Revision: 21580
http://sourceforge.net/p/jmol/code/21580
Author: hansonr
Date: 2017-04-30 20:40:31 +0000 (Sun, 30 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.3"
bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
bug fix: JVXL reader not reading Gaussian files with "1" in the third line, 5th
field
bug fix: CIP chirality may not show M/P for atropisomeric atoms
test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java 2017-04-30
02:04:08 UTC (rev 21579)
+++ trunk/Jmol/src/org/jmol/renderbio/NucleicRenderer.java 2017-04-30
20:40:31 UTC (rev 21580)
@@ -114,12 +114,16 @@
}
bsr.renderHermiteConic(i, false, 4);
colix = bsr.getLeadColix(i);
- if (bsr.setBioColix(colix))
- renderNucleicBaseStep(i);
+ if (bsr.setBioColix(colix)) {
+ if (cartoonRibose && bsVisible.get(i + 1))
+ renderNucleicBaseStep(i, pts[i + 1], screens[i + 1]);
+ else
+ renderNucleicBaseStep(i, null, null);
+ }
}
}
- private void renderNucleicBaseStep(int im) {
+ private void renderNucleicBaseStep(int im, T3 ptPnext, T3 scrPnext) {
if (bsr.isPhosphorusOnly)
return;
NucleicMonomer nucleotide = (NucleicMonomer) bsr.monomers[im];
@@ -201,7 +205,10 @@
renderEdge(rScr, rPt, 3, 6); // C4' - C5'
renderEdge(rScr, rPt, 6, 7); // C5' - O5'
renderEdge(rScr, rPt, 7, 8); // O5' - P'
+ renderEdge(rScr, rPt, 0, 4); // C1' - O4'
renderCyl(rScr[0], baseScreen, rPt[0], basePt); // C1' - N1 or N9
+ if (ptPnext != null)
+ renderCyl(rScr[5], (P3) scrPnext, rPt[5], (P3) ptPnext); // O3' - P(+1)
drawEdges(rScr, rPt, 5);
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-30 02:04:08 UTC
(rev 21579)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-30 20:40:31 UTC
(rev 21580)
@@ -905,12 +905,18 @@
boolean isAlkene;
/**
- * parent atom of a second alkene or cumulene atom
+ * first atom of an alkene or cumulene atom
*/
CIPAtom alkeneParent;
/**
+ * last atom of an alkene or cumulene atom
+ */
+
+ CIPAtom alkeneChild;
+
+ /**
* a flag used in Rule 3 to indicate the second carbon of a double bond
*/
@@ -1154,7 +1160,9 @@
} else {
isAlkeneAtom2 = true;
}
+ parent.alkeneChild = null;
alkeneParent = (parent.alkeneParent == null ? parent :
parent.alkeneParent);
+ alkeneParent.alkeneChild = this;
if (parent.alkeneParent == null)
parent.nextSP2 = this;
}
@@ -1606,7 +1614,7 @@
* the root atom. This must be reconstructed, because until this point we
* have not carried out many of the necessary comparisons.
*
- * @return [1: "Zaux", 2: "Eaux", 3: no chirality]
+ * @return one of [STEREO_Z, STEREO_E, NO_CHIRALITY]
*/
private int getEZaux() {
// this is the second atom of the alkene, checked as the parent of the
next atom
@@ -1791,11 +1799,11 @@
int n = aStr.length();
if (n == 0 || n != bStr.length())
return TIED;
- char aref = aStr.charAt(0);
- char bref = bStr.charAt(0);
+ char aref = fixMataRef(aStr.charAt(0));
+ char bref = fixMataRef(bStr.charAt(0));
for (int c = 1; c < n; c++) {
- boolean alike = (aref == aStr.charAt(c));
- boolean blike = (bref == bStr.charAt(c));
+ boolean alike = (aref == fixMataRef(aStr.charAt(c)));
+ boolean blike = (bref == fixMataRef(bStr.charAt(c)));
if (alike != blike)
return (isRSTest ? c : 1) * (alike ? A_WINS : B_WINS);
}
@@ -1810,6 +1818,20 @@
return aref < bref ? A_WINS : B_WINS;
}
+ private char fixMataRef(char c) {
+ switch (c) {
+ case 'R':
+ case 'M':
+ case 'Z':
+ return 'R';
+ case 'S':
+ case 'P':
+ case 'E':
+ return 'S';
+ default:
+ return c;
+ }
+ }
/**
* Retrieve the Mata Rule 4b list for a given atom.
*
@@ -2056,6 +2078,12 @@
if (!done) {
s = "?" + sphere;
subRS = "[" + subRS + "]";
+ } else if (isAlkene && alkeneChild != null) {
+ // this does not work. Is "E" a "chiral unit"?
+// int ez = alkeneChild.getEZaux();
+// s = (ez == STEREO_Z ? "D" : ez == STEREO_E ? "E" : "~");
+// System.out.println(myPath + s);
+// System.out.println("?");
} else if (!isRoot && (bondCount == 4 && nPriorities >= 3 -
Math.abs(adj)
|| bondCount == 3 && elemNo > 10 && nPriorities >= 2 -
Math.abs(adj))) {
// if here, adj is TIED (0), A_WINS (-1), or B_WINS (1)
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2017-04-30 02:04:08 UTC
(rev 21579)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2017-04-30 20:40:31 UTC
(rev 21580)
@@ -1256,8 +1256,8 @@
tokens = PT.getTokens(line3);
if (tokens[0].indexOf(".") > 0)
return (line3.length() >= 60 || tokens.length != 3 ? null :
"VaspChgcar"); // M40 files are > 60 char
- if (nAtoms >= 0)
- return (tokens.length == 4 ? "Cube" : null); //Can't be a Jvxl file;
+ if (nAtoms >= 0)
+ return (tokens.length == 4 || tokens.length == 5 &&
tokens[4].equals("1") ? "Cube" : null); //Can't be a Jvxl file;
nAtoms = -nAtoms;
for (int i = 4 + nAtoms; --i >= 0;)
if ((line = br.readLineWithNewline()) == null)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-30 02:04:08 UTC
(rev 21579)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-30 20:40:31 UTC
(rev 21580)
@@ -51,6 +51,8 @@
Jmol.___JmolVersion="14.15.3"
+bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
+bug fix: JVXL reader not reading Gaussian files with "1" in the third line,
5th field
bug fix: CIP chirality may not show M/P for atropisomeric atoms
test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
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