aromaticDefined = ((flags & Edge.FLAG_AROMATIC_DEFINED) != 0);
+ boolean aromaticStrict = ((flags & FLAG_AROMATIC_STRICT) != 0);
+ boolean aromaticDefined = ((flags & FLAG_AROMATIC_DEFINED) != 0);
if (aromaticStrict && vRings == null)
vRings = AU.createArrayOfArrayList(4);
if (aromaticDefined && needAromatic) {
@@ -406,11 +417,13 @@
*
*/
- ignoreStereochemistry = ((flags & Edge.FLAG_IGNORE_STEREOCHEMISTRY) != 0);
- invertStereochemistry = ((flags & Edge.FLAG_INVERT_STEREOCHEMISTRY) != 0);
- noAromatic = ((flags & Edge.FLAG_NO_AROMATIC) != 0);
- noncanonical = ((flags & Edge.FLAG_AROMATIC_NONCANONICAL) != 0);
- aromaticDouble = ((flags & Edge.FLAG_AROMATIC_DOUBLE) != 0);
+ // flags are passed on from SmilesParser
+ aromaticDouble = ((flags & FLAG_AROMATIC_DOUBLE) != 0);
+ ignoreStereochemistry = ((flags & FLAG_IGNORE_STEREOCHEMISTRY) != 0);
+ invertStereochemistry = ((flags & FLAG_INVERT_STEREOCHEMISTRY) != 0);
+ noAromatic = ((flags & FLAG_NO_AROMATIC) != 0);
+ noncanonical = ((flags & FLAG_AROMATIC_NONCANONICAL) != 0);
+ openSMILES = ((flags & JC.SMILES_TYPE_OPENSMILES) ==
JC.SMILES_TYPE_OPENSMILES);
if (Logger.debugging && !isSilent)
Logger.debug("SmilesSearch processing " + pattern);
@@ -928,8 +941,8 @@
if (!noAromatic && !patternAtom.aromaticAmbiguous
&& isAromatic != bsAromatic.get(iAtom)) {
if (!noncanonical
- || patternAtom.getExplicitHydrogenCount() !=
- atom.getCovalentHydrogenCount())
+ || patternAtom.getExplicitHydrogenCount() != atom
+ .getCovalentHydrogenCount())
break;
}
@@ -985,33 +998,41 @@
+ atom.getImplicitHydrogenCount())
break;
- // r <n> ring of a given size
- if (ringData != null && patternAtom.ringSize >= -1) {
- if (patternAtom.ringSize <= 0) {
- if ((ringCounts[iAtom] == 0) != (patternAtom.ringSize == 0))
- break;
- } else {
- BS rd = ringData[patternAtom.ringSize == 500 ? 5
- : patternAtom.ringSize == 600 ? 6 : patternAtom.ringSize];
- if (rd == null || !rd.get(iAtom))
- break;
- if (!noAromatic)
- if (patternAtom.ringSize == 500) {
- if (!bsAromatic5.get(iAtom))
- break;
- } else if (patternAtom.ringSize == 600) {
- if (!bsAromatic6.get(iAtom))
- break;
- }
+ if (openSMILES) {
+ if (!Float.isNaN(patternAtom.osClass)
+ && patternAtom.osClass !=
atom.getFloatProperty("property_osclass"))
+ break;
+ }
+
+ if (ringData != null) {
+ // r <n> ring of a given size
+ if (patternAtom.ringSize >= -1) {
+ if (patternAtom.ringSize <= 0) {
+ if ((ringCounts[iAtom] == 0) != (patternAtom.ringSize == 0))
+ break;
+ } else {
+ BS rd = ringData[patternAtom.ringSize == 500 ? 5
+ : patternAtom.ringSize == 600 ? 6 : patternAtom.ringSize];
+ if (rd == null || !rd.get(iAtom))
+ break;
+ if (!noAromatic)
+ if (patternAtom.ringSize == 500) {
+ if (!bsAromatic5.get(iAtom))
+ break;
+ } else if (patternAtom.ringSize == 600) {
+ if (!bsAromatic6.get(iAtom))
+ break;
+ }
+ }
+ // R <n> a certain number of rings
+ if (patternAtom.ringMembership >= -1) {
+ // R --> -1 implies "!R0"
+ if (patternAtom.ringMembership == -1 ? ringCounts[iAtom] == 0
+ : ringCounts[iAtom] != patternAtom.ringMembership)
+ break;
+ }
}
}
- // R <n> a certain number of rings
- if (ringData != null && patternAtom.ringMembership >= -1) {
- // R --> -1 implies "!R0"
- if (patternAtom.ringMembership == -1 ? ringCounts[iAtom] == 0
- : ringCounts[iAtom] != patternAtom.ringMembership)
- break;
- }
// x <n>
if (patternAtom.ringConnectivity >= 0) {
// default > 0
Modified: branches/v14_4/Jmol/src/org/jmol/util/Edge.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/Edge.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/util/Edge.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -104,13 +104,6 @@
public int index = -1;
public int order;
- final public static int FLAG_AROMATIC_NONCANONICAL = 64;
- final public static int FLAG_AROMATIC_DOUBLE = 32;
- final public static int FLAG_AROMATIC_DEFINED = 16;
- final public static int FLAG_AROMATIC_STRICT = 8;
- final public static int FLAG_INVERT_STEREOCHEMISTRY = 4;
- final public static int FLAG_IGNORE_STEREOCHEMISTRY = 2;
- public final static int FLAG_NO_AROMATIC = 1;
abstract public int getAtomIndex1();
Modified: branches/v14_4/Jmol/src/org/jmol/util/Node.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/Node.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/util/Node.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -43,7 +43,14 @@
public int getIsotopeNumber();
public int getValence();
public void set(float x, float y, float z);
+
+ /**
+ * @param property "property_xxxx"
+ * @return value or Float.NaN
+ */
+ public float getFloatProperty(String property);
+
// abstracts out the essential pieces for SMARTS processing
public BS findAtomsLike(String substring);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -1067,6 +1067,7 @@
public static final int SMILES_TYPE_SMILES = 0x1;
public static final int SMILES_TYPE_SMARTS = 0x2;
+ public static final int SMILES_TYPE_OPENSMILES = 0x5;
public static final int SMILES_MATCH_ALL = 0x10;
public static final int SMILES_MATCH_ONE = 0x20;
Modified: trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java 2016-03-06
18:23:15 UTC (rev 20981)
+++ trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java 2016-03-07
04:22:42 UTC (rev 20982)
@@ -45,9 +45,8 @@
int ac, BS bsSelected,
int flags) throws Exception;
- public abstract void getSubstructureSets(String[] smarts, Node[] atoms, int
ac,
- int flags,
- BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings)
throws Exception;
+ public abstract void getMMFF94AtomTypes(String[] smarts, Node[] atoms, int
ac,
+ BS bsSelected, Lst<BS> bitSets,
Lst<BS>[] vRings) throws Exception;
public abstract String getSmiles(Node[] atoms, int ac, BS bsSelected,
String bioComment, int flags) throws
Exception;
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
2016-03-06 18:23:15 UTC (rev 20981)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
2016-03-07 04:22:42 UTC (rev 20982)
@@ -25,15 +25,13 @@
package org.jmol.minimize.forcefield;
import java.io.BufferedReader;
+import java.util.Hashtable;
+import java.util.Map;
import javajs.util.AU;
import javajs.util.Lst;
import javajs.util.PT;
-import java.util.Hashtable;
-
-import java.util.Map;
-
import org.jmol.api.SmilesMatcherInterface;
import org.jmol.java.BS;
import org.jmol.minimize.MinAngle;
@@ -47,7 +45,6 @@
import org.jmol.util.BSUtil;
import org.jmol.util.Elements;
import org.jmol.util.Escape;
-import org.jmol.util.Edge;
import org.jmol.util.Logger;
import org.jmol.viewer.JmolAsyncException;
@@ -870,8 +867,7 @@
// identifies that atom's MMFF94 type.
try {
- smartsMatcher.getSubstructureSets(smarts, atoms, atoms.length,
- Edge.FLAG_AROMATIC_STRICT | Edge.FLAG_AROMATIC_DOUBLE,
+ smartsMatcher.getMMFF94AtomTypes(smarts, atoms, atoms.length,
bsConnected, bitSets, vRings);
} catch (Exception e) {
Logger.error(e.toString());
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2016-03-06 18:23:15 UTC (rev
20981)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2016-03-07 04:22:42 UTC (rev
20982)
@@ -33,6 +33,7 @@
import javajs.util.T3;
import javajs.util.V3;
+import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolModulationSet;
import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
@@ -1420,4 +1421,18 @@
return (m.isBioModel ? ((BioModel) m).getUnitID(this, flags) : "");
}
+ @Override
+ public float getFloatProperty(String property) {
+ Object data = group.chain.model.ms.vwr.getDataObj(property, null,
+ JmolDataManager.DATA_TYPE_AF);
+ float f = 0;
+ if (data != null) {
+ try {
+ f = ((float[]) data)[i];
+ } catch (Exception e) {
+ }
+ }
+ return f;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -1272,7 +1272,8 @@
&& args[1].tok != T.off ? SV.sValue(args[1]) : "");
boolean isSequence = !isList && sFind.equalsIgnoreCase("SEQUENCE");
boolean isSeq = !isList && sFind.equalsIgnoreCase("SEQ");
- boolean isSmiles = !isList && sFind.equalsIgnoreCase("SMILES");
+ boolean isOpenSmiles = !isList && sFind.equalsIgnoreCase("OPENSMILES");
+ boolean isSmiles = isOpenSmiles || !isList &&
sFind.equalsIgnoreCase("SMILES");
boolean isSMARTS = !isList && sFind.equalsIgnoreCase("SMARTS");
boolean isChemical = !isList && sFind.equalsIgnoreCase("CHEMICAL");
boolean isMF = !isList && sFind.equalsIgnoreCase("MF");
@@ -1365,7 +1366,8 @@
| JC.SMILES_RETURN_FIRST);
ret = (map.length > 0 ? vwr.ms.getDihedralMap(map[0]) : new
int[0]);
} else {
- int smilesFlags = (isSmiles ? JC.SMILES_TYPE_SMILES
+ int smilesFlags = (isOpenSmiles ? JC.SMILES_TYPE_OPENSMILES
+ : isSmiles ? JC.SMILES_TYPE_SMILES
: JC.SMILES_TYPE_SMARTS)
| (isON && sFind.length() == 0 ? JC.SMILES_BIO_COV_CROSSLINK
| JC.SMILES_BIO_COMMENT : 0);
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -180,6 +180,7 @@
private Node matchingNode;
public boolean hasSubpattern;
public int mapIndex = -1; // in CCC we have atoms 0, 1, and 2
+ public float osClass = Float.NaN; // OpenSMILES atom class is an integer
public SmilesAtom setAll(int iComponent, int ptAtom, int atomicNumber,
int charge) {
@@ -716,18 +717,21 @@
}
/**
+ *
+ * called from SmilesGenerator
*
* @param atomicNumber
* @param isotopeNumber
* @param valence set -1 to force brackets
* @param charge
+ * @param osclass OpenSMILES value
* @param nH
* @param isAromatic
* @param stereo
* @return label
*/
static String getAtomLabel(int atomicNumber, int isotopeNumber, int valence,
- int charge, int nH, boolean isAromatic,
+ int charge, float osclass, int nH, boolean
isAromatic,
String stereo) {
String sym = Elements.elementSymbolFromNumber(atomicNumber);
if (isAromatic) {
@@ -735,15 +739,20 @@
if (atomicNumber != 6)
valence = Integer.MAX_VALUE; // force [n]
}
- int count = (stereo == null || stereo.length() > 0 || isotopeNumber != 0
|| charge != 0 ? -1
+ int count = (isotopeNumber != 0
+ || stereo != null && stereo.length() > 0
+ || charge != 0 || osclass != 0 ? -1
: getDefaultCount(atomicNumber, false));
return (count == valence ? sym :
+ // rearranged 14.5.3_2016.03.06 to
"["
- + (isotopeNumber <= 0 ? "" : "" + isotopeNumber) + sym
+ + (isotopeNumber <= 0 ? "" : "" + isotopeNumber)
+ + sym
+ + (stereo == null ? "" : stereo)
+ + (nH > 1 ? "H" + nH : nH == 1 ? "H" : "")
+ (charge < 0 && charge != Integer.MIN_VALUE ? "" + charge
: charge > 0 ? "+" + charge : "")
- + (stereo == null ? "" : stereo)
- + (nH > 1 ? "H" + nH : nH == 1 ? "H" : "")
+ + (osclass == 0 ? "" : ":" + (int) osclass)
+ "]");
}
@@ -807,4 +816,11 @@
+ "]";
}
+ @Override
+ public float getFloatProperty(String property) {
+ if (property == "property_osclass") // == is OK here.
+ return osClass;
+ return Float.NaN;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -86,6 +86,7 @@
private boolean addAtomComment;
private boolean noBioComment;
private boolean noStereo;
+ private boolean openSMILES;
public P3 stereoReference;
private SmilesStereo smilesStereo;
private boolean isPolyhedral;
@@ -99,13 +100,15 @@
return "";
this.atoms = atoms;
this.ac = ac;
- addAtomComment = ((flags & JC.SMILES_ATOM_COMMENT) ==
JC.SMILES_ATOM_COMMENT);
bsSelected = BSUtil.copy(bsSelected);
-
+
+ // note -- some of these are 2-bit flags, so we need to use (flags & X) ==
X
if ((flags & JC.SMILES_BIO) == JC.SMILES_BIO)
return getBioSmiles(bsSelected, comment, flags);
this.bsSelected = bsSelected;
+ openSMILES = ((flags & JC.SMILES_TYPE_OPENSMILES) ==
JC.SMILES_TYPE_OPENSMILES);
+ addAtomComment = ((flags & JC.SMILES_ATOM_COMMENT) ==
JC.SMILES_ATOM_COMMENT);
explicitH = ((flags & JC.SMILES_EXPLICIT_H) == JC.SMILES_EXPLICIT_H);
topologyOnly = ((flags & JC.SMILES_TOPOLOGY) == JC.SMILES_TOPOLOGY);
getAromatic = !((flags & JC.SMILES_NOAROMATIC) == JC.SMILES_NOAROMATIC);
@@ -704,6 +707,7 @@
int charge = atom.getFormalCharge();
int isotope = atom.getIsotopeNumber();
int valence = atom.getValence();
+ float osclass = (openSMILES ? atom.getFloatProperty("property_osclass") :
0);
String atomName = atom.getAtomName();
String groupType = (atom instanceof BNode ?
((BNode)atom).getBioStructureTypeName() : "");
// for bioSMARTS we provide the connecting atom if
@@ -717,7 +721,7 @@
addBracketedBioName(sb, atom, "." + atomName, false);
else
sb.append(SmilesAtom
- .getAtomLabel(atomicNumber, isotope, (forceBrackets ? -1 : valence),
charge, nH, isAromatic,
+ .getAtomLabel(atomicNumber, isotope, (forceBrackets ? -1 : valence),
charge, osclass, nH, isAromatic,
atat != null ? atat : noStereo ? null : checkStereoPairs(atom,
atomIndex, stereo, stereoFlag)));
sb.appendSB(sMore);
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -285,16 +285,17 @@
}
/**
- * called by ForceFieldMMFF.setAtomTypes
+ * called by ForceFieldMMFF.setAtomTypes only
*
*/
@Override
- public void getSubstructureSets(String[] smarts, Node[] atoms, int ac,
- int flags, BS bsSelected, Lst<BS> ret,
+ public void getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac,
+ BS bsSelected, Lst<BS> ret,
Lst<BS>[] vRings) throws Exception {
InvalidSmilesException.clear();
SmilesParser sp = new SmilesParser(true);
SmilesSearch search = null;
+ int flags = (SmilesSearch.FLAG_AROMATIC_STRICT |
SmilesSearch.FLAG_AROMATIC_DOUBLE);
search = sp.parse("");
search.firstMatchOnly = false;
search.matchAllAtoms = false;
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -25,16 +25,16 @@
package org.jmol.smiles;
+import java.util.Hashtable;
+import java.util.Map;
+
import javajs.util.Lst;
import javajs.util.PT;
import javajs.util.SB;
-import java.util.Hashtable;
-import java.util.Map;
-
import org.jmol.util.Elements;
-import org.jmol.util.Edge;
import org.jmol.util.Logger;
+import org.jmol.viewer.JC;
/**
* Parses a SMILES String to create a <code>SmilesMolecule</code>.
@@ -121,6 +121,7 @@
private int braceCount;
private int branchLevel;
private boolean ignoreStereochemistry;
+ private boolean openSMILES;
public static SmilesSearch getMolecule(String pattern, boolean isSmarts)
throws InvalidSmilesException {
@@ -160,23 +161,27 @@
String strFlags = getSubPattern(pattern, 0, '/').toUpperCase();
pattern = pattern.substring(strFlags.length() + 2);
if (strFlags.indexOf("NONCANONICAL") >= 0)
- flags |= Edge.FLAG_AROMATIC_NONCANONICAL;
+ flags |= SmilesSearch.FLAG_AROMATIC_NONCANONICAL;
+ if (strFlags.indexOf("OPENSMILES") >= 0) {
+ flags |= JC.SMILES_TYPE_OPENSMILES;
+ openSMILES = true;
+ }
if (strFlags.indexOf("NOAROMATIC") >= 0)
- flags |= Edge.FLAG_NO_AROMATIC;
+ flags |= SmilesSearch.FLAG_NO_AROMATIC;
if (strFlags.indexOf("AROMATICSTRICT") >= 0)
- flags |= Edge.FLAG_AROMATIC_STRICT;
+ flags |= SmilesSearch.FLAG_AROMATIC_STRICT;
if (strFlags.indexOf("AROMATICDEFINED") >= 0)
- flags |= Edge.FLAG_AROMATIC_DEFINED;
+ flags |= SmilesSearch.FLAG_AROMATIC_DEFINED;
if (strFlags.indexOf("AROMATICDOUBLE") >= 0)
- flags |= Edge.FLAG_AROMATIC_DOUBLE;
+ flags |= SmilesSearch.FLAG_AROMATIC_DOUBLE;
if (strFlags.indexOf("NOSTEREO") >= 0) {
- flags |= Edge.FLAG_IGNORE_STEREOCHEMISTRY;
+ flags |= SmilesSearch.FLAG_IGNORE_STEREOCHEMISTRY;
ignoreStereochemistry = true;
} else if (strFlags.indexOf("INVERTSTEREO") >= 0) {
- if ((flags & Edge.FLAG_INVERT_STEREOCHEMISTRY) != 0)
- flags &= ~Edge.FLAG_INVERT_STEREOCHEMISTRY;
+ if ((flags & SmilesSearch.FLAG_INVERT_STEREOCHEMISTRY) != 0)
+ flags &= ~SmilesSearch.FLAG_INVERT_STEREOCHEMISTRY;
else
- flags |= Edge.FLAG_INVERT_STEREOCHEMISTRY;
+ flags |= SmilesSearch.FLAG_INVERT_STEREOCHEMISTRY;
}
}
if (pattern.indexOf("$") >= 0)
@@ -920,6 +925,11 @@
index = SmilesStereo.checkChirality(pattern, index,
molecule.patternAtoms[newAtom.index]);
break;
+ case ':': //openSmiles application-dependent atom class
+ index = getDigits(pattern, index + 1, ret);
+ if (openSMILES)
+ newAtom.osClass = ret[0];
+ break;
default:
// SMARTS has ambiguities in terms of chaining without &.
// H alone is "one H atom"
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-03-06 18:23:15 UTC
(rev 20981)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -40,6 +40,7 @@
import org.jmol.util.JmolMolecule;
import org.jmol.util.Logger;
import org.jmol.util.Node;
+import org.jmol.viewer.JC;
/**
* -- was SmilesMolecule,
@@ -58,7 +59,16 @@
sb.append("\nmolecular formula: " + getMolecularFormula(true, null,
false));
return sb.toString();
}
+
+ final static int FLAG_AROMATIC_NONCANONICAL = 0x400;
+ final static int FLAG_AROMATIC_DOUBLE = 0x200;
+ final static int FLAG_AROMATIC_DEFINED = 0x100;
+ final static int FLAG_AROMATIC_STRICT = 0x080;
+ final static int FLAG_INVERT_STEREOCHEMISTRY = 0x040;
+ final static int FLAG_IGNORE_STEREOCHEMISTRY = 0x020;
+ final static int FLAG_NO_AROMATIC = 0x010;
+
private final static int INITIAL_ATOMS = 16;
SmilesAtom[] patternAtoms = new SmilesAtom[INITIAL_ATOMS];
@@ -131,6 +141,7 @@
private boolean noAromatic;
private boolean aromaticDouble;
private boolean noncanonical;
+ private boolean openSMILES;
void setAtomArray() {
@@ -186,7 +197,7 @@
needAromatic = false;
if (needAromatic)
needRingData = true;
- boolean noAromatic = ((flags & Edge.FLAG_NO_AROMATIC) != 0);
+ boolean noAromatic = ((flags & FLAG_NO_AROMATIC) != 0);
needAromatic &= (bsA == null) & !noAromatic;
// when using "xxx".find("search","....")
// or $(...), the aromatic set has already been determined
@@ -203,8 +214,8 @@
@SuppressWarnings("unchecked")
void getRingData(boolean needRingData, int flags, Lst<BS>[] vRings)
throws InvalidSmilesException {
- boolean aromaticStrict = ((flags & Edge.FLAG_AROMATIC_STRICT) != 0);
- boolean aromaticDefined = ((flags & Edge.FLAG_AROMATIC_DEFINED) != 0);
+ boolean aromaticStrict = ((flags & FLAG_AROMATIC_STRICT) != 0);
+ boolean aromaticDefined = ((flags & FLAG_AROMATIC_DEFINED) != 0);
if (aromaticStrict && vRings == null)
vRings = AU.createArrayOfArrayList(4);
if (aromaticDefined && needAromatic) {
@@ -406,11 +417,13 @@
*
*/
- ignoreStereochemistry = ((flags & Edge.FLAG_IGNORE_STEREOCHEMISTRY) != 0);
- invertStereochemistry = ((flags & Edge.FLAG_INVERT_STEREOCHEMISTRY) != 0);
- noAromatic = ((flags & Edge.FLAG_NO_AROMATIC) != 0);
- noncanonical = ((flags & Edge.FLAG_AROMATIC_NONCANONICAL) != 0);
- aromaticDouble = ((flags & Edge.FLAG_AROMATIC_DOUBLE) != 0);
+ // flags are passed on from SmilesParser
+ aromaticDouble = ((flags & FLAG_AROMATIC_DOUBLE) != 0);
+ ignoreStereochemistry = ((flags & FLAG_IGNORE_STEREOCHEMISTRY) != 0);
+ invertStereochemistry = ((flags & FLAG_INVERT_STEREOCHEMISTRY) != 0);
+ noAromatic = ((flags & FLAG_NO_AROMATIC) != 0);
+ noncanonical = ((flags & FLAG_AROMATIC_NONCANONICAL) != 0);
+ openSMILES = ((flags & JC.SMILES_TYPE_OPENSMILES) ==
JC.SMILES_TYPE_OPENSMILES);
if (Logger.debugging && !isSilent)
Logger.debug("SmilesSearch processing " + pattern);
@@ -928,8 +941,8 @@
if (!noAromatic && !patternAtom.aromaticAmbiguous
&& isAromatic != bsAromatic.get(iAtom)) {
if (!noncanonical
- || patternAtom.getExplicitHydrogenCount() !=
- atom.getCovalentHydrogenCount())
+ || patternAtom.getExplicitHydrogenCount() != atom
+ .getCovalentHydrogenCount())
break;
}
@@ -985,33 +998,41 @@
+ atom.getImplicitHydrogenCount())
break;
- // r <n> ring of a given size
- if (ringData != null && patternAtom.ringSize >= -1) {
- if (patternAtom.ringSize <= 0) {
- if ((ringCounts[iAtom] == 0) != (patternAtom.ringSize == 0))
- break;
- } else {
- BS rd = ringData[patternAtom.ringSize == 500 ? 5
- : patternAtom.ringSize == 600 ? 6 : patternAtom.ringSize];
- if (rd == null || !rd.get(iAtom))
- break;
- if (!noAromatic)
- if (patternAtom.ringSize == 500) {
- if (!bsAromatic5.get(iAtom))
- break;
- } else if (patternAtom.ringSize == 600) {
- if (!bsAromatic6.get(iAtom))
- break;
- }
+ if (openSMILES) {
+ if (!Float.isNaN(patternAtom.osClass)
+ && patternAtom.osClass !=
atom.getFloatProperty("property_osclass"))
+ break;
+ }
+
+ if (ringData != null) {
+ // r <n> ring of a given size
+ if (patternAtom.ringSize >= -1) {
+ if (patternAtom.ringSize <= 0) {
+ if ((ringCounts[iAtom] == 0) != (patternAtom.ringSize == 0))
+ break;
+ } else {
+ BS rd = ringData[patternAtom.ringSize == 500 ? 5
+ : patternAtom.ringSize == 600 ? 6 : patternAtom.ringSize];
+ if (rd == null || !rd.get(iAtom))
+ break;
+ if (!noAromatic)
+ if (patternAtom.ringSize == 500) {
+ if (!bsAromatic5.get(iAtom))
+ break;
+ } else if (patternAtom.ringSize == 600) {
+ if (!bsAromatic6.get(iAtom))
+ break;
+ }
+ }
+ // R <n> a certain number of rings
+ if (patternAtom.ringMembership >= -1) {
+ // R --> -1 implies "!R0"
+ if (patternAtom.ringMembership == -1 ? ringCounts[iAtom] == 0
+ : ringCounts[iAtom] != patternAtom.ringMembership)
+ break;
+ }
}
}
- // R <n> a certain number of rings
- if (ringData != null && patternAtom.ringMembership >= -1) {
- // R --> -1 implies "!R0"
- if (patternAtom.ringMembership == -1 ? ringCounts[iAtom] == 0
- : ringCounts[iAtom] != patternAtom.ringMembership)
- break;
- }
// x <n>
if (patternAtom.ringConnectivity >= 0) {
// default > 0
Modified: trunk/Jmol/src/org/jmol/util/Edge.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Edge.java 2016-03-06 18:23:15 UTC (rev
20981)
+++ trunk/Jmol/src/org/jmol/util/Edge.java 2016-03-07 04:22:42 UTC (rev
20982)
@@ -104,13 +104,6 @@
public int index = -1;
public int order;
- final public static int FLAG_AROMATIC_NONCANONICAL = 64;
- final public static int FLAG_AROMATIC_DOUBLE = 32;
- final public static int FLAG_AROMATIC_DEFINED = 16;
- final public static int FLAG_AROMATIC_STRICT = 8;
- final public static int FLAG_INVERT_STEREOCHEMISTRY = 4;
- final public static int FLAG_IGNORE_STEREOCHEMISTRY = 2;
- public final static int FLAG_NO_AROMATIC = 1;
abstract public int getAtomIndex1();
Modified: trunk/Jmol/src/org/jmol/util/Node.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Node.java 2016-03-06 18:23:15 UTC (rev
20981)
+++ trunk/Jmol/src/org/jmol/util/Node.java 2016-03-07 04:22:42 UTC (rev
20982)
@@ -43,7 +43,14 @@
public int getIsotopeNumber();
public int getValence();
public void set(float x, float y, float z);
+
+ /**
+ * @param property "property_xxxx"
+ * @return value or Float.NaN
+ */
+ public float getFloatProperty(String property);
+
// abstracts out the essential pieces for SMARTS processing
public BS findAtomsLike(String substring);
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2016-03-06 18:23:15 UTC (rev
20981)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2016-03-07 04:22:42 UTC (rev
20982)
@@ -1067,23 +1067,24 @@
public static final int SMILES_TYPE_SMILES = 0x1;
public static final int SMILES_TYPE_SMARTS = 0x2;
+ public static final int SMILES_TYPE_OPENSMILES = 0x5;
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_NOSTEREO = 0x00800;
- public static final int SMILES_POLYHEDRAL = 0x01000;
- public static final int SMILES_BIO = 0x10000;
- public static final int SMILES_BIO_ALLOW_UNMATCHED_RINGS = 0x11000;
- public static final int SMILES_BIO_COV_CROSSLINK = 0x12000;
- public static final int SMILES_BIO_HH_CROSSLINK = 0x16000;
- public static final int SMILES_BIO_COMMENT = 0x30000;
- public static final int SMILES_BIO_NOCOMMENTS = 0x50000;
- public static final int SMILES_ATOM_COMMENT = 0x80000;
+ public static final int SMILES_EXPLICIT_H = 0x000100;
+ public static final int SMILES_TOPOLOGY = 0x000200;
+ public static final int SMILES_NOAROMATIC = 0x000400;
+ public static final int SMILES_NOSTEREO = 0x000800;
+ public static final int SMILES_POLYHEDRAL = 0x001000;
+ public static final int SMILES_ATOM_COMMENT = 0x002000;
+ public static final int SMILES_BIO = 0x010000;
+ public static final int SMILES_BIO_ALLOW_UNMATCHED_RINGS = 0x030000;
+ public static final int SMILES_BIO_COV_CROSSLINK = 0x050000;
+ public static final int SMILES_BIO_HH_CROSSLINK = 0x090000;
+ public static final int SMILES_BIO_COMMENT = 0x110000;
+ public static final int SMILES_BIO_NOCOMMENTS = 0x210000;
public static final int JSV_NOT = -1;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-06 18:23:15 UTC
(rev 20981)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-07 04:22:42 UTC
(rev 20982)
@@ -67,6 +67,17 @@
Jmol.___JmolVersion="14.5.3_2016.03.06"
+new feature: optional processing of OpenSMILES [CH2:002] ":<n>" atom class.
+ -- positive integer value only
+ -- checks the atom property property_osclass
+ -- for SMARTS, [:0] means "without an osclass"
+ -- for SMARTS, [!:0] means "any non-zero osclass"
+ -- for SMARTS, same as [$(select property_osclass=n)]
+ -- only enabled with Jmol SMILES directive "/opensmiles/"; otherwise ignored
+
+new feature: {*}.find("OPENSMILES")
+ -- adds atom class if property_osclass is nonzero
+
bug fix: Inconsistent use of "DIASTEREOMERS" (preferred) and "DIASTERIOMERS"
(incorrect)
JmolVersion="14.5.3_2016.03.05"
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
