Revision: 20759
http://sourceforge.net/p/jmol/code/20759
Author: hansonr
Date: 2015-09-06 20:54:56 +0000 (Sun, 06 Sep 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.09.06"
bug fix: after atom deletion, atom iterator still finds atoms.
-- was not reinitializing the binary search after atom deletion
-- affects polyhedra, within()
$ load $caffeine
$ delete _N
4 atoms deleted
$ print {*}.count
20
$ print within(14.0, {c6}).count
24
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Added Paths:
-----------
trunk/Jmol/src/org/jmol/smiles/PolyhedronStereoSorter.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-09-06 04:11:42 UTC
(rev 20758)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-09-06 20:54:56 UTC
(rev 20759)
@@ -3047,6 +3047,7 @@
am[i].dssrCache = null;
}
deleteBonds(bsBonds, false);
+ validateBspf(false);
}
// atom addition //
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-09-06 04:11:42 UTC
(rev 20758)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-09-06 20:54:56 UTC
(rev 20759)
@@ -193,7 +193,7 @@
case T.search:
case T.smiles:
case T.substructure:
- return evaluateSubstructure(mp, args, tok);
+ return evaluateSubstructure(mp, args, tok, op.tok == T.propselector);
case T.sort:
case T.count:
return evaluateSort(mp, args, tok);
@@ -2624,19 +2624,21 @@
}
private boolean evaluateSubstructure(ScriptMathProcessor mp, SV[] args,
- int tok) throws ScriptException {
+ int tok, boolean isSelector)
+ throws ScriptException {
// select substucture(....) legacy - was same as smiles(), now search()
// select smiles(...)
// select search(...) now same as substructure
- if (args.length == 0)
+ // print {*}.search(...)
+ if (args.length == 0 || isSelector && args.length != 1)
return false;
BS bs = new BS();
String pattern = SV.sValue(args[0]);
if (pattern.length() > 0)
try {
- BS bsSelected = (args.length == 2 && args[1].tok == T.bitset ? SV
- .bsSelectVar(args[1]) : null);
- // BS bsSelected, boolean isSmarts, boolean
firstMatchOnly
+ BS bsSelected = (isSelector ? SV.bsSelectVar(mp.getX())
+ : args.length == 2 && args[1].tok == T.bitset ? SV
+ .bsSelectVar(args[1]) : null);
bs = vwr.getSmilesMatcher().getSubstructureSet(pattern, vwr.ms.at,
vwr.ms.ac, bsSelected,
(tok == T.smiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS));
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-09-06 04:11:42 UTC
(rev 20758)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedra.java 2015-09-06 20:54:56 UTC
(rev 20759)
@@ -86,7 +86,7 @@
private int nVertices;
float faceCenterOffset;
- float distanceFactor = Float.NaN;
+// float distanceFactor = Float.NaN;
boolean isCollapsed;
private boolean iHaveCenterBitSet;
@@ -109,7 +109,8 @@
if ("init" == propertyName) {
faceCenterOffset = DEFAULT_FACECENTEROFFSET;
- distanceFactor = planarParam = Float.NaN;
+ //distanceFactor =
+ planarParam = Float.NaN;
radius = 0.0f;
nVertices = 0;
nPoints = 0;
@@ -190,7 +191,8 @@
if ("distanceFactor" == propertyName) {
// not a general user option
- distanceFactor = ((Float) value).floatValue();
+ // ignore
+ //distanceFactor = ((Float) value).floatValue();
return;
}
@@ -588,9 +590,9 @@
int nj = vertexCount - 1;
float planarParam = (Float.isNaN(this.planarParam) ? DEFAULT_PLANAR_PARAM
: this.planarParam);
- float factor = (!Float.isNaN(distanceFactor) ? distanceFactor
- : DEFAULT_DISTANCE_FACTOR);
- BS bs = BS.newN(vertexCount);
+// float factor = (!Float.isNaN(distanceFactor) ? distanceFactor
+// : DEFAULT_DISTANCE_FACTOR);
+// BS bs = BS.newN(vertexCount);
// here we are assuring that at least ONE face is drawn to
// all matching vertices -- skip this for BOND polyhedra
@@ -600,43 +602,43 @@
for (int i = 0; i < vertexCount; i++)
ptAve.add(points[i]);
ptAve.scale(1f / vertexCount);
- float distMax = 0;
- if (checkDist) {
- float dAverage = 0;
- for (int i = 0; i < vertexCount; i++)
- dAverage += points[vertexCount].distance(points[i]);
- dAverage /= vertexCount;
- boolean isOK = (dAverage == 0);
- while (!isOK && factor < 10.0f) {
- distMax = dAverage * factor;
- bs.setBits(0, vertexCount);
- for (int i = 0; i < ni; i++)
- for (int j = i + 1; j < nj; j++) {
- if (points[i].distance(points[j]) > distMax)
- continue;
- for (int k = j + 1; k < vertexCount; k++) {
- if (points[i].distance(points[k]) > distMax
- || points[j].distance(points[k]) > distMax)
- continue;
- bs.clear(i);
- bs.clear(j);
- bs.clear(k);
- }
- }
- isOK = true;
- for (int i = 0; i < vertexCount; i++)
- if (bs.get(i)) {
- isOK = false;
- factor *= 1.05f;
- if (Logger.debugging) {
- Logger.debug("Polyhedra distanceFactor for " + vertexCount
- + " atoms increased to " + factor + " in order to include "
- + points[i]);
- }
- break;
- }
- }
- }
+// float distMax = 0;
+// if (checkDist) {
+// float dAverage = 0;
+// for (int i = 0; i < vertexCount; i++)
+// dAverage += points[vertexCount].distance(points[i]);
+// dAverage /= vertexCount;
+// boolean isOK = (dAverage == 0);
+// while (!isOK && factor < 10.0f) {
+// distMax = dAverage * factor;
+// bs.setBits(0, vertexCount);
+// for (int i = 0; i < ni; i++)
+// for (int j = i + 1; j < nj; j++) {
+// if (points[i].distance(points[j]) > distMax)
+// continue;
+// for (int k = j + 1; k < vertexCount; k++) {
+// if (points[i].distance(points[k]) > distMax
+// || points[j].distance(points[k]) > distMax)
+// continue;
+// bs.clear(i);
+// bs.clear(j);
+// bs.clear(k);
+// }
+// }
+// isOK = true;
+// for (int i = 0; i < vertexCount; i++)
+// if (bs.get(i)) {
+// isOK = false;
+// factor *= 1.05f;
+// if (Logger.debugging) {
+// Logger.debug("Polyhedra distanceFactor for " + vertexCount
+// + " atoms increased to " + factor + " in order to include "
+// + points[i]);
+// }
+// break;
+// }
+// }
+// }
/* Start by defining a face to be when all three distances
* are < distanceFactor * (longest central) but if a vertex is missed,
* then expand the range. The collapsed trick is to introduce
@@ -676,15 +678,15 @@
V3 vTemp = vAC;
for (int i = 0, pt = 0; i < ni; i++)
for (int j = i + 1; j < nj; j++) {
- if (checkDist && points[i].distance(points[j]) > distMax) {
- pt += vertexCount - j - 1;
- continue;
- }
+// if (checkDist && points[i].distance(points[j]) > distMax) {
+// pt += vertexCount - j - 1;
+// continue;
+// }
for (int k = j + 1; k < vertexCount; k++, pt++) {
- if (checkDist
- && (points[i].distance(points[k]) > distMax || points[j]
- .distance(points[k]) > distMax))
- continue;
+// if (checkDist
+// && (points[i].distance(points[k]) > distMax || points[j]
+// .distance(points[k]) > distMax))
+// continue;
if (planeCount >= fmax) {
Logger.error("Polyhedron error: maximum face(" + fmax
+ ") -- reduce RADIUS");
Added: trunk/Jmol/src/org/jmol/smiles/PolyhedronStereoSorter.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/PolyhedronStereoSorter.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/smiles/PolyhedronStereoSorter.java 2015-09-06
20:54:56 UTC (rev 20759)
@@ -0,0 +1,59 @@
+package org.jmol.smiles;
+
+import java.util.Comparator;
+
+import javajs.util.P3;
+import javajs.util.T3;
+import javajs.util.V3;
+
+class PolyhedronStereoSorter implements Comparator<Object[]> {
+
+ private V3 vTemp = new V3();
+ private V3 vRef;
+
+ PolyhedronStereoSorter() {
+ }
+
+ void setRef(V3 vRef) {
+ this.vRef = vRef;
+ }
+
+ /**
+ * Comparison is by torsion angle, as set previously and passed in as Float
a[1] and b[1].
+ * If these two are within 1 degree of each other, then we compare the dot
product of
+ * the reference vector and the vector from a to b, from points stored as
a[2] and b[2].
+ */
+ @Override
+ public int compare(Object[] a, Object[] b) {
+ float torA = ((Float) a[1]).floatValue();
+ float torB = ((Float) b[1]).floatValue();
+ if (Math.abs(torA - torB) < 1f) {
+ torA = 0;
+ vTemp.sub2((P3) b[2], (P3) a[2]);
+ torB = vRef.dot(vTemp);
+ }
+ return (torA < torB ? 1 : torA > torB ? -1 : 0);
+ }
+
+ private V3 align1 = new V3();
+ private V3 align2 = new V3();
+
+ private static final float MIN_ALIGNED = (float) (10f/180*Math.PI);
+
+ /**
+ * check alignment, within 10 degrees is considered aligned.
+ *
+ * @param pt1
+ * @param pt2
+ * @param pt3
+ * @return true if within 10 degrees
+ */
+ boolean isAligned(T3 pt1, T3 pt2, T3 pt3) {
+ align1.sub2(pt1, pt2);
+ align2.sub2(pt2, pt3);
+ float angle = align1.angle(align2);
+ return (angle < MIN_ALIGNED);
+ }
+
+
+}
\ No newline at end of file
Property changes on: trunk/Jmol/src/org/jmol/smiles/PolyhedronStereoSorter.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2015-09-06 04:11:42 UTC
(rev 20758)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2015-09-06 20:54:56 UTC
(rev 20759)
@@ -24,25 +24,22 @@
package org.jmol.smiles;
-import java.util.Comparator;
+import java.util.Hashtable;
import java.util.Iterator;
-import java.util.Hashtable;
import java.util.Map;
import javajs.util.Lst;
+import javajs.util.P3;
import javajs.util.SB;
-import javajs.util.P3;
import org.jmol.java.BS;
-
-
+import org.jmol.util.BNode;
import org.jmol.util.BSUtil;
+import org.jmol.util.Edge;
import org.jmol.util.Elements;
-import org.jmol.util.Edge;
import org.jmol.util.JmolMolecule;
-import org.jmol.util.BNode;
+import org.jmol.util.Logger;
import org.jmol.util.Node;
-import org.jmol.util.Logger;
import org.jmol.viewer.JC;
/**
@@ -90,6 +87,7 @@
private boolean noBioComment;
private boolean noStereo;
public P3 stereoReference;
+ private SmilesStereo smilesStereo;
// generation of SMILES strings
@@ -510,7 +508,13 @@
Edge[] bonds = atom.getEdges();
if (stereoReference != null) {
allowBranches = false;
- SmilesStereo.sortBondsByStereo(atom, prevAtom, stereoReference, bonds,
aTemp);
+ if (smilesStereo == null)
+ try {
+ smilesStereo = SmilesStereo.newStereo(null);
+ } catch (InvalidSmilesException e) {
+ // not possible
+ }
+ smilesStereo.sortBondsByStereo(atom, prevAtom, stereoReference, bonds,
vTemp.vA);
}
Node aH = null;
int stereoFlag = (isAromatic ? 10 : 0);
@@ -663,7 +667,7 @@
String atat = null;
if (!allowBranches && !noStereo && stereoReference == null && (v.size() ==
5 || v.size() == 6))
- atat = sortInorganic(atom, v);
+ atat = sortInorganic(atom, v, vTemp);
for (int i = 0; i < v.size(); i++) {
Edge bond = v.get(i);
if (bond == bond0)
@@ -744,8 +748,6 @@
return atomNext;
}
- private Object[] aTemp;
-
/**
* We must sort the bond vector such that a diaxial pair is
* first and last. Then we assign stereochemistry based on what
@@ -755,9 +757,10 @@
*
* @param atom
* @param v
+ * @param vTemp
* @return "@" or "@@" or ""
*/
- private String sortInorganic(Node atom, Lst<Edge> v) {
+ private String sortInorganic(Node atom, Lst<Edge> v, VTemp vTemp) {
int atomIndex = atom.getIndex();
int n = v.size();
Lst<Edge[]> axialPairs = new Lst<Edge[]>();
@@ -929,18 +932,6 @@
return Math.min(i0, i1) + "_" + Math.max(i0, i1);
}
- class PolyhedronStereoSorter implements Comparator<Object> {
-
- protected PolyhedronStereoSorter() { }
-
- @Override
- public int compare(Object a, Object b) {
- float torA = ((Float) ((Object[]) a)[1]).floatValue();
- float torB = ((Float) ((Object[]) b)[1]).floatValue();
- return (torA < torB ? 1 : torA > torB ? -1 : 0);
- }
- }
-
//static {
// T3 atom = P3.new3(0, 0.0001f, -1);
// T3 atomPrev = P3.new3(0, 0 , 1);
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2015-09-06 04:11:42 UTC
(rev 20758)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2015-09-06 20:54:56 UTC
(rev 20759)
@@ -898,7 +898,7 @@
break;
case '@':
if (molecule.stereo == null)
- molecule.stereo = new SmilesStereo(0, 0, 0, null, null);
+ molecule.stereo = SmilesStereo.newStereo(null);
index = SmilesStereo.checkChirality(pattern, index,
molecule.patternAtoms[newAtom.index]);
break;
default:
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2015-09-06 04:11:42 UTC
(rev 20758)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2015-09-06 20:54:56 UTC
(rev 20759)
@@ -33,7 +33,6 @@
import javajs.util.T3;
import javajs.util.V3;
-import org.jmol.smiles.SmilesGenerator.PolyhedronStereoSorter;
import org.jmol.util.Edge;
import org.jmol.util.Escape;
import org.jmol.util.Logger;
@@ -42,7 +41,7 @@
//import org.jmol.util.Logger;
/**
- * This class relates to stereochemical issues.
+ * This class relates to stereochemical issues.
*/
public class SmilesStereo {
@@ -66,13 +65,15 @@
return ("0;PH;AL;33;TH;TP;OH;77;SP;".indexOf(xx) + 1) / 3;
}
- public static SmilesStereo newStereo(SmilesStereo stereo) throws
InvalidSmilesException {
- SmilesStereo s = new SmilesStereo(stereo.chiralClass, stereo.chiralOrder,
- stereo.atomCount, stereo.details, stereo.directives);
- return s;
+ public static SmilesStereo newStereo(SmilesStereo stereo)
+ throws InvalidSmilesException {
+ return (stereo == null ? new SmilesStereo(0, 0, 0, null, null)
+ : new SmilesStereo(stereo.chiralClass, stereo.chiralOrder,
+ stereo.atomCount, stereo.details, stereo.directives));
}
- SmilesStereo(int chiralClass, int chiralOrder, int atomCount, String
details, String directives) throws InvalidSmilesException {
+ SmilesStereo(int chiralClass, int chiralOrder, int atomCount, String details,
+ String directives) throws InvalidSmilesException {
this.chiralClass = chiralClass;
this.chiralOrder = chiralOrder;
this.atomCount = atomCount;
@@ -84,8 +85,8 @@
private int[][] polyhedralOrders;
private boolean isNot;
- static PolyhedronStereoSorter polyhedronStereoSorter;
-
+ private PolyhedronStereoSorter sorter;
+
private void getPolyhedralOrders() throws InvalidSmilesException {
int[][] po = polyhedralOrders = AU.newInt2(atomCount);
if (details == null)
@@ -127,8 +128,8 @@
default:
index = SmilesParser.getRingNumber(s, index, ch, ret);
pt = temp[n++] = ret[0] - 1;
- if (pt == atomPt)
- msg = "Atom cannot connect to itself";
+ if (pt == atomPt)
+ msg = "Atom cannot connect to itself";
else if (pt < 0 || pt >= atomCount)
msg = "Connection number outside of range (1-" + atomCount + ")";
else if (n >= atomCount)
@@ -234,9 +235,8 @@
return false;
int chiralClass = atom.stereo.chiralClass;
int chiralOrder = atom.stereo.chiralOrder;
- Node a2 = (chiralClass == STEREOCHEMISTRY_ALLENE
- || chiralClass == 3 ? a2 = jmolAtoms[sAtom2.getMatchingAtomIndex()]
- : null);
+ Node a2 = (chiralClass == STEREOCHEMISTRY_ALLENE || chiralClass == 3 ? a2
= jmolAtoms[sAtom2
+ .getMatchingAtomIndex()] : null);
// set the chirality center at the origin
atom.set(0, 0, 0);
@@ -349,11 +349,11 @@
v.sub((P3) jn[i]);
}
if (v.length() == 0) {
- v.setT(((P3)jn[4]));
+ v.setT(((P3) jn[4]));
doSwitch = false;
} else {
- v.scaleAdd2(n + 1,(P3) getJmolAtom(sAtom.getMatchingAtomIndex()), v);
- doSwitch = search.isSmilesFind || doSwitch ;
+ v.scaleAdd2(n + 1, (P3) getJmolAtom(sAtom.getMatchingAtomIndex()),
v);
+ doSwitch = search.isSmilesFind || doSwitch;
}
jn[pt] = new SmilesAtom().setIndex(-1);
((P3) jn[pt]).setT(v);
@@ -377,50 +377,52 @@
jn[pt - 1] = a;
}
}
-
private Node getJmolAtom(int i) {
return (i < 0 || i >= jmolAtoms.length ? null : jmolAtoms[i]);
}
/**
- * Sort bond array as ccw rotation around the axis connecting the
- * atom and the reference point (polyhedron center) as seen from
- * outside the polyhedron looking in.
+ * Sort bond array as ccw rotation around the axis connecting the atom and
the
+ * reference point (polyhedron center) as seen from outside the polyhedron
+ * looking in.
*
* Since we are allowing no branching, all atoms will appear as separate
* components with only numbers after them. These numbers will be processed
- * and listed in this order.
+ * and listed in this order.
*
* @param atom
* @param atomPrev
* @param ref
* @param bonds
- * @param aTemp
+ * @param vTemp
*/
- static void sortBondsByStereo(Node atom, Node atomPrev, T3 ref, Edge[]
bonds, Object[] aTemp) {
+ void sortBondsByStereo(Node atom, Node atomPrev, T3 ref, Edge[] bonds,
+ V3 vTemp) {
if (bonds.length < 2 || !(atom instanceof T3))
return;
if (atomPrev == null)
atomPrev = bonds[0].getOtherAtomNode(atom);
- if (aTemp == null || aTemp.length != bonds.length)
- aTemp = new Object[bonds.length];
+ Object[][] aTemp = new Object[bonds.length][0];
+ if (sorter == null)
+ sorter = new PolyhedronStereoSorter();
+ vTemp.sub2((T3)atomPrev, ref);
+ sorter.setRef(vTemp);
for (int i = bonds.length; --i >= 0;) {
Node a = bonds[i].getOtherAtomNode(atom);
- float f = (a == atomPrev ? 0 : Measure.computeTorsion((T3) atom,
(T3)atomPrev, ref, (T3) a, true));
- if (Float.isNaN(f))
- f = 180; // directly across the center from the previous atom
+ float f = (a == atomPrev ? 0 :
+ sorter.isAligned((T3) a, ref, (T3) atomPrev) ? -999 :
+ Measure.computeTorsion((T3) atom,
+ (T3) atomPrev, ref, (T3) a, true));
if (bonds.length > 2)
f += 360;
- aTemp[i] = new Object[] {bonds[i], Float.valueOf(f) };
+ aTemp[i] = new Object[] { bonds[i], Float.valueOf(f), a };
}
- if (polyhedronStereoSorter == null)
- polyhedronStereoSorter = new SmilesGenerator().new
PolyhedronStereoSorter();
- Arrays.sort(aTemp, polyhedronStereoSorter);
+ Arrays.sort(aTemp, sorter);
if (Logger.debugging)
- Logger.info(Escape.e(aTemp)) ;
+ Logger.info(Escape.e(aTemp));
for (int i = bonds.length; --i >= 0;)
- bonds[i] = (Edge) ((Object[]) aTemp[i])[0];
+ bonds[i] = (Edge) aTemp[i][0];
}
public boolean checkStereoChemistry(SmilesSearch smilesSearch, VTemp v) {
@@ -430,7 +432,7 @@
boolean invertStereochemistry = smilesSearch.invertStereochemistry;
if (Logger.debugging)
- Logger.debug("checking stereochemistry...");
+ Logger.debug("checking sstereochemistry...");
//for debugging, first try SET DEBUG
//for (int i = 0; i < ac; i++) {
@@ -484,9 +486,9 @@
// can't process this unless it is tetrahedral or perhaps square
planar
if (sAtom.getBondCount() != 3)
return false;
- v.vA.set(0, 0, 0);
+ v.vA.set(0, 0, 0);
for (int j = 0; j < 3; j++)
- v.vA.add((T3)bonds[j].getOtherAtom(sAtom0).getMatchingAtom());
+ v.vA.add((T3) bonds[j].getOtherAtom(sAtom0).getMatchingAtom());
v.vA.scale(0.3333f);
v.vA.sub2((T3) atom0, v.vA);
v.vA.add((T3) atom0);
@@ -498,8 +500,9 @@
if (orders == null || orders.length < 2)
continue;
// the atom we are looking down
- pt = (j > jHpt ? j - nH: j);
- T3 ta1 = (j == jHpt ? v.vA : (T3)
bonds[pt].getOtherAtom(sAtom).getMatchingAtom());
+ pt = (j > jHpt ? j - nH : j);
+ T3 ta1 = (j == jHpt ? v.vA : (T3) bonds[pt].getOtherAtom(sAtom)
+ .getMatchingAtom());
float flast = (isNot ? Float.MAX_VALUE : 0);
T3 ta2 = null;
for (int k = 0; k < orders.length; k++) {
@@ -633,8 +636,8 @@
&& !setSmilesCoordinates(sAtom0, sAtom, sAtom2, new Node[] { atom1,
atom2, atom3, atom4, atom5, atom6 }))
return false;
- if (!checkStereochemistryAll(isNot, atom0,
- chiralClass, order, atom1, atom2, atom3, atom4, atom5, atom6, v))
+ if (!checkStereochemistryAll(isNot, atom0, chiralClass, order, atom1,
+ atom2, atom3, atom4, atom5, atom6, v))
return false;
continue;
@@ -652,7 +655,7 @@
* @param atoms
* @param nAtoms
* @param v
- * @return String
+ * @return String
*/
static String getStereoFlag(Node atom0, Node[] atoms, int nAtoms, VTemp v) {
Node atom1 = atoms[0];
@@ -668,23 +671,29 @@
case 5:
case 6:
// like tetrahedral
- return (checkStereochemistryAll(false, atom0, chiralClass, 1, atom1,
atom2, atom3, atom4, atom5, atom6, v)? "@" : "@@");
+ return (checkStereochemistryAll(false, atom0, chiralClass, 1, atom1,
+ atom2, atom3, atom4, atom5, atom6, v) ? "@" : "@@");
case 2: // allene
case 4: // tetrahedral, square planar
if (atom3 == null || atom4 == null)
return "";
- float d = SmilesAromatic.getNormalThroughPoints(atom1, atom2, atom3,
v.vTemp, v.vA, v.vB);
+ float d = SmilesAromatic.getNormalThroughPoints(atom1, atom2, atom3,
+ v.vTemp, v.vA, v.vB);
if (Math.abs(distanceToPlane(v.vTemp, d, (P3) atom4)) < 0.2f) {
chiralClass = STEREOCHEMISTRY_SQUARE_PLANAR;
- if (checkStereochemistryAll(false, atom0, chiralClass, 1, atom1,
atom2, atom3, atom4, atom5, atom6, v))
+ if (checkStereochemistryAll(false, atom0, chiralClass, 1, atom1, atom2,
+ atom3, atom4, atom5, atom6, v))
return "@SP1";
- if (checkStereochemistryAll(false, atom0, chiralClass, 2, atom1,
atom2, atom3, atom4, atom5, atom6, v))
+ if (checkStereochemistryAll(false, atom0, chiralClass, 2, atom1, atom2,
+ atom3, atom4, atom5, atom6, v))
return "@SP2";
- if (checkStereochemistryAll(false, atom0, chiralClass, 3, atom1,
atom2, atom3, atom4, atom5, atom6, v))
- return "@SP3";
+ if (checkStereochemistryAll(false, atom0, chiralClass, 3, atom1, atom2,
+ atom3, atom4, atom5, atom6, v))
+ return "@SP3";
} else {
- return (checkStereochemistryAll(false, atom0, chiralClass, 1, atom1,
atom2, atom3, atom4, atom5, atom6, v)? "@" : "@@");
- }
+ return (checkStereochemistryAll(false, atom0, chiralClass, 1, atom1,
+ atom2, atom3, atom4, atom5, atom6, v) ? "@" : "@@");
+ }
}
return "";
}
@@ -817,8 +826,8 @@
case 'O': //OH
case 'S': //SP
case 'T': //TH, TP
- stereoClass = (index + 1 < len ? getChiralityClass(pattern
- .substring(index, index + 2)) : -1);
+ stereoClass = (index + 1 < len ? getChiralityClass(pattern.substring(
+ index, index + 2)) : -1);
index += 2;
break;
default:
@@ -838,8 +847,7 @@
details = SmilesParser.getSubPattern(pattern, pt, '(');
pt += details.length() + 2;
}
- }
- else {
+ } else {
order = n;
}
} catch (NumberFormatException e) {
@@ -851,7 +859,8 @@
if (order < 1 || stereoClass < 0)
throw new InvalidSmilesException("Invalid stereochemistry descriptor");
}
- newAtom.stereo = new SmilesStereo(stereoClass, order, atomCount, details,
directives);
+ newAtom.stereo = new SmilesStereo(stereoClass, order, atomCount, details,
+ directives);
if (SmilesParser.getChar(pattern, index) == '?') {
Logger.info("Ignoring '?' in stereochemistry");
index++;
@@ -859,5 +868,4 @@
return index;
}
-
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-06 04:11:42 UTC
(rev 20758)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-06 20:54:56 UTC
(rev 20759)
@@ -59,8 +59,21 @@
TODO: image off stops JSmol
TODO: Rolf's errors in Safari due to move + zoomto
-Jmol.___JmolVersion="14.3.16_2015.09.05"
+Jmol.___JmolVersion="14.3.16_2015.09.06"
+bug fix: after atom deletion, atom iterator still finds atoms.
+ -- was not reinitializing the binary search after atom deletion
+ -- affects polyhedra, within()
+ $ load $caffeine
+ $ delete _N
+ 4 atoms deleted
+ $ print {*}.count
+ 20
+ $ print within(14.0, {c6}).count
+ 24
+
+JmolVersion="14.3.16_2015.09.05"
+
new feature: POLYHEDRA
-- same as POLYHEDRA BONDS {selected}
new feature: POLYHEDRA 4
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