Revision: 21597
http://sourceforge.net/p/jmol/code/21597
Author: hansonr
Date: 2017-05-14 12:06:00 +0000 (Sun, 14 May 2017)
Log Message:
-----------
CIP trimmed up and documented; 955 lines
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 2017-05-14 12:01:39 UTC
(rev 21596)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-14 12:06:00 UTC
(rev 21597)
@@ -91,8 +91,9 @@
*
* 5/06/16 validated for 236 compound set AY-236.
*
- * 5/13/16 validated for mixed Rule 4b systems involving auxiliary R/S, M/P,
and seqCis/seqTrans; 958 lines
+ * 5/13/16 Jmol 14.15.4. validated for mixed Rule 4b systems involving
auxiliary R/S, M/P, and seqCis/seqTrans; 959 lines
*
+ * 5/14/16 Jmol 14.15.5. trimmed up and documented; 955 lines
*
* NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE! NOTE!
NOTE!
*
@@ -257,7 +258,6 @@
static final int DIASTEREOMERIC = Integer.MAX_VALUE;
static final int IGNORE = Integer.MIN_VALUE;
static final int NOT_RELEVANT = Integer.MIN_VALUE;
- static final int STEREO_SAME = Integer.MAX_VALUE;
static final int STEREO_UNDETERMINED = -1;
@@ -274,8 +274,7 @@
static final int STEREO_Z = JC.CIP_CHIRALITY_Z_FLAG;
static final int STEREO_E = JC.CIP_CHIRALITY_E_FLAG;
- static final int STEREO_BOTH_RS = STEREO_R | STEREO_S;
- static final int STEREO_BOTH_EZ = STEREO_Z | STEREO_E;
+ static final int STEREO_BOTH = STEREO_R | STEREO_S; // must be the number 3
static final int RULE_1a = 1;
static final int RULE_1b = 2;
@@ -765,7 +764,7 @@
public int getAtomChirality(Node atom) {
init();
int rs = getAtomChiralityLimited(atom, null, null, RULE_5);
- return (rs == NO_CHIRALITY ? STEREO_BOTH_RS : rs);
+ return (rs == NO_CHIRALITY ? STEREO_BOTH : rs);
}
/**
@@ -964,7 +963,7 @@
{
e.printStackTrace();
}
- return STEREO_BOTH_RS;
+ return STEREO_BOTH;
}
return rs;
}
@@ -2074,7 +2073,7 @@
&& (auxEZ = alkeneParent.auxEZ) == STEREO_UNDETERMINED) {
auxEZ = getEneWinnerChirality(alkeneParent, this, RULE_3, false);
if (auxEZ == NO_CHIRALITY)
- auxEZ = STEREO_BOTH_EZ;
+ auxEZ = STEREO_BOTH;
}
alkeneParent.auxEZ = auxEZ;
if (Logger.debugging)
@@ -2541,7 +2540,7 @@
// case we have a simple E or Z, and there is no need to check
AND
// it does not contribute to the Mata sequence (so would mess it
up).
boolean isAxial = (((alkeneChild.sphere - sphere) % 2) == 0);
- if (isAxial || auxEZ == STEREO_BOTH_EZ
+ if (isAxial || auxEZ == STEREO_BOTH
&& alkeneChild.bondCount >= 2 && !isKekuleAmbigous) {
rs = getEneWinnerChirality(this, alkeneChild, RULE_5,
isAxial);
@@ -2701,7 +2700,7 @@
int score = i1 + rs.indexOf(rs2.charAt(i));
if (score == 0)
continue;
- if (score != STEREO_BOTH_RS)
+ if (score != STEREO_BOTH)
return DIASTEREOMERIC;
if (finalScore == TIED)
finalScore = (i1 == STEREO_R ? A_WINS : B_WINS);
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