Revision: 21522
http://sourceforge.net/p/jmol/code/21522
Author: hansonr
Date: 2017-04-18 02:52:35 +0000 (Tue, 18 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.14.1"
new feature: CALCULATE CHIRALITY {atom set}
-- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
-- continues with Rules 3-5, which require full-molecule analysis.
-- work in progress:
-- Rules 1 and 2 complete
-- Rule 3 (E/Z) implemented
-- Rule 4 partially implemented
-- simple linear sequences of R/S ok
-- Rule 5 implemented
-- caveates
-- no pseudochirality
-- not cyclitols
-- does not distinguish rings, so inserts "Z" into ring bonds
-- only validated on
-- optionally limited to the given atom set (or the currently selected atoms
by default)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-18 02:08:41 UTC
(rev 21521)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-18 02:52:35 UTC
(rev 21522)
@@ -54,7 +54,7 @@
// Very rough Pseudocode:
//
- // individual "standard" carbon-based R/S stereochemistry (Rules 1-2)
+ // individual "standard" carbon-based R/S and E/Z stereochemistry (Rules 1,
2, and 3)
//
// getChirality(atom) {
// if (atom.getCovalentBondCount() != 4) exit NO_CHIRALITY
@@ -194,7 +194,7 @@
* Jmol viewer that created this CIPChirality object
*
*/
- Viewer vwr;
+ private Viewer vwr;
/**
* incremental pointer providing a unique ID to every CIPAtom for debugging
@@ -238,9 +238,16 @@
* @param bsAtoms
*/
public void getChiralityForAtoms(Node[] atoms, BS bsAtoms) {
+
+ // Initial Rules 1-3 only
+
BS bsToDo = BSUtil.copy(bsAtoms);
for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1))
{
Node atom = atoms[i];
+
+ // This call checks to be sure we do not already have it and also
+ // indirectly calls getAtomChirality(Node atom)
+
String c = atom.getCIPChirality(true);
if (c.length() > 0) {
bsToDo.clear(i);
@@ -247,6 +254,8 @@
}
}
+ // E/Z -- Rule 3
+
for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1))
{
Node atom = atoms[i];
Edge[] bonds = atom.getEdges();
@@ -260,6 +269,8 @@
}
}
+ // Necessary? Perhaps for pseudo-chirality
+
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1)) {
Node a = atoms[i];
if (a.getCovalentBondCount() != 4)
@@ -436,13 +447,6 @@
}
- static CIPAtom getCommonAncestor(CIPAtom a, CIPAtom b) {
- if ((a.parent == null) != (b.parent == null))
- System.out.println("OHOH3");
- while ((a = a.parent) != (b = b.parent)){}
- return a;
- }
-
final static int[] PRIORITY_SHIFT = new int[] {24, 20, 12, 8, 4, 0};
private class CIPAtom implements Comparable<CIPAtom>, Cloneable {
@@ -469,22 +473,22 @@
/**
* first atom in this atom's root branch
*/
- CIPAtom rootSubstituent;
+ private CIPAtom rootSubstituent;
/**
* Rule 1 element number
*/
- int elemNo;
+ private int elemNo;
/**
* Rule 2 nominal atomic mass; may be a rounded value so that 12C is the
same as C
*/
- int massNo;
+ private int massNo;
/**
* bond distance from the root atom to this atom
*/
- int sphere;
+ private int sphere;
/**
* the array of indices of the associated atoms in the path to this atom
@@ -500,12 +504,12 @@
*
*/
- int rootDistance;
+ private int rootDistance;
/**
* number of substituent atoms (non-null atoms[] entries)
*/
- int nAtoms;
+ private int nAtoms;
/**
* the number of distinct priorities determined for this atom for the
current rule
@@ -538,7 +542,7 @@
* a flag to prevent finalization of an atom node more than once
*
*/
- boolean isSet;
+ private boolean isSet;
/**
* a flag to indicate atom that is a duplicate of another, either due to
ring closure or multiple bonding
@@ -552,13 +556,13 @@
* a flag to indicate an atom that has no substituents; a branch end
point; typically H or a halogen (F, Cl, Br, I)
*
*/
- boolean isTerminal;
+ private boolean isTerminal;
/**
* a flag used in Rule 3 to indicate the second carbon of a double bond
*/
- boolean isAlkeneAtom2;
+ private boolean isAlkeneAtom2;
/**
* the substituents -- up to four supported here at this time
@@ -571,7 +575,7 @@
* due to equivaliencies at a given rule level, these numbers may duplicate
* and have gaps - for example, [1 1 3 4]
*/
- int[] priorities = new int[4];
+ private int[] priorities = new int[4];
/**
* a number that encodes a substituent's priority prior to any comparisons
by previous rules;
@@ -692,7 +696,7 @@
return !isTerminal;
}
- void fillNull(int pt) {
+ private void fillNull(int pt) {
for (; pt < atoms.length; pt++)
atoms[pt] = new CIPAtom(null, this, true);
}
@@ -705,7 +709,7 @@
* @param isDuplicate
* @return new atom or null
*/
- CIPAtom addAtom(int i, Node other, boolean isDuplicate) {
+ private CIPAtom addAtom(int i, Node other, boolean isDuplicate) {
if (i >= atoms.length) {
if (Logger.debugging)
Logger.info(" too many bonds on " + atom);
@@ -855,7 +859,7 @@
* @param b
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
- int checkDuplicate(CIPAtom b) {
+ private int checkDuplicate(CIPAtom b) {
return b.isDuplicate == isDuplicate ? TIED : b.isDuplicate ? A_WINS :
B_WINS;
}
@@ -867,7 +871,7 @@
* @return 1 to indicate this is the winner, -1 to indicate b is the
winner; 0
* for a tie
*/
- int breakTie(CIPAtom b) {
+ private int breakTie(CIPAtom b) {
// Do a duplicate check -- if that is not a TIE we do not have to go any
further.
@@ -991,7 +995,7 @@
* @param b
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
- int checkRule1a(CIPAtom b) {
+ private int checkRule1a(CIPAtom b) {
return b.atom == atom ? TIED : b.atom == null ? A_WINS : atom == null ?
B_WINS
: b.elemNo < elemNo ? A_WINS : b.elemNo > elemNo ? B_WINS : TIED;
}
@@ -1003,7 +1007,7 @@
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
- int checkRule1b(CIPAtom b) {
+ private int checkRule1b(CIPAtom b) {
return !b.isDuplicate || !isDuplicate ? TIED
: b.rootDistance < rootDistance ?
B_WINS
@@ -1018,7 +1022,7 @@
* @param b
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
- int checkRule2(CIPAtom b) {
+ private int checkRule2(CIPAtom b) {
return b.massNo < massNo ? A_WINS : b.massNo > massNo ? B_WINS : TIED;
}
@@ -1087,7 +1091,7 @@
return auxiliaryEZ;
}
- Lst<CIPAtom> getReturnPath(CIPAtom a) {
+ private Lst<CIPAtom> getReturnPath(CIPAtom a) {
Lst<CIPAtom> path = new Lst<CIPAtom>();
while (a.parent != null && a.parent.atoms[0] != null) {
if (Logger.debugging)
@@ -1156,7 +1160,7 @@
private int checkRule4(CIPAtom b) {
if (Logger.debugging)
Logger.info("Checking Rule 4 for " + this + " and " + b);
- int l = getCommonAncestor(this, b).knownChiralityPath.length();
+ int l = getCommonAncestor(b).knownChiralityPath.length();
if (l >= knownChiralityPath.length())
return TIED; // some H atoms
String ac = knownChiralityPath.substring(l);
@@ -1174,6 +1178,15 @@
return TIED;
}
+ private CIPAtom getCommonAncestor(CIPAtom b) {
+ CIPAtom a = this;
+ if ((a.parent == null) != (b.parent == null))
+ System.out.println("OHOH3");
+ while ((a = a.parent) != (b = b.parent)){}
+ return a;
+ }
+
+
/**
* Chapter 9 Rule 5. Implemented only for R and Z.
*
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