Revision: 21640
http://sourceforge.net/p/jmol/code/21640
Author: hansonr
Date: 2017-06-25 20:37:45 +0000 (Sun, 25 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.19.1"
bug fix: CIPChirality: minor fixes for Rule 4b and 5 for BH64_012-015; better
atropisomer check
bug fix; SPIN QUATERNION
bug fix: CENTERAT ABSOLUTE broken (since forever?)
bug fix: SPIN QUATERNION {0 0 -1 0} still does a positive, not negative,
rotation
(solution is to apply a miniscule rotation of 1e-10 degrees)
bug fix: script array context [3 -0] becomes [3], as in [3 - 0]
new feature: WRITE "SDF" implements atom value V nnn ... information
-- requires assigning the data property name "atom_values" in the model's
molData property
-- for example:
$ load $2,3-dichlorobutane
$ molData = {"atom_values":"chirality"}
$ model properties "molData" molData
$ write diol.sdf
-- note that if the model already has a molData property, then use the
following to append to it:
$ molData = (_M.molData ? _M.molData : {})
$ molData.atom_values = "chirality"
$ model properties "molData" molData
new feature: x = load("filename","JSON")
-- loads JSON data into variable
bug fix: SET ANTIALIASDISPLAY requires click [via resizeImage()]
bug fix: CIP gives wrong alkene root distance for cyclopropene
bug fix: WRITE of structure file does not report number of atoms and warn if
selected is different from this molecule
bug fix: WRITE MOL using format 10f.5 instead of 10f.4 for x, y, z coordinates
bug fix: MOL/SDF files should truncate lines at 80 characters.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-06-22 16:44:35 UTC
(rev 21639)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-06-25 20:37:45 UTC
(rev 21640)
@@ -5819,7 +5819,10 @@
int direction = 1;
int tok;
Quat q = null;
+ boolean qGT180 = false;
boolean helicalPath = false;
+ boolean isDegreesPerSecond = false;
+ boolean isSeconds = false;
Lst<P3> ptsB = null;
BS bsCompare = null;
P3 invPoint = null;
@@ -5876,11 +5879,11 @@
// rotate spin BRANCH <DihedralList> [seconds]
if (degreesPerSecond == PT.FLOAT_MIN_SAFE) {
degreesPerSecond = floatParameter(i);
- continue;
} else if (endDegrees == Float.MAX_VALUE) {
endDegrees = degreesPerSecond;
degreesPerSecond = floatParameter(i);
- continue;
+ } else {
+ invArg();
}
} else {
// rotate ... [endDegrees]
@@ -5887,14 +5890,21 @@
// rotate ... [endDegrees] [degreesPerSecond]
if (endDegrees == Float.MAX_VALUE) {
endDegrees = floatParameter(i);
- continue;
} else if (degreesPerSecond == PT.FLOAT_MIN_SAFE) {
degreesPerSecond = floatParameter(i);
isSpin = true;
- continue;
+ } else {
+ invArg();
}
}
- invArg();
+ if (i == slen - 2 && (tokAt(i + 1) == T.misc || tokAt(i + 1) ==
T.string)) {
+ String s = paramAsStr(++i).toLowerCase();
+ if (s.equals("dps")) {
+ isDegreesPerSecond = true;
+ } else if (s.equals("sec")) {
+ isSeconds = true;
+ }
+ }
break;
case T.minus:
direction = -1;
@@ -5925,8 +5935,9 @@
if (q != null) {
if (tok == T.best && !(isMolecular = isSelected)) // yes, setting
isMolecular here.
q = q.div(vwr.tm.getRotationQ());
- if (q.q0 == 0 && isSpin)
+ if (q.q0 == 0)
q.q0 = 1e-10f;
+ qGT180 = (q.q0 < 0);
rotAxis.setT(q.getNormal());
endDegrees = q.getTheta();
}
@@ -5945,7 +5956,8 @@
return;
pts = new P3[3];
for (int j = 0; j < 3; j++)
- pts[j] = vwr.ms.getAtomSetCenter(SV.getBitSet(lst.get(n - 3 + j),
false));
+ pts[j] = vwr.ms.getAtomSetCenter(SV.getBitSet(lst.get(n - 3 + j),
+ false));
} else if (isArrayParameter(i + 1)) {
pts = getPointArray(++i, -1, false);
i = iToken;
@@ -5960,7 +5972,7 @@
if (n < 3)
return;
q = Quat.getQuaternionFrame(pts[n - 3], pts[n - 2], pts[n - 1]);
- q = Quat.new4(1,0,0,0).mulQ(q.inv().div(vwr.tm.getRotationQ()));
+ q = Quat.new4(1, 0, 0, 0).mulQ(q.inv().div(vwr.tm.getRotationQ()));
rotAxis.setT(q.getNormal());
endDegrees = q.getTheta();
break;
@@ -6008,8 +6020,8 @@
int symop = intParameter(++i);
if (chk)
continue;
- Map<String, Object> info = vwr.getSymTemp().getSpaceGroupInfo(
- vwr.ms, null, -1);
+ Map<String, Object> info = vwr.getSymTemp().getSpaceGroupInfo(vwr.ms,
+ null, -1);
Object[] op = (info == null ? null : (Object[])
info.get("operations"));
if (symop == 0 || op == null || op.length < Math.abs(symop))
invArg();
@@ -6104,12 +6116,23 @@
if (bsAtoms == null)
bsAtoms = bsCompare;
}
+ if (isSpin && qGT180) {
+ endDegrees = (endDegrees >= 0 ? 360 : -360) - endDegrees;
+ rotAxis.scale(-1);
+ }
+ if (q != null && !isSeconds && !isDegreesPerSecond) {
+ isDegreesPerSecond = (degreesPerSecond > 0);
+ isSeconds = !isDegreesPerSecond;
+ }
float rate = (degreesPerSecond == PT.FLOAT_MIN_SAFE ? 10
: endDegrees == Float.MAX_VALUE ? degreesPerSecond
- : (degreesPerSecond < 0) == (endDegrees > 0) ?
- // -n means number of seconds, not degreesPerSecond
- -endDegrees / degreesPerSecond
- : degreesPerSecond);
+ : isDegreesPerSecond ? degreesPerSecond
+ : isSeconds ? (endDegrees < 0 ? -1 : 1) * Math.abs(endDegrees
/ degreesPerSecond)
+ : (degreesPerSecond < 0) == (q == null ? endDegrees > 0
+ : true) ?
+ // -n means number of seconds, not degreesPerSecond
+ -endDegrees / degreesPerSecond
+ : degreesPerSecond);
if (dihedralList != null) {
if (!isSpin) {
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-22 16:44:35 UTC
(rev 21639)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-25 20:37:45 UTC
(rev 21640)
@@ -108,8 +108,10 @@
*
* code history:
*
- * 6/12/2017 Jmo 14.18.2 tested for Rule 1b sphere (AY236.53, 163, 173, 192);
957 lines
+ * 6/25/17 Jmol 14.19.1 minor fixes for Rule 4b and 5 for BH64_012-015; better
atropisomer check
*
+ * 6/12/2017 Jmol 14.18.2 tested for Rule 1b sphere (AY236.53, 163, 173, 192);
957 lines
+ *
* 6/8/2017 Jmol 14.18.2 removed unnecessary presort for Rule 1b
*
* 5/27/17 Jmol 14.17.2 fully interfaced using SimpleNode and SimpleEdge
@@ -437,7 +439,6 @@
// for reflection
//System.out.println("TESTING ALLOWRULE1B");
//allowRule1bAlkenes = false;
- System.out.println("TESTING SPHERE+1");
}
/**
@@ -1696,7 +1697,7 @@
}
// if this is Rule 4 or 5, then we do a check of the forward-based
stereochemical path
- boolean checkRule4List = (rule4List != null && currentRule > RULE_4a);
+ boolean checkRule4List = (rule4List != null && (currentRule == RULE_4b
|| currentRule == RULE_5));
for (int i = 0; i < 4; i++) {
CIPAtom a = atoms[i];
for (int j = i + 1; j < 4; j++) {
@@ -1781,6 +1782,7 @@
CIPAtom[] newAtoms = new CIPAtom[4];
int[] newPriorities = new int[4];
+ String[] newRule4List = (rule4List == null ? null : new String[4]);
BS bs = new BS();
for (int i = 0; i < 4; i++) {
@@ -1787,11 +1789,14 @@
int pt = indices[i];
CIPAtom a = newAtoms[pt] = atoms[i];
newPriorities[pt] = priorities[i];
+ if (rule4List != null)
+ newRule4List[pt] = rule4List[i];
if (a.atom != null)
bs.set(priorities[i]);
}
atoms = newAtoms;
priorities = newPriorities;
+ rule4List = newRule4List;
nPriorities = bs.cardinality();
// Check for pseudochirality
@@ -2050,13 +2055,12 @@
case RULE_3:
return checkRule3(b); // can be IGNORE
case RULE_4a:
- return checkRules4a(b, " sr SR PM");
+ return checkRules4ac(b, " sr SR PM");
+ case RULE_4c:
+ return checkRules4ac(b, " s r p m");
case RULE_4b:
- case RULE_4c:
case RULE_5:
return TIED; // not carried out here because these need access to a
full list of ligands
- // case RULE_4c: // taken care of by RULE_4bc
- // return checkRules4a4c(b, " s r");
}
}
@@ -2265,7 +2269,7 @@
}
/**
- * Chapter 9 Rules 4 and 5: like vs. unlike
+ * Chapter 9 Rules 4b and 5: like vs. unlike
*
* Compare two strings such as RSSSR and SRSRR for like and unlike and find
* a winner. Return IGNORE if they are identical; return A_WINS or B_WINS
if
@@ -2282,57 +2286,60 @@
// resolved as "r" or "s"
// but generally we will want to process this as "R" and "S"
// note that this analysis cannot be done ahead of time
- String aStr = rule4List[ia].substring(1), bStr =
rule4List[ib].substring(1);
- if (currentRule == RULE_4c) {
- aStr = PT.rep(aStr, "~", "");
- bStr = PT.rep(bStr, "~", "");
+ String aStr = rule4List[ia].substring(1), bStr = rule4List[ib]
+ .substring(1);
+ boolean haveRSOptions = false, isRule5 = (currentRule == RULE_5);
+ String sa = "", sb = "";
+ if (atoms[ia].nextChiralBranch != null) {
+ sa = atoms[ia].nextChiralBranch.getMataList(getFirstRef(aStr),
isRule5);
+ }
+ if (atoms[ib].nextChiralBranch != null) {
+ sb = atoms[ib].nextChiralBranch.getMataList(getFirstRef(bStr),
isRule5);
+ }
+ haveRSOptions = (sa.indexOf("|") >= 0 || sb.indexOf("|") >= 0);
+ if (haveRSOptions) {
+ aStr += "|" + sa;
+ bStr += "|" + sb;
} else {
- boolean haveRS = false, isRule5 = (currentRule == RULE_5);
- if (atoms[ia].nextChiralBranch != null) {
- String s = atoms[ia].getMataList(getFirstRef(aStr), isRule5);
- haveRS = (s.indexOf("|") >= 0);
- aStr = (haveRS ? s : aStr + s);
- }
- if (atoms[ib].nextChiralBranch != null) {
- String s = atoms[ib].getMataList(getFirstRef(bStr), isRule5);
- haveRS |= (s.indexOf("|") >= 0);
- bStr = (s.indexOf("|") < 0 ? bStr + s : s);
- }
- if (Logger.debugging)
- Logger.info(dots() + this + " comparing " + atoms[ia] + " " + aStr
- + " to " + atoms[ib] + " " + bStr); // Logger
- if (isRule5 || !haveRS && aStr.length() != bStr.length()) {
- // note that these two strings can be different lengths
- // if we have sXX and ~
- return sign(aStr.compareTo(bStr));
- }
- aStr = cleanRule4Str(aStr);
- bStr = cleanRule4Str(bStr);
- if (haveRS) {
- // Mata(2005) Figure 9
- // We are trying to ascertain that
- // R lull R luuu
- // S luuu is the same as S lull
- //
- // Solution is to SUM all winners. If that is 0, then they are the
same
- String[] aList = PT.split(aStr, "|"), bList = PT.split(bStr, "|");
- int minScore = Integer.MAX_VALUE, sumScore = 0;
- aStr = aList[0];
- bStr = bList[0];
- for (int i = aList.length; --i >= 0;) {
- for (int j = bList.length; --j >= 0;) {
- int score = compareRule4PairStr(aList[i], bList[j], true);
- sumScore += score;
- if (score != TIED && Math.abs(score) <= minScore) {
- minScore = Math.abs(score);
- aStr = aList[i];
- bStr = bList[j];
- }
+ aStr += sa;
+ bStr += sb;
+ }
+
+ if (true || Logger.debugging)
+ Logger.info(dots() + this + " comparing " + atoms[ia] + " " + aStr
+ + " to " + atoms[ib] + " " + bStr); // Logger
+ if (isRule5 || !haveRSOptions && aStr.length() != bStr.length()) {
+ // note that these two strings can be different lengths
+ // if we have sXX and ~
+ return sign(aStr.compareTo(bStr));
+ }
+ aStr = cleanRule4Str(aStr);
+ bStr = cleanRule4Str(bStr);
+ if (haveRSOptions) {
+ // Mata(2005) Figure 9
+ // We are trying to ascertain that
+ // R lull R luuu
+ // S luuu is the same as S lull
+ //
+ // Solution is to SUM all winners. If that is 0, then they are the same
+ String[] aList = PT.split(aStr, "|"), bList = PT.split(bStr, "|");
+ int minScore = Integer.MAX_VALUE, sumScore = 0;
+ aStr = aList[0] + aList[1];
+ bStr = bList[0] + bList[1];
+ for (int i = aList.length; --i >= 1;) {
+ for (int j = bList.length; --j >= 1;) {
+ int score = compareRule4PairStr(aList[0] + aList[i], bList[0]
+ + bList[j], true);
+ sumScore += score;
+ if (score != TIED && Math.abs(score) <= minScore) {
+ minScore = Math.abs(score);
+ aStr = aList[0] + aList[i];
+ bStr = bList[0] + bList[j];
}
}
- if (sumScore == TIED)
- return TIED;
}
+ if (sumScore == TIED)
+ return TIED;
}
if (aStr.length() == 1 && "RS".indexOf(aStr) < 0) {
int score = checkEnantiomer(aStr, bStr, 0, aStr.length(), " rs");
@@ -2360,7 +2367,7 @@
*/
private String getFirstRef(String aStr) {
int r = aStr.indexOf("R"), s = aStr.indexOf("S");
- return (r < 0 && s < 0 ? null : r < 0 ? "S" : "R");
+ return (r < 0 && s < 0 ? null : s > 0 && (r < 0 || r > s) ? "S" : "R");
}
/**
@@ -2407,7 +2414,7 @@
/**
* This is the key Mata method -- getting the correct sequence of R and S
- * from a set of diasteromorphic paths. Given a specific reference
+ * from a set of diastereomorphic paths. Given a specific reference
* designation, the task is to sort the paths based on priority (we can't
* change the base priority already determined using Rules 1-3) and
* reference.
@@ -2596,7 +2603,7 @@
case A_WINS:
case B_WINS:
isBranch = true;
- noPseudo = subRS.indexOf("r") >= 0;
+ noPseudo = (subRS.indexOf("r") >= 0);
// enantiomers -- we have an r/s situation
// process to determine chirality, but then set ret[0] to be null
subRS = "";
@@ -2713,7 +2720,6 @@
}
if (noPseudo)
s = s.toUpperCase(); // Rule 4c or diasteriomers // AY-236.148
- auxChirality = s;
subRS = "";
//if (ret != null)
//ret[0] = null;
@@ -2730,6 +2736,7 @@
parent.addMataRef(sphere, priority, rs);
}
}
+ auxChirality = s;
}
}
}
@@ -2812,8 +2819,17 @@
return NOT_RELEVANT;
if (rs1.equals(rs2))
return TIED;
- boolean haveRS = (rs1.indexOf("R") >= 0 || rs1.indexOf("S") >= 0);
- String rs = (haveRS ? "~RS" : "~rs");
+ String rs = rs1 + rs2;
+ //System.out.println("compareRule4aIsomers:" + rs1 + " vs. " + rs2);
+ boolean haveRS = (rs.indexOf("R") >= 0 || rs.indexOf("S") >= 0);
+ if ((rs.indexOf("r") >= 0 || rs.indexOf("s") >= 0)) {
+ // consider Rule 4a here -- Sr beats R~ BH64_014
+ if (rs1.endsWith("~"))
+ return (DIASTEREOMERIC_B_WINS);
+ if (rs2.endsWith("~"))
+ return (DIASTEREOMERIC_A_WINS);
+ }
+ rs = (haveRS ? "~RS" : "~rs");
if (haveRS) {
rs1 = PT.replaceAllCharacters(rs1, "rs", "~");
rs2 = PT.replaceAllCharacters(rs2, "rs", "~");
@@ -2840,7 +2856,7 @@
* @param m
* @param n
* @param rs
- * @return DIASTEROMERIC, A_WINS, or B_WINS
+ * @return DIASTEREOMERIC, A_WINS, or B_WINS
*/
private int checkEnantiomer(String rs1, String rs2, int m, int n, String
rs) {
int finalScore = TIED; // not a possible return
@@ -2921,11 +2937,15 @@
* String to test against; depends upon subrule being checked
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
- private int checkRules4a(CIPAtom b, String test) {
+ private int checkRules4ac(CIPAtom b, String test) {
if (isTerminal || isDuplicate)
return TIED;
int isRa = test.indexOf(auxChirality), isRb =
test.indexOf(b.auxChirality);
- return (isRa > isRb + 1 ? A_WINS : isRb > isRa + 1 ? B_WINS : TIED);
+ return (isRa > isRb + 1 ?
+ A_WINS
+ : isRb > isRa + 1 ?
+ B_WINS
+ : TIED);
}
/**
@@ -2967,6 +2987,7 @@
a.htPathPoints = htPathPoints;
a.doCheckPseudo = false;
a.alkeneParent = null;
+ a.auxChirality = "~";
for (int i = 0; i < 4; i++)
if (atoms[i] != null)
a.atoms[i] = atoms[i];
@@ -2978,7 +2999,9 @@
public String toString() {
return (atom == null ? "<null>" : "[" + currentRule + "." + sphere + ","
+ id + "." + atom.getAtomName()
- + (isDuplicate ? "*(" + rootDistance + ")": "") + "]");
+ + (isDuplicate ? "*(" + rootDistance + ")": "")
+ + (auxChirality == null ? "" : auxChirality)
+ + "]");
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-06-22 16:44:35 UTC
(rev 21639)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-06-25 20:37:45 UTC
(rev 21640)
@@ -768,7 +768,10 @@
CIPChirality cip = getCIPChirality(vwr);
BS bsAtropisomer = null, bsHelixM = null, bsHelixP = null;
try {
- bsAtropisomer = vwr.getSmartsMatch("a-a", bsAtoms);
+// four ortho groups required: bsAtropisomer =
vwr.getSmartsMatch("[!H](.t3:-20,20)a1(.t3).[!H](.t1:-20,20)a(.t1)a1(.t1)(.t2:-20,20)(.t3)(.t4:-20,20)-{a}2(.t1)(.t2)(.t3)(.t4)a(.t2)[!H](.t2).a2(.t4)[!H](.t4)",
bsAtoms);
+// three ortho groups required: bsAtropisomer =
vwr.getSmartsMatch("[!H](.t3:-20,20)a1(.t3).[!H](.t1:-20,20)a(.t1){a}1(.t1)(.t2:-20,20)(.t3)-{a}(.t1)(.t2)(.t3)a(.t2)[!H](.t2)",
bsAtoms);
+// one ortho group on each ring required:
+ bsAtropisomer =
vwr.getSmartsMatch("[!H](.t1:-20,20)a{a(.t2:-20,20)-a}a[!H]", bsAtoms);
bsHelixM = vwr.getSmartsMatch("A{a}(.t:-10,-40)a(.t:-10,-40)aaa",
bsAtoms);
bsHelixP = vwr.getSmartsMatch("A{a}(.t:10,40)a(.t:10,40)aaa", bsAtoms);
} catch (Exception e) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-22 16:44:35 UTC
(rev 21639)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-25 20:37:45 UTC
(rev 21640)
@@ -58,11 +58,13 @@
Jmol.___JmolVersion="14.19.1"
+bug fix: CIPChirality: minor fixes for Rule 4b and 5 for BH64_012-015; better
atropisomer check
+bug fix; SPIN QUATERNION
bug fix: CENTERAT ABSOLUTE broken (since forever?)
-bug fix: SPIN quaternion {0 0 -1 0} still does a positive, not negative,
rotation
+bug fix: SPIN QUATERNION {0 0 -1 0} still does a positive, not negative,
rotation
(solution is to apply a miniscule rotation of 1e-10 degrees)
-bug fix: scirpt array context [3 -0] becomes [3], as in [3 - 0]
+bug fix: script array context [3 -0] becomes [3], as in [3 - 0]
new feature: WRITE "SDF" implements atom value V nnn ... information
-- requires assigning the data property name "atom_values" in the model's
molData property
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