Revision: 21572
http://sourceforge.net/p/jmol/code/21572
Author: hansonr
Date: 2017-04-29 18:56:28 +0000 (Sat, 29 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.2" // 4/29/17
bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for
cumulenes
bug fix: CIP chirality adds atropisomer chirality (M/P[Ra/Sa], m/p[ra/sa]) for
biaryls
bug fix: CIP chirality adds cumulene E/Z chirality
-- 816 lines
-- validation data are at
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
-- validates for 160 structures (some duplicates; both cip_examples.zip and
stereo_test_cases.sdf)
-- validates for all cases considered:
-- simple R/S and E/Z
-- small-ring removal of E/Z
-- parallel-strand Rule 4b and Rule 5 (Mata)
-- pseudochiral r/s and m/p
-- odd and even cumulenes
-- atropisomers
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-29 18:49:38 UTC
(rev 21571)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-29 18:56:28 UTC
(rev 21572)
@@ -233,6 +233,9 @@
static final int STEREO_R = JC.CIP_CHIRALITY_R_FLAG;
static final int STEREO_S = JC.CIP_CHIRALITY_S_FLAG;
+ static final int STEREO_M = JC.CIP_CHIRALITY_M_FLAG;
+ static final int STEREO_P = JC.CIP_CHIRALITY_P_FLAG;
+
static final int STEREO_Z = JC.CIP_CHIRALITY_Z_FLAG;
static final int STEREO_E = JC.CIP_CHIRALITY_E_FLAG;
@@ -807,13 +810,10 @@
int c = NO_CHIRALITY;
if (atop >= 0 && btop >= 0) {
if (isAxial) {
- c = (isRa(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_R
- : STEREO_S);
- if (c != NO_CHIRALITY) {
- c |= JC.CIP_CHIRALITY_AXIAL_FLAG;
- if ((a2.ties == null) != (b2.ties == null))
- c |= JC.CIP_CHIRALITY_PSEUDO_FLAG;
- }
+ c = (isPos(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_P
+ : STEREO_M);
+ if ((a2.ties == null) != (b2.ties == null))
+ c |= JC.CIP_CHIRALITY_PSEUDO_FLAG;
} else {
c = (isCis(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_Z
: STEREO_E);
@@ -847,7 +847,8 @@
}
/**
- *
+ * Checks the torsion angle and returns true if it is positive
+ *
* @param a
* @param b
* @param c
@@ -854,10 +855,9 @@
* @param d
* @return true if torsion angle is
*/
- boolean isRa(CIPAtom a, CIPAtom b, CIPAtom c, CIPAtom d) {
- float angle = Measure.computeTorsion(a.atom.getXYZ(), b.atom.getXYZ(),
c.atom.getXYZ(),
- d.atom.getXYZ(), true);
- return angle < 0;
+ boolean isPos(CIPAtom a, CIPAtom b, CIPAtom c, CIPAtom d) {
+ return (Measure.computeTorsion(a.atom.getXYZ(), b.atom.getXYZ(),
c.atom.getXYZ(),
+ d.atom.getXYZ(), true) > 0);
}
final static int[] PRIORITY_SHIFT = new int[] { 24, 20, 12, 8, 4, 0 };
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2017-04-29 18:49:38 UTC (rev
21571)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2017-04-29 18:56:28 UTC (rev
21572)
@@ -48,18 +48,21 @@
public final static int CIP_CHIRALITY_R_FLAG = 1;
public final static int CIP_CHIRALITY_S_FLAG = 2;
public final static int CIP_CHIRALITY_NONE = 3;
- public final static int CIP_CHIRALITY_PSEUDO_FLAG = 4;
- public final static int CIP_CHIRALITY_r_FLAG = CIP_CHIRALITY_R_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
- public final static int CIP_CHIRALITY_s_FLAG = CIP_CHIRALITY_S_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
public final static int CIP_CHIRALITY_CANTDETERMINE = 7;
+
public final static int CIP_CHIRALITY_Z_FLAG = 1 << 3; // 0x08
public final static int CIP_CHIRALITY_E_FLAG = 2 << 3; // 0x10 Z|E is "no
chirality"
+
public final static int CIP_CHIRALITY_AXIAL_FLAG = 4 << 3;
- public final static int CIP_CHIRALITY_Ra_FLAG = CIP_CHIRALITY_R_FLAG |
CIP_CHIRALITY_AXIAL_FLAG;
- public final static int CIP_CHIRALITY_Sa_FLAG = CIP_CHIRALITY_S_FLAG |
CIP_CHIRALITY_AXIAL_FLAG;
- public final static int CIP_CHIRALITY_ra_FLAG = CIP_CHIRALITY_Ra_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
- public final static int CIP_CHIRALITY_sa_FLAG = CIP_CHIRALITY_Sa_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
+ public final static int CIP_CHIRALITY_M_FLAG = CIP_CHIRALITY_R_FLAG |
CIP_CHIRALITY_AXIAL_FLAG;
+ public final static int CIP_CHIRALITY_P_FLAG = CIP_CHIRALITY_S_FLAG |
CIP_CHIRALITY_AXIAL_FLAG;
+ public final static int CIP_CHIRALITY_PSEUDO_FLAG = 4;
+ public final static int CIP_CHIRALITY_r_FLAG = CIP_CHIRALITY_R_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
+ public final static int CIP_CHIRALITY_s_FLAG = CIP_CHIRALITY_S_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
+ public final static int CIP_CHIRALITY_m_FLAG = CIP_CHIRALITY_M_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
+ public final static int CIP_CHIRALITY_p_FLAG = CIP_CHIRALITY_P_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
+
public static String getCIPChiralityName(int flags) {
switch (flags) {
case CIP_CHIRALITY_Z_FLAG:
@@ -66,10 +69,10 @@
return "Z";
case CIP_CHIRALITY_E_FLAG:
return "E";
- case CIP_CHIRALITY_Ra_FLAG:
- return "Ra";
- case CIP_CHIRALITY_Sa_FLAG:
- return "Sa";
+ case CIP_CHIRALITY_M_FLAG:
+ return "M";
+ case CIP_CHIRALITY_P_FLAG:
+ return "P";
case CIP_CHIRALITY_R_FLAG:
return "R";
case CIP_CHIRALITY_S_FLAG:
@@ -78,10 +81,10 @@
return "r";
case CIP_CHIRALITY_s_FLAG:
return "s";
- case CIP_CHIRALITY_ra_FLAG:
- return "ra";
- case CIP_CHIRALITY_sa_FLAG:
- return "sa";
+ case CIP_CHIRALITY_m_FLAG:
+ return "m";
+ case CIP_CHIRALITY_p_FLAG:
+ return "p";
case CIP_CHIRALITY_CANTDETERMINE:
return "?";
case CIP_CHIRALITY_NONE:
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-29 18:49:38 UTC
(rev 21571)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-29 18:56:28 UTC
(rev 21572)
@@ -51,12 +51,19 @@
Jmol.___JmolVersion="14.15.2" // 4/29/17
-bug fix: CIP chirality adds axial chirality (Ra/Sa, ra/sa) for cumulenes
-bug fix: CIP chirality adds atropisomer chirality (Ra/Sa, ra/sa) for biaryls
+bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for
cumulenes
+bug fix: CIP chirality adds atropisomer chirality (M/P[Ra/Sa], m/p[ra/sa]) for
biaryls
bug fix: CIP chirality adds cumulene E/Z chirality
+ -- 816 lines
+ -- validation data are at
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
-- validates for 160 structures (some duplicates; both cip_examples.zip and
stereo_test_cases.sdf)
- -- 817 lines
-
+ -- validates for all cases considered:
+ -- simple R/S and E/Z
+ -- small-ring removal of E/Z
+ -- parallel-strand Rule 4b and Rule 5 (Mata)
+ -- pseudochiral r/s and m/p
+ -- odd and even cumulenes
+ -- atropisomers
JmolVersion="14.15.1" // 4/28/17
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