Revision: 21620
http://sourceforge.net/p/jmol/code/21620
Author: hansonr
Date: 2017-05-27 20:31:36 +0000 (Sat, 27 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.17.2"
code: CIPChirality.java fully interfaced using SimpleNode and SimpleEdge
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/Bond.java
trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
trunk/Jmol/src/org/jmol/smiles/SmilesBond.java
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/util/Edge.java
trunk/Jmol/src/org/jmol/util/JmolMolecule.java
trunk/Jmol/src/org/jmol/util/Node.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Added Paths:
-----------
trunk/Jmol/src/org/jmol/util/SimpleEdge.java
trunk/Jmol/src/org/jmol/util/SimpleNode.java
Modified: trunk/Jmol/src/org/jmol/modelset/Bond.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Bond.java 2017-05-27 17:45:55 UTC (rev
21619)
+++ trunk/Jmol/src/org/jmol/modelset/Bond.java 2017-05-27 20:31:36 UTC (rev
21620)
@@ -28,7 +28,7 @@
import org.jmol.java.BS;
import org.jmol.util.C;
import org.jmol.util.Edge;
-import org.jmol.util.Node;
+import org.jmol.util.SimpleNode;
import org.jmol.viewer.JC;
public class Bond extends Edge {
@@ -38,7 +38,7 @@
public Atom atom1;
public Atom atom2;
- public short mad;
+ public short mad;
public short colix;
public int shapeVisibilityFlags;
@@ -162,7 +162,7 @@
}
@Override
- public Node getOtherAtomNode(Node thisAtom) {
+ public SimpleNode getOtherNode(SimpleNode thisAtom) {
return (atom1 == thisAtom ? atom2 : atom2 == thisAtom || thisAtom == null
? atom1 : null);
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -36,6 +36,7 @@
import org.jmol.util.Edge;
import org.jmol.util.Logger;
import org.jmol.util.Node;
+import org.jmol.util.SimpleNode;
public class SmilesAromatic {
@@ -98,7 +99,7 @@
Edge[] aedges = a.getEdges();
int ai = a.getIndex();
for (int j = aedges.length; --j >= 0;) {
- Node a2 = aedges[j].getOtherAtomNode(a);
+ SimpleNode a2 = aedges[j].getOtherNode(a);
int a2i = a2.getIndex();
if (a2i > ai && bs.get(a2i))
edges.addLast(aedges[j]);
@@ -439,7 +440,7 @@
// just check that the connected atom is either C or flat-aromatic
// if it is, assign 1 pi electron; if it is not, set it to 0 as
long
// we are not being strict or discard this ring if we are.
- Node het = b.getOtherAtomNode(atom);
+ SimpleNode het = b.getOtherNode(atom);
n = (het.getElementNumber() == 6 || bsAromatic.get(het.getIndex())
? 1
: strictness > 0 ? -100 : 0);
break;
@@ -516,7 +517,7 @@
Edge[] bonds = jmolAtoms[i].getEdges();
int naro = 0;
for (int j = bonds.length; --j >= 0;) {
- Node otherAtom = bonds[j].getOtherAtomNode(jmolAtoms[i]);
+ SimpleNode otherAtom = bonds[j].getOtherNode(jmolAtoms[i]);
int order = bonds[j].getCovalentOrder();
int ai2 = otherAtom.getIndex();
boolean isJAro = bsAromatic.get(ai2);
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesBond.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -25,7 +25,7 @@
package org.jmol.smiles;
import org.jmol.util.Edge;
-import org.jmol.util.Node;
+import org.jmol.util.SimpleNode;
/**
* Bond in a SmilesMolecule
@@ -270,7 +270,7 @@
}
@Override
- public Node getOtherAtomNode(Node atom) {
+ public SimpleNode getOtherNode(SimpleNode atom) {
return (atom == atom1 ? atom2 : atom == atom2 || atom == null ? atom1 :
null);
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -40,6 +40,7 @@
import org.jmol.util.JmolMolecule;
import org.jmol.util.Logger;
import org.jmol.util.Node;
+import org.jmol.util.SimpleNode;
import org.jmol.viewer.JC;
/**
@@ -73,8 +74,8 @@
private BS bsBondsUp = new BS();
private BS bsBondsDn = new BS();
private BS bsToDo;
- private Node prevAtom;
- private Node[] prevSp2Atoms;
+ private SimpleNode prevAtom;
+ private SimpleNode[] prevSp2Atoms;
// outputs
@@ -403,7 +404,7 @@
* @param atomFrom
* @return the correct character '/', '\\', '\0' (meaning "no
stereochemistry")
*/
- private char getBondStereochemistry(Edge bond, Node atomFrom) {
+ private char getBondStereochemistry(Edge bond, SimpleNode atomFrom) {
if (bond == null)
return '\0';
int i = bond.index;
@@ -433,27 +434,27 @@
for (int k = 0; k < bonds.length; k++) {
Edge bond = bonds[k];
int index = bond.index;
- Node atom2;
+ SimpleNode atom2;
if (bsDone.get(index) || bond.getCovalentOrder() != 2
- || SmilesSearch.isRingBond(ringSets, null, i, (atom2 =
bond.getOtherAtomNode(atom1)).getIndex()))
+ || SmilesSearch.isRingBond(ringSets, null, i, (atom2 =
bond.getOtherNode(atom1)).getIndex()))
continue;
bsDone.set(index);
int nCumulene = 0;
- Node a10 = atom1;
+ SimpleNode a10 = atom1;
while (atom2.getCovalentBondCount() == 2 && atom2.getValence() == 4) {
- Edge[] e2 = atom2.getEdges();
- Edge e = e2[e2[0].getOtherAtomNode(atom2) == a10 ? 1 : 0];
+ Edge[] e2 = (Edge[]) atom2.getEdges();
+ Edge e = e2[e2[0].getOtherNode(atom2) == a10 ? 1 : 0];
bsDone.set(e.index);
a10 = atom2;
- atom2 = e.getOtherAtomNode(atom2);
+ atom2 = e.getOtherNode(atom2);
nCumulene++;
}
if (nCumulene % 2 == 1)
continue;
Edge b0 = null;
- Node a0 = null;
+ SimpleNode a0 = null;
int i0 = 0;
- Node[] atom12 = new Node[] { atom1, atom2 };
+ SimpleNode[] atom12 = new SimpleNode[] { atom1, atom2 };
int edgeCount = 1;
// OK, so we have a double bond. Only looking at single bonds around
it.
@@ -463,10 +464,10 @@
for (int j = 0; j < 2 && edgeCount > 0 && edgeCount < 3; j++) {
edgeCount = 0;
- Node atomA = atom12[j];
- Edge[] bb = atomA.getEdges();
+ SimpleNode atomA = atom12[j];
+ Edge[] bb = ((Node) atomA).getEdges();
for (int b = 0; b < bb.length; b++) {
- if (bb[b].getCovalentOrder() != 1 ||
bb[b].getOtherAtomNode(atomA).getElementNumber() == 1)
+ if (bb[b].getCovalentOrder() != 1 ||
bb[b].getOtherNode(atomA).getElementNumber() == 1)
continue;
edges[j][edgeCount++] = bb[b];
if (getBondStereochemistry(bb[b], atomA) != '\0') {
@@ -503,7 +504,7 @@
// could ever get that with a real molecule.
char c0 = getBondStereochemistry(b0, atom12[i0]);
- a0 = b0.getOtherAtomNode(atom12[i0]);
+ a0 = b0.getOtherNode(atom12[i0]);
if (a0 == null)
continue;
for (int j = 0; j < 2; j++)
@@ -512,7 +513,7 @@
if (b1 == null || b1 == b0)
continue;
int bi = b1.index;
- Node a1 = b1.getOtherAtomNode(atom12[j]);
+ SimpleNode a1 = b1.getOtherNode(atom12[j]);
if (a1 == null)
continue;
char c1 = getBondStereochemistry(b1, atom12[j]);
@@ -544,7 +545,7 @@
}
}
- private Node getSmilesAt(SB sb, Node atom,
+ private Node getSmilesAt(SB sb, SimpleNode atom,
boolean allowConnectionsToOutsideWorld,
boolean allowBranches, boolean forceBrackets) {
int atomIndex = atom.getIndex();
@@ -562,12 +563,12 @@
Lst<Edge> v = new Lst<Edge>();
Edge bondNext = null;
Edge bondPrev = null;
- Edge[] bonds = atom.getEdges();
+ Edge[] bonds = (Edge[])atom.getEdges();
if (polySmilesCenter != null) {
allowBranches = false;
sortBonds(atom, prevAtom, polySmilesCenter);
}
- Node aH = null;
+ SimpleNode aH = null;
int stereoFlag = (isAromatic ? 10 : 0);
if (Logger.debugging)
Logger.debug(sb.toString());
@@ -580,7 +581,7 @@
Edge bond = bonds[i];
if (!bond.isCovalent())
continue;
- Node atom1 = bonds[i].getOtherAtomNode(atom);
+ SimpleNode atom1 = bonds[i].getOtherNode(atom);
int index1 = atom1.getIndex();
if (index1 == prevIndex) {
bondPrev = bonds[i];
@@ -615,7 +616,7 @@
// add the bond from the previous atom and carry over the prev atom in
case it is sp2
- Node[] sp2Atoms = prevSp2Atoms;
+ SimpleNode[] sp2Atoms = prevSp2Atoms;
int nSp2Atoms = (sp2Atoms == null ? 1 : 2);
if (sp2Atoms == null)
sp2Atoms = new Node[5];
@@ -635,9 +636,9 @@
if (allowBranches)
for (int i = 0; i < nBonds; i++) {
Edge bond = v.get(i);
- Node a = bond.getOtherAtomNode(atom);
+ SimpleNode a = bond.getOtherNode(atom);
int n = a.getCovalentBondCount()
- - (includeHs ? 0 : a.getCovalentHydrogenCount());
+ - (includeHs ? 0 : ((Node) a).getCovalentHydrogenCount());
int order = bond.getCovalentOrder();
if (n == 1 && (bondNext != null || i < nBonds - 1)) {
bsBranches.set(bond.index);
@@ -647,7 +648,7 @@
bondNext = bond;
}
}
- Node atomNext = (bondNext == null ? null :
bondNext.getOtherAtomNode(atom));
+ Node atomNext = (bondNext == null ? null : (Node)
bondNext.getOtherNode(atom));
int orderNext = (bondNext == null ? 0 : bondNext.getCovalentOrder());
if (isAromatic || orderNext == 2 && nH > 1 || atomNext != null
@@ -656,7 +657,7 @@
}
// initialize stereo[] for stereochemistry
- Node[] stereo = new Node[7];
+ SimpleNode[] stereo = new Node[7];
if (stereoFlag < 7 && bondPrev != null) {
if (havePreviousSp2Atoms && bondPrev.getCovalentOrder() == 2 &&
orderNext == 2
@@ -693,7 +694,7 @@
Edge bond = v.get(i);
if (!bsBranches.get(bond.index))
continue;
- Node a = bond.getOtherAtomNode(atom);
+ SimpleNode a = bond.getOtherNode(atom);
SB s2 = new SB();
prevAtom = atom;
prevSp2Atoms = null;
@@ -733,7 +734,7 @@
Edge bond = v.get(i);
if (bond == bondNext)
continue;
- Node a = bond.getOtherAtomNode(atom);
+ SimpleNode a = bond.getOtherNode(atom);
strPrev = getBondOrder(bond, atomIndex, a.getIndex(), isAromatic);
if (!deferStereo) {
chBond = getBondStereochemistry(bond, atom);
@@ -776,10 +777,10 @@
int charge = atom.getFormalCharge();
int isotope = atom.getIsotopeNumber();
int valence = atom.getValence();
- float osclass = (openSMILES ? atom.getFloatProperty("property_atomclass")
+ float osclass = (openSMILES ?
((Node)atom).getFloatProperty("property_atomclass")
: Float.NaN);
String atomName = atom.getAtomName();
- String groupType = atom.getBioStructureTypeName();
+ String groupType = ((Node)atom).getBioStructureTypeName();
// 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
@@ -788,7 +789,7 @@
if (topologyOnly)
sb.append("*");
else if (isExtension && groupType.length() != 0 && atomName.length() != 0)
- addBracketedBioName(sb, atom, "." + atomName, false);
+ addBracketedBioName(sb, (Node)atom, "." + atomName, false);
else
sb.append(SmilesAtom.getAtomLabel(
atomicNumber,
@@ -841,7 +842,7 @@
return atomNext;
}
- private Node[] atemp;
+ private SimpleNode[] atemp;
/**
* swap slices of an array [i0 i1) with [i1 i2)
* @param a
@@ -849,7 +850,7 @@
* @param i1
* @param i2
*/
- private void swapArray(Node[] a, int i0, int i1, int i2) {
+ private void swapArray(SimpleNode[] a, int i0, int i1, int i2) {
int n = i1 - i0;
if (atemp == null || atemp.length < n)
atemp = new Node[n];
@@ -895,7 +896,7 @@
return false;
}
- void sortBonds(Node atom, Node refAtom, P3 center) {
+ void sortBonds(SimpleNode atom, SimpleNode refAtom, P3 center) {
if (smilesStereo == null)
try {
smilesStereo = SmilesStereo.newStereo(null);
@@ -917,22 +918,22 @@
* @param vTemp
* @return "@" or "@@" or ""
*/
- private String sortInorganic(Node atom, Lst<Edge> v, VTemp vTemp) {
+ private String sortInorganic(SimpleNode atom, Lst<Edge> v, VTemp vTemp) {
int atomIndex = atom.getIndex();
int n = v.size();
Lst<Edge[]> axialPairs = new Lst<Edge[]>();
Lst<Edge> bonds = new Lst<Edge>();
- Node a1, a2, a01 = null, a02 = null;
+ SimpleNode a1, a2, a01 = null, a02 = null;
Edge bond1, bond2;
BS bsDone = new BS();
Edge[] pair0 = null;
- Node[] stereo = new Node[6];
+ SimpleNode[] stereo = new Node[6];
boolean isOK = true; // AX6 or AX5
String s = "";
int naxial = 0;
for (int i = 0; i < n; i++) {
bond1 = v.get(i);
- stereo[0] = a1 = bond1.getOtherAtomNode(atom);
+ stereo[0] = a1 = bond1.getOtherNode(atom);
// just looking for the opposite atom not being identical
if (i == 0)
s = addStereoCheck(0, atomIndex, a1, "", null);
@@ -946,7 +947,7 @@
if (bsDone.get(j))
continue;
bond2 = v.get(j);
- a2 = bond2.getOtherAtomNode(atom);
+ a2 = bond2.getOtherNode(atom);
if (SmilesStereo.isDiaxial(atom, atom, a1, a2, vTemp, -0.95f)) {
switch (++naxial) {
case 1:
@@ -984,7 +985,7 @@
return "";
pair0 = axialPairs.get(0);
bond1 = pair0[0];
- stereo[0] = bond1.getOtherAtomNode(atom);
+ stereo[0] = bond1.getOtherNode(atom);
// now sort them into the ligand vector in the proper order
v.clear();
@@ -1000,10 +1001,10 @@
for (int i = 0; i < bonds.size(); i++) {
bond1 = bonds.get(i);
v.addLast(bond1);
- stereo[i + 1] = bond1.getOtherAtomNode(atom);
+ stereo[i + 1] = bond1.getOtherNode(atom);
}
v.addLast(pair0[1]);
- stereo[n - 1] = pair0[1].getOtherAtomNode(atom);
+ stereo[n - 1] = pair0[1].getOtherNode(atom);
// now deterimine the stereochemistry
@@ -1010,8 +1011,8 @@
return SmilesStereo.getStereoFlag(atom, stereo, n, vTemp);
}
- private String checkStereoPairs(Node atom, int atomIndex,
- Node[] stereo, int stereoFlag) {
+ private String checkStereoPairs(SimpleNode atom, int atomIndex,
+ SimpleNode[] stereo, int stereoFlag) {
if (stereoFlag < 4)
return "";
if (stereoFlag == 4 && (atom.getElementNumber()) == 6) {
@@ -1041,14 +1042,14 @@
* @param bsDone
* @return null if duplicate
*/
- private String addStereoCheck(int level, int atomIndex, Node atom, String s,
+ private String addStereoCheck(int level, int atomIndex, SimpleNode atom,
String s,
BS bsDone) {
if (bsDone != null)
bsDone.set(atomIndex);
//System.out.println("level=" + level + " atomIndex=" + atomIndex + "
atom=" + atom + " s=" + s);
- int n = atom.getAtomicAndIsotopeNumber();
+ int n = ((Node)atom).getAtomicAndIsotopeNumber();
int nx = atom.getCovalentBondCount();
- int nh = (n == 6 && !explicitH ? atom.getCovalentHydrogenCount() : 0);
+ int nh = (n == 6 && !explicitH ? ((Node) atom).getCovalentHydrogenCount()
: 0);
// only carbon or singly-connected atoms are checked
// for C we use nh -- CH3, for example.
// for other atoms, we use number of bonds.
@@ -1064,12 +1065,12 @@
case 2:
if (bsDone == null)
return s;
- Edge[] edges = atom.getEdges();
+ Edge[] edges = ((Node)atom).getEdges();
String s2 = "";
String sa2 = "";
int nunique = (nh == 2 ? 0 : 3);
for (int j = atom.getBondCount(); --j >= 0;) {
- Node a2 = edges[j].getOtherAtomNode(atom);
+ SimpleNode a2 = edges[j].getOtherNode(atom);
int i2 = a2.getIndex();
if (bsDone.get(i2) || !edges[j].isCovalent() ||
a2.getElementNumber() == 1)
continue;
@@ -1094,7 +1095,7 @@
// must check isotopes for CH3
int ndt = 0;
for (int j = 0; j < nx && ndt < 3; j++) {
- int ia = atom.getBondedAtomIndex(j);
+ int ia = ((Node)atom).getBondedAtomIndex(j);
if (ia == atomIndex)
continue;
ndt += atoms[ia].getAtomicAndIsotopeNumber();
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -40,6 +40,7 @@
import org.jmol.util.JmolMolecule;
import org.jmol.util.Logger;
import org.jmol.util.Node;
+import org.jmol.util.SimpleNode;
import org.jmol.viewer.JC;
/**
@@ -654,7 +655,7 @@
// clear out all atoms connected to the last atom only
jmolBonds = a.getEdges();
for (int k = 0; k < jmolBonds.length; k++)
- bs.set(jmolBonds[k].getOtherAtomNode(a).getIndex());
+ bs.set(jmolBonds[k].getOtherNode(a).getIndex());
}
}
boolean skipGroup = ((newPatternAtom.isBioAtomWild));
@@ -1509,9 +1510,9 @@
while (sAtom2.getBondCount() == 2 && sAtom2.getValence() == 4) {
nCumulene++;
Edge[] e2 = sAtom2.getEdges();
- Edge e = e2[e2[0].getOtherAtomNode(sAtom2) == a10 ? 1 : 0];
+ Edge e = e2[e2[0].getOtherNode(sAtom2) == a10 ? 1 : 0];
a10 = sAtom2;
- sAtom2 = (SmilesAtom) e.getOtherAtomNode(sAtom2);
+ sAtom2 = (SmilesAtom) e.getOtherNode(sAtom2);
}
if (nCumulene % 2 == 1)
continue;
@@ -1577,7 +1578,7 @@
Node a11 = Edge.getAtropismNode(b.matchingBond.order, a1, isFirst);
SmilesBond[] b1 = s1.bonds;
for (int i = s1.getBondCount(); --i >= 0;)
- if (((SmilesAtom) b1[i].getOtherAtomNode(s1)).getMatchingAtom() == a11)
+ if (((SmilesAtom) b1[i].getOtherNode(s1)).getMatchingAtom() == a11)
return i + 1;
return 0;
}
@@ -1644,8 +1645,8 @@
Edge bond = bonds[k];
if (bond.order == Edge.BOND_COVALENT_DOUBLE)
continue;
- Node atom = bond.getOtherAtomNode(dbAtom1);
- atom.set(-1, (nBonds++ == 0) ? -1 : 1, 0);
+ SimpleNode atom = bond.getOtherNode(dbAtom1);
+ ((Node) atom).set(-1, (nBonds++ == 0) ? -1 : 1, 0);
int mode = (bond.getAtomIndex2() == dbAtom1.getIndex() ? nBonds :
-nBonds);
switch (bond.order) {
case Edge.BOND_STEREO_NEAR:
@@ -1657,15 +1658,15 @@
}
int dir2 = 0;
nBonds = 0;
- Node[] atoms = new Node[2];
+ SimpleNode[] atoms = new Node[2];
bonds = dbAtom2.getEdges();
for (int k = bonds.length; --k >= 0;) {
Edge bond = bonds[k];
if (bond.order == Edge.BOND_COVALENT_DOUBLE)
continue;
- Node atom = bond.getOtherAtomNode(dbAtom2);
+ SimpleNode atom = bond.getOtherNode(dbAtom2);
atoms[nBonds] = atom;
- atom.set(1, (nBonds++ == 0) ? 1 : -1, 0);
+ ((Node) atom).set(1, (nBonds++ == 0) ? 1 : -1, 0);
int mode = (bond.getAtomIndex2() == dbAtom2.getIndex() ? nBonds :
-nBonds);
switch (bond.order) {
case Edge.BOND_STEREO_NEAR:
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -37,6 +37,8 @@
import org.jmol.util.Escape;
import org.jmol.util.Logger;
import org.jmol.util.Node;
+import org.jmol.util.SimpleEdge;
+import org.jmol.util.SimpleNode;
//import org.jmol.util.Logger;
@@ -477,7 +479,7 @@
}
int n = bonds.length;
for (int k = 0; k < n; k++) {
- SmilesAtom bAtom = (SmilesAtom) bonds[k].getOtherAtomNode(atom);
+ SmilesAtom bAtom = (SmilesAtom) bonds[k].getOtherNode(atom);
if (bAtom == cAtom) {
map[i] = (k + 1) * 10 + n000 + i;
return true;
@@ -505,12 +507,12 @@
* @param bonds
* @param vTemp
*/
- void sortBondsByStereo(Node atom, Node atomPrev, T3 ref, Edge[] bonds,
+ void sortBondsByStereo(SimpleNode atom, SimpleNode atomPrev, T3 ref,
SimpleEdge[] bonds,
V3 vTemp) {
if (bonds.length < 2 || !(atom instanceof T3))
return;
if (atomPrev == null)
- atomPrev = bonds[0].getOtherAtomNode(atom);
+ atomPrev = bonds[0].getOtherNode(atom);
Object[][] aTemp = new Object[bonds.length][0];
if (sorter == null)
sorter = new PolyhedronStereoSorter();
@@ -517,7 +519,7 @@
vTemp.sub2((T3)atomPrev, ref);
sorter.setRef(vTemp);
for (int i = bonds.length; --i >= 0;) {
- Node a = bonds[i].getOtherAtomNode(atom);
+ SimpleNode a = bonds[i].getOtherNode(atom);
float f = (a == atomPrev ? 0 :
sorter.isAligned((T3) a, ref, (T3) atomPrev) ? -999 :
Measure.computeTorsion((T3) atom,
@@ -809,13 +811,13 @@
* @param v
* @return String
*/
- static String getStereoFlag(Node atom0, Node[] atoms, int nAtoms, VTemp v) {
- Node atom1 = atoms[0];
- Node atom2 = atoms[1];
- Node atom3 = atoms[2];
- Node atom4 = atoms[3];
- Node atom5 = atoms[4];
- Node atom6 = atoms[5];
+ static String getStereoFlag(SimpleNode atom0, SimpleNode[] atoms, int
nAtoms, VTemp v) {
+ SimpleNode atom1 = atoms[0];
+ SimpleNode atom2 = atoms[1];
+ SimpleNode atom3 = atoms[2];
+ SimpleNode atom4 = atoms[3];
+ SimpleNode atom5 = atoms[4];
+ SimpleNode atom6 = atoms[5];
int chiralClass = TETRAHEDRAL;
// what about POLYHEDRAL?
switch (nAtoms) {
@@ -850,10 +852,10 @@
return "";
}
- private static boolean checkStereochemistryAll(boolean isNot, Node atom0,
+ private static boolean checkStereochemistryAll(boolean isNot, SimpleNode
atom0,
int chiralClass, int order,
- Node atom1, Node atom2, Node atom3,
- Node atom4, Node atom5, Node atom6,
+ SimpleNode atom1, SimpleNode atom2,
SimpleNode atom3,
+ SimpleNode atom4, SimpleNode atom5,
SimpleNode atom6,
VTemp v) {
switch (chiralClass) {
@@ -927,7 +929,7 @@
}
}
- static boolean isDiaxial(Node atomA, Node atomB, Node atom1, Node atom2,
+ static boolean isDiaxial(SimpleNode atomA, SimpleNode atomB, SimpleNode
atom1, SimpleNode atom2,
VTemp v, float f) {
v.vA.sub2((P3) atomA, (P3) atom1);
v.vB.sub2((P3) atomB, (P3) atom2);
@@ -947,7 +949,7 @@
* @param v
* @return 1 for "@", 2 for "@@"
*/
- static int getHandedness(Node a, Node b, Node c, Node pt, VTemp v) {
+ 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);
// System.out.println("$ draw p1 " + P3.newP((P3)a) +" color red '"+a+"
[2]'");
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -13,9 +13,9 @@
import org.jmol.java.BS;
import org.jmol.util.BSUtil;
-import org.jmol.util.Edge;
import org.jmol.util.Logger;
-import org.jmol.util.Node;
+import org.jmol.util.SimpleEdge;
+import org.jmol.util.SimpleNode;
import org.jmol.viewer.JC;
/**
@@ -56,7 +56,7 @@
*
* - reports atom descriptor along with the rule that ultimately decided it
*
- * Primary 236-compound Chapter-9 validation set (AY-236) provided by Andres
+ * Primary 236-compound Chapter-9 validation set (AY-236) provided by Andrey
* Yerin, ACD/Labs (Moscow).
*
* Mikko Vainio also supplied a 64-compound testing suite (MV-64), which is
@@ -68,7 +68,7 @@
* Additional thanks to the IUPAC Blue Book Revision project, specifically
* Karl-Heinz Hellwich for alerting me to the errata page for the 2013 IUPAC
* specs (http://www.chem.qmul.ac.uk/iupac/bibliog/BBerrors.html), Gerry Moss
- * for discussions, Andres Yerin for discussion and digraph checking.
+ * for discussions, Andrey Yerin for discussion and digraph checking.
*
* Many thanks to the members of the BlueObelisk-Discuss group, particularly
* Mikko Vainio, John Mayfield (aka John May), Wolf Ihlenfeldt, and Egon
Willighagen, for
@@ -108,6 +108,8 @@
*
* code history:
*
+ * 5/27/17 Jmol 14.17.2 fully interfaced using SimpleNode and SimpleEdge
+ *
* 5/27/17 Jmol 14.17.1 fully validated; simplified code; 978 lines
*
* 5/17/17 Jmol 14.16.1. adds helicene M/P chirality; 959 lines validated using
@@ -449,7 +451,7 @@
* aromatic atoms at the end of a positive helical turn;
* smarts("A{a}(.t:10,40)a(.t:10,40)aaa")
*/
- public void getChiralityForAtoms(Node[] atoms, BS bsAtoms,
+ public void getChiralityForAtoms(SimpleNode[] atoms, BS bsAtoms,
BS bsAtropisomeric, BS bsHelixM, BS
bsHelixP) {
if (bsAtoms.isEmpty())
return;
@@ -473,7 +475,7 @@
// set atom chiralities
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1)) {
- Node a = atoms[i];
+ SimpleNode a = atoms[i];
a.setCIPChirality(0);
ptID = 0;
int c = getAtomChiralityLimited(a, null, null, RULE_5);
@@ -525,10 +527,10 @@
* @return a bit set of bridgehead nitrogens. I just liked the name
* "azacyclic".
*/
- private BS getAzacyclic(Node[] atoms, BS bsAtoms) {
+ private BS getAzacyclic(SimpleNode[] atoms, BS bsAtoms) {
BS bsAza = null;
for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1))
{
- Node atom = atoms[i];
+ SimpleNode atom = atoms[i];
if (atom.getElementNumber() != 7 || atom.getCovalentBondCount() != 3
|| bsKekuleAmbiguous.get(i))
continue;
@@ -543,10 +545,10 @@
if (nr < 2)
continue;
BS bsSubs = new BS();
- Edge[] bonds = atom.getEdges();
+ SimpleEdge[] bonds = atom.getEdges();
for (int b = bonds.length; --b >= 0;)
if (bonds[b].isCovalent())
- bsSubs.set(bonds[b].getOtherAtomNode(atom).getIndex());
+ bsSubs.set(bonds[b].getOtherNode(atom).getIndex());
BS bsBoth = new BS();
BS bsAll = new BS();
for (int j = 0; j < nr - 1 && bsAll != null; j++) {
@@ -580,7 +582,7 @@
* @param bsToDo
* @return whether we have any alkenes that could be EZ
*/
- private boolean preFilterAtomList(Node[] atoms, BS bsToDo) {
+ private boolean preFilterAtomList(SimpleNode[] atoms, BS bsToDo) {
boolean haveAlkenes = false;
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1)) {
if (!couldBeChiralAtom(atoms[i])) {
@@ -602,7 +604,7 @@
* @return true for selected atoms and hybridizations
*
*/
- private boolean couldBeChiralAtom(Node a) {
+ private boolean couldBeChiralAtom(SimpleNode a) {
boolean mustBePlanar = false;
switch (a.getCovalentBondCount()) {
default:
@@ -642,13 +644,13 @@
break;
}
// check that the atom has at most one 1H atom and whether it must be
planar and has a double bond
- Edge[] edges = a.getEdges();
+ SimpleEdge[] edges = a.getEdges();
int nH = 0;
boolean haveDouble = false;
for (int j = edges.length; --j >= 0;) {
if (mustBePlanar && edges[j].getCovalentOrder() == 2)
haveDouble = true;
- if (edges[j].getOtherAtomNode(a).getAtomicAndIsotopeNumber() == 1)
+ if (edges[j].getOtherNode(a).getIsotopeNumber() == 1)
nH++;
}
return (nH < 2 && (haveDouble || mustBePlanar == Math.abs(getTrigonality(a,
@@ -665,7 +667,7 @@
* optional other atom
* @return if the atom could be an EZ node
*/
- private int couldBeChiralAlkene(Node a, Node b) {
+ private int couldBeChiralAlkene(SimpleNode a, SimpleNode b) {
switch (a.getCovalentBondCount()) {
default:
return STEREO_UNDETERMINED;
@@ -680,13 +682,13 @@
return STEREO_UNDETERMINED;
break;
}
- Edge[] bonds = a.getEdges();
+ SimpleEdge[] bonds = a.getEdges();
int n = 0;
for (int i = bonds.length; --i >= 0;)
if (bonds[i].getCovalentOrder() == 2) {
if (++n > 1)
return STEREO_M; //central allenes
- Node other = bonds[i].getOtherAtomNode(a);
+ SimpleNode other = bonds[i].getOtherNode(a);
if (!isFirstRow(other))
return STEREO_UNDETERMINED;
if (b != null && (other != b || b.getCovalentBondCount() == 1)) {
@@ -703,7 +705,7 @@
* @param a
* @return elemno > 2 && elemno <= 10
*/
- boolean isFirstRow(Node a) {
+ boolean isFirstRow(SimpleNode a) {
int n = a.getElementNumber();
return (n > 2 && n <= 10);
}
@@ -716,7 +718,7 @@
* @param atoms
* @return bsKekuleAmbiguous
*/
- private BS getKekule(Node[] atoms) {
+ private BS getKekule(SimpleNode[] atoms) {
int nRings = lstSmallRings.size();
BS bs = new BS(), bsDone = new BS();
for (int i = nRings; --i >= 0;) {
@@ -729,7 +731,7 @@
}
int nPI = 0;
for (int j = bsRing.nextSetBit(0); j >= 0; j = bsRing.nextSetBit(j + 1))
{
- Node a = atoms[j];
+ SimpleNode a = atoms[j];
if (bs.get(a.getIndex())) {
nPI++;
continue;
@@ -736,12 +738,12 @@
}
int nb = a.getCovalentBondCount();
if (nb == 3 || nb == 2) {
- Edge[] bonds = a.getEdges();
+ SimpleEdge[] bonds = a.getEdges();
for (int k = bonds.length; --k >= 0;) {
- Edge b = bonds[k];
+ SimpleEdge b = bonds[k];
if (b.getCovalentOrder() != 2)
continue;
- if (bsRing.get(b.getOtherAtomNode(a).getIndex())) {
+ if (bsRing.get(b.getOtherNode(a).getIndex())) {
nPI++;
break;
}
@@ -764,7 +766,7 @@
* @param bs
* tracks all atoms in this molecular unit
*/
- private void getSmallRings(Node atom, BS bs) {
+ private void getSmallRings(SimpleNode atom, BS bs) {
root = new CIPAtom().create(atom, null, false, false);
addSmallRings(root, bs);
}
@@ -783,13 +785,13 @@
bs.clear(a.atom.getIndex());
if (a.isTerminal || a.isDuplicate || a.atom.getCovalentBondCount() > 4)
return;
- Node atom2;
+ SimpleNode atom2;
int pt = 0;
- Edge[] bonds = a.atom.getEdges();
+ SimpleEdge[] bonds = a.atom.getEdges();
for (int i = bonds.length; --i >= 0;) {
- Edge bond = bonds[i];
+ SimpleEdge bond = bonds[i];
if (!bond.isCovalent()
- || (atom2 = bond.getOtherAtomNode(a.atom)).getCovalentBondCount() ==
1
+ || (atom2 = bond.getOtherNode(a.atom)).getCovalentBondCount() == 1
|| a.parent != null && atom2 == a.parent.atom)
continue;
CIPAtom r = a.addAtom(pt++, atom2, false, false);
@@ -808,7 +810,7 @@
* @param atoms
* @param lstEZ
*/
- private void clearSmallRingEZ(Node[] atoms, Lst<int[]> lstEZ) {
+ private void clearSmallRingEZ(SimpleNode[] atoms, Lst<int[]> lstEZ) {
for (int j = lstSmallRings.size(); --j >= 0;)
lstSmallRings.get(j).andNot(bsAtropisomeric);
for (int i = lstEZ.size(); --i >= 0;) {
@@ -834,18 +836,15 @@
* @return distance from plane of first three covalently bonded nodes to this
* node
*/
- float getTrigonality(Node a, V3 vNorm) {
- P3[] pts = new P3[3];
- Edge[] bonds = a.getEdges();
- Node other;
- for (int n = bonds.length, i = n, pt = 0; --i >= 0 && pt < 3;)
- if (bonds[i].isCovalent()
- && ((other = bonds[i].getOtherAtomNode(a))
- .getAtomicAndIsotopeNumber() != 1 || n < 4))
- pts[pt++] = other.getXYZ();
+ float getTrigonality(SimpleNode a, V3 vNorm) {
+ P3[] pts = new P3[4];
+ SimpleEdge[] bonds = a.getEdges();
+ for (int n = bonds.length, i = n, pt = 0; --i >= 0 && pt < 4;)
+ if (bonds[i].isCovalent())
+ pts[pt++] = bonds[i].getOtherNode(a).getXYZ();
P4 plane = Measure.getPlaneThroughPoints(pts[0], pts[1], pts[2], vNorm,
vTemp, new P4());
- return Measure.distanceToPlane(plane, a.getXYZ());
+ return Measure.distanceToPlane(plane, (pts[3] == null ? a.getXYZ() :
pts[3]));
}
/**
@@ -857,17 +856,17 @@
* @param bsToDo
*/
- private void getAtomBondChirality(Node atom, Lst<int[]> lstEZ, BS bsToDo) {
+ private void getAtomBondChirality(SimpleNode atom, Lst<int[]> lstEZ, BS
bsToDo) {
int index = atom.getIndex();
- Edge[] bonds = atom.getEdges();
+ SimpleEdge[] bonds = atom.getEdges();
int c = NO_CHIRALITY;
boolean isAtropic = bsAtropisomeric.get(index);
for (int j = bonds.length; --j >= 0;) {
- Edge bond = bonds[j];
- Node atom1;
+ SimpleEdge bond = bonds[j];
+ SimpleNode atom1;
int index1;
if (isAtropic) {
- atom1 = bonds[j].getOtherAtomNode(atom);
+ atom1 = bonds[j].getOtherNode(atom);
index1 = atom1.getIndex();
if (!bsAtropisomeric.get(index1))
continue;
@@ -901,10 +900,10 @@
* @param parents
* @return the terminal atom of this alkene or cumulene
*/
- private Node getLastCumuleneAtom(Edge bond, Node atom, int[] nSP2,
- Node[] parents) {
+ private SimpleNode getLastCumuleneAtom(SimpleEdge bond, SimpleNode atom,
int[] nSP2,
+ SimpleNode[] parents) {
// we know this is a double bond
- Node atom2 = bond.getOtherAtomNode(atom);
+ SimpleNode atom2 = bond.getOtherNode(atom);
if (parents != null) {
parents[0] = atom2;
parents[1] = atom;
@@ -916,9 +915,9 @@
while (true) {
if (atom2.getCovalentBondCount() != 2)
return atom2;
- Edge[] edges = atom2.getEdges();
+ SimpleEdge[] edges = atom2.getEdges();
for (int i = edges.length; --i >= 0;) {
- Node atom3 = (bond = edges[i]).getOtherAtomNode(atom2);
+ SimpleNode atom3 = (bond = edges[i]).getOtherNode(atom2);
if (atom3 == atom)
continue;
// connected atom must only have one other bond, and it must be double
to continue
@@ -957,7 +956,7 @@
* @return if parent != null: [0:none, 1:R, 2:S] otherwise [0:none, 1:
* atoms[0] is higher, 2: atoms[1] is higher]
*/
- private int getAtomChiralityLimited(Node atom, CIPAtom cipAtom,
+ private int getAtomChiralityLimited(SimpleNode atom, CIPAtom cipAtom,
CIPAtom parent, int ruleMax) {
int rs = NO_CHIRALITY;
boolean isChiral = false, isAlkene = false;
@@ -1038,16 +1037,16 @@
* @return one of: {NO_CHIRALITY | STEREO_Z | STEREO_E | STEREO_Ra |
STEREO_Sa
* | STEREO_ra | STEREO_sa}
*/
- private int getBondChiralityLimited(Edge bond, Node a, int ruleMax) {
+ private int getBondChiralityLimited(SimpleEdge bond, SimpleNode a, int
ruleMax) {
if (Logger.debugging)
Logger.info("get Bond Chirality " + bond);
if (a == null)
- a = bond.getOtherAtomNode(null);
- if (couldBeChiralAlkene(a, bond.getOtherAtomNode(a)) ==
STEREO_UNDETERMINED)
+ a = bond.getOtherNode(null);
+ if (couldBeChiralAlkene(a, bond.getOtherNode(a)) == STEREO_UNDETERMINED)
return NO_CHIRALITY;
int[] nSP2 = new int[1];
- Node[] parents = new Node[2];
- Node b = getLastCumuleneAtom(bond, a, nSP2, parents);
+ SimpleNode[] parents = new SimpleNode[2];
+ SimpleNode b = getLastCumuleneAtom(bond, a, nSP2, parents);
boolean isAxial = nSP2[0] % 2 == 1;
return setBondChirality(a, parents[0], parents[1], b, isAxial, ruleMax);
}
@@ -1064,7 +1063,7 @@
* @return one of: {NO_CHIRALITY | STEREO_Z | STEREO_E | STEREO_M | STEREO_P
|
* STEREO_m | STEREO_p}
*/
- private int setBondChirality(Node a, Node pa, Node pb, Node b,
+ private int setBondChirality(SimpleNode a, SimpleNode pa, SimpleNode pb,
SimpleNode b,
boolean isAxial, int ruleMax) {
CIPAtom a1 = new CIPAtom().create(a, null, false, true);
int atop = getAlkeneEndTopPriority(a1, pa, isAxial, ruleMax);
@@ -1118,7 +1117,7 @@
* @param ruleMax
* @return -1, 0, or 1
*/
- private int getAlkeneEndTopPriority(CIPAtom a, Node pa, boolean isAxial,
+ private int getAlkeneEndTopPriority(CIPAtom a, SimpleNode pa, boolean
isAxial,
int ruleMax) {
a.canBePseudo = a.isAxialRoot = isAxial;
return getAtomChiralityLimited(a.atom, a,
@@ -1165,7 +1164,7 @@
* this in SMILES or Jmol
*
*/
- Node atom;
+ SimpleNode atom;
/**
* unique ID for this CIPAtom for debugging only
@@ -1426,7 +1425,7 @@
* @param isAlkene
* @return this
*/
- CIPAtom create(Node atom, CIPAtom parent, boolean isDuplicate,
+ CIPAtom create(SimpleNode atom, CIPAtom parent, boolean isDuplicate,
boolean isAlkene) {
this.id = ++ptID;
this.parent = parent;
@@ -1502,13 +1501,13 @@
* @return an averaged element number
*/
private float getKekuleElementNumber() {
- Edge[] edges = atom.getEdges();
- Edge bond;
+ SimpleEdge[] edges = atom.getEdges();
+ SimpleEdge bond;
float ave = 0;
int n = 0;
for (int i = edges.length; --i >= 0;)
if ((bond = edges[i]).isCovalent()) {
- Node other = bond.getOtherAtomNode(atom);
+ SimpleNode other = bond.getOtherNode(atom);
if (bsKekuleAmbiguous.get(other.getIndex())) {
n++;
ave += other.getElementNumber();
@@ -1549,16 +1548,16 @@
if (isDuplicate)
return true;
- Edge[] bonds = atom.getEdges();
+ SimpleEdge[] bonds = atom.getEdges();
int nBonds = bonds.length;
if (Logger.debuggingHigh)
Logger.info("set " + this);
int pt = 0;
for (int i = 0; i < nBonds; i++) {
- Edge bond = bonds[i];
+ SimpleEdge bond = bonds[i];
if (!bond.isCovalent())
continue;
- Node other = bond.getOtherAtomNode(atom);
+ SimpleNode other = bond.getOtherNode(atom);
boolean isParentBond = (parent != null && parent.atom == other);
int order = bond.getCovalentOrder();
if (order == 2) {
@@ -1641,7 +1640,7 @@
* @param isAlkene
* @return new atom or null
*/
- CIPAtom addAtom(int i, Node other, boolean isDuplicate, boolean isAlkene) {
+ CIPAtom addAtom(int i, SimpleNode other, boolean isDuplicate, boolean
isAlkene) {
if (i >= atoms.length) {
if (Logger.debugging)
Logger.info(" too many bonds on " + atom);
@@ -1649,7 +1648,7 @@
}
if (parent == null) {
// For top level, we do not allow two 1H atoms.
- int atomIsotope = other.getAtomicAndIsotopeNumber();
+ int atomIsotope = other.getIsotopeNumber();
if (atomIsotope == 1) {
if (++h1Count > 1) {
if (Logger.debuggingHigh)
@@ -1797,7 +1796,9 @@
if (ties != null) {
switch (ties.size()) {
case 1:
- switch (checkPseudoHandedness(ties.get(0), indices)) {
+ // in the case of an alkene, we are just checking for a winner on
one atom
+ // otherwise we need to check the chirality of this tie
+ switch (isAlkene ? STEREO_R : checkPseudoHandedness(ties.get(0),
indices)) {
case STEREO_R:
case STEREO_S:
isPseudo = canBePseudo;
@@ -2909,8 +2910,8 @@
CIPAtom atom1;
// critical here that we do NOT include the tied branches
atom1 = (CIPAtom) clone();
- atom1.atoms[ia] = new CIPAtom().create(null, atom1, false, isAlkene);
- atom1.atoms[ib] = new CIPAtom().create(null, atom1, false, isAlkene);
+ atom1.atoms[ia] = new CIPAtom().create(null, atom1, false, false);
+ atom1.atoms[ib] = new CIPAtom().create(null, atom1, false, false);
atom1.addReturnPath(null, this);
// We are guaranteed that only RULE_1a is necessary, because one of our
// paths goes all the way back to the root, without a duplicate atom,
and any
@@ -2966,7 +2967,7 @@
* Determine the ordered CIP winding of this atom. For this, we just take
* the directed normal through the plane containing the top three
* substituent atoms and dot that with the vector from any one of them to
- * the root atom. If this is positive, we have R.
+ * the fourth ligand (or the root atom if trigonal pyramidal). If this is
positive, we have R.
*
* @return 1 for "R", 2 for "S"
*/
@@ -2973,9 +2974,12 @@
int checkHandedness() {
P3 p1 = atoms[0].atom.getXYZ(), p2 = atoms[1].atom.getXYZ(), p3 =
atoms[2].atom.getXYZ();
Measure.getNormalThroughPoints(p1, p2, p3, vNorm, vTemp);
- vTemp.setT(atom.getXYZ());
+ vTemp.setT((atoms[3].atom == null ? atom : atoms[3].atom).getXYZ());
vTemp.sub(p1);
- return (vTemp.dot(vNorm) > 0 ? STEREO_R : STEREO_S);
+ float f = vTemp.dot(vNorm);
+ System.out.println("draw d1 vector " + P3.newP(atom.getXYZ()) + " " +
vNorm);
+ System.out.println("draw d2 vector " + P3.newP(atom.getXYZ()) + " " +
vTemp);
+ return (f > 0 ? STEREO_R : STEREO_S);
}
/**
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -26,6 +26,17 @@
import java.util.Map;
+import javajs.util.Lst;
+import javajs.util.M3;
+import javajs.util.M4;
+import javajs.util.Matrix;
+import javajs.util.P3;
+import javajs.util.P3i;
+import javajs.util.Quat;
+import javajs.util.SB;
+import javajs.util.T3;
+import javajs.util.V3;
+
import org.jmol.api.AtomIndexIterator;
import org.jmol.api.Interface;
import org.jmol.api.SymmetryInterface;
@@ -33,28 +44,14 @@
import org.jmol.bspt.CubeIterator;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
-import org.jmol.modelset.Bond;
import org.jmol.modelset.ModelSet;
-import javajs.util.Lst;
-
+import org.jmol.util.Escape;
import org.jmol.util.JmolMolecule;
-import javajs.util.P3;
-
-import org.jmol.util.Escape;
-import org.jmol.util.Tensor;
import org.jmol.util.Logger;
import org.jmol.util.SimpleUnitCell;
+import org.jmol.util.Tensor;
import org.jmol.viewer.Viewer;
-import javajs.util.M3;
-import javajs.util.M4;
-import javajs.util.Matrix;
-import javajs.util.P3i;
-import javajs.util.Quat;
-import javajs.util.SB;
-import javajs.util.T3;
-import javajs.util.V3;
-
public class Symmetry implements SymmetryInterface {
// NOTE: THIS CLASS IS VERY IMPORTANT.
// IN ORDER TO MODULARIZE IT, IT IS REFERENCED USING
Modified: trunk/Jmol/src/org/jmol/util/Edge.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Edge.java 2017-05-27 17:45:55 UTC (rev
21619)
+++ trunk/Jmol/src/org/jmol/util/Edge.java 2017-05-27 20:31:36 UTC (rev
21620)
@@ -25,7 +25,7 @@
package org.jmol.util;
-public abstract class Edge {
+public abstract class Edge implements SimpleEdge {
/**
@@ -132,10 +132,10 @@
abstract public int getAtomIndex2();
+ @Override
abstract public int getCovalentOrder();
- abstract public Node getOtherAtomNode(Node atom);
-
+ @Override
abstract public boolean isCovalent();
abstract public boolean isHydrogen();
@@ -224,7 +224,7 @@
public static Node getAtropismNode(int order, Node a1, boolean isFirst) {
int i1 = (order >> (ATROPISOMER_SHIFT + (isFirst ? 2 : 0))) & 3;
- return a1.getEdges()[i1 - 1].getOtherAtomNode(a1);
+ return (Node) a1.getEdges()[i1 - 1].getOtherNode(a1);
}
public static boolean isAtropism(int order) {
@@ -346,10 +346,17 @@
}
+ /**
+ * @param c
+ */
public void setCIPChirality(int c) {
// default is no action
}
+ /**
+ * @param doCalculate
+ * @return CIP chirality label
+ */
public String getCIPChirality(boolean doCalculate) {
return "";
}
Modified: trunk/Jmol/src/org/jmol/util/JmolMolecule.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/JmolMolecule.java 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/util/JmolMolecule.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -318,7 +318,7 @@
for (int i = bonds.length; --i >= 0;) {
Edge bond = bonds[i];
if (bond != null && bond.isCovalent()
- && !getCovalentlyConnectedBitSet(atoms, bond.getOtherAtomNode(atom),
+ && !getCovalentlyConnectedBitSet(atoms, (Node)
bond.getOtherNode(atom),
bsToTest, allowCyclic, allowBioResidue, biobranches, bsResult))
return false;
}
Modified: trunk/Jmol/src/org/jmol/util/Node.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Node.java 2017-05-27 17:45:55 UTC (rev
21619)
+++ trunk/Jmol/src/org/jmol/util/Node.java 2017-05-27 20:31:36 UTC (rev
21620)
@@ -29,24 +29,32 @@
import org.jmol.java.BS;
-public interface Node {
+public interface Node extends SimpleNode {
// abstracts out the essential pieces for SMILES processing
public int getAtomicAndIsotopeNumber();
+ @Override
public String getAtomName();
public int getAtomSite();
public int getBondedAtomIndex(int j);
+ @Override
public int getCovalentBondCount();
public int getCovalentHydrogenCount();
+ @Override
public Edge[] getEdges();
+ @Override
public int getElementNumber();
public int getFormalCharge();
+ @Override
public int getIndex();
+ @Override
public int getIsotopeNumber();
+ @Override
public int getValence();
public void set(float x, float y, float z);
public int getMoleculeNumber(boolean inModel);
+ @Override
public int getNominalMass();
@@ -62,8 +70,6 @@
public BS findAtomsLike(String substring);
public String getAtomType();
public int getModelIndex();
- // could include hydrogen bonds
- public int getBondCount();
public int getAtomNumber();
/**
* can be > 0 for PDB model with no H atoms or for SMILES string CCC
@@ -99,7 +105,9 @@
char getBioSmilesType();
String getCIPChirality(boolean doCalculate);
int getCIPChiralityCode();
+ @Override
void setCIPChirality(int c);
+ @Override
public P3 getXYZ();
}
Added: trunk/Jmol/src/org/jmol/util/SimpleEdge.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SimpleEdge.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/util/SimpleEdge.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -0,0 +1,12 @@
+package org.jmol.util;
+
+
+public interface SimpleEdge {
+
+ int getCovalentOrder();
+
+ SimpleNode getOtherNode(SimpleNode a);
+
+ boolean isCovalent();
+
+}
Property changes on: trunk/Jmol/src/org/jmol/util/SimpleEdge.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: trunk/Jmol/src/org/jmol/util/SimpleNode.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SimpleNode.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/util/SimpleNode.java 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -0,0 +1,37 @@
+package org.jmol.util;
+
+
+import javajs.util.P3;
+
+/**
+ * Just the bare minimum to accomplish CIP and non-BioSMILES
+ */
+public interface SimpleNode {
+
+ void setCIPChirality(int rs);
+
+ int getIsotopeNumber();
+
+ String getAtomName();
+
+ // could include hydrogen bonds
+ int getBondCount();
+
+ int getCovalentBondCount();
+
+ SimpleEdge[] getEdges();
+
+ int getElementNumber();
+
+ int getFormalCharge();
+
+ int getIndex();
+
+ int getNominalMass();
+
+ int getValence();
+
+ P3 getXYZ();
+
+
+}
Property changes on: trunk/Jmol/src/org/jmol/util/SimpleNode.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-27 17:45:55 UTC
(rev 21619)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-27 20:31:36 UTC
(rev 21620)
@@ -56,8 +56,12 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.17.1" // 2017.05.27
+Jmol.___JmolVersion="14.17.2"
+code: CIPChirality.java fully interfaced using SimpleNode and SimpleEdge
+
+JmolVersion="14.17.1" // 2017.05.27
+
new feature: atom property x.cipRule
-- CIP sequence rule deciding this center
-- one of 1a, 1b, 2, 3, 4a, 4b, 4c, 5, or blank
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