Revision: 20801
http://sourceforge.net/p/jmol/code/20801
Author: hansonr
Date: 2015-10-01 06:12:01 +0000 (Thu, 01 Oct 2015)
Log Message:
-----------
JmolVersion="14.3.16_2015.09.30"
new feature: calculate hydrogen TRUE
-- calculates hydrogen and multiple bonding
bug fix: calculate aromatic should not touch atoms with 4 groups or H atoms
bug fix: calculate hydrogen should consider backbone N sp2.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-09-29
21:53:26 UTC (rev 20800)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-10-01
06:12:01 UTC (rev 20801)
@@ -1301,7 +1301,8 @@
// 2 bonds needed R2C or R-N or R2C=C or O
// or RC=C or C=C
boolean isEne = (hybridization == 2 || atomicNumber == 5 || nBonds
== 1
- && targetValence == 4 || atomicNumber == 7 &&
isAdjacentSp2(atom));
+ && targetValence == 4
+ || atomicNumber == 7 && isAdjacentSp2(atom));
getHybridizationAndAxes(i, atomicNumber, z, x, (isEne ? "sp2b"
: targetValence == 3 ? "sp3c" : "lpa"), false, true);
pt = P3.newP(z);
@@ -1332,7 +1333,8 @@
continue;
}
if (getHybridizationAndAxes(i, atomicNumber, z, x,
(hybridization == 2 || atomicNumber == 5
- || atomicNumber == 7 && isAdjacentSp2(atom)
+ || atomicNumber == 7
+ && (atom.group.getNitrogenAtom() == atom ||
isAdjacentSp2(atom))
? "sp2c"
: "sp3d"), true, false) != null) {
pt = P3.newP(z);
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-09-29
21:53:26 UTC (rev 20800)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-10-01
06:12:01 UTC (rev 20801)
@@ -478,15 +478,26 @@
Bond bond;
isAll = (bsBonds == null);
i0 = (isAll ? bondCount - 1 : bsBonds.nextSetBit(0));
+ BS bsTest = new BS();
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsBonds.nextSetBit(i + 1))) {
bond = bo[i];
if (!bond.is(Edge.BOND_AROMATIC)
|| bsAromaticDouble.get(i) || bsAromaticSingle.get(i))
continue;
- if (!assignAromaticDouble(bond))
- assignAromaticSingle(bond);
- System.out.println(bond + " "+ bond.order);
+ bsTest.set(i);
+ if (bond.atom1.getElementNumber() == 8 ||
bond.atom2.getElementNumber() == 8) {
+ if (!assignAromaticDouble(bond))
+ assignAromaticSingle(bond);
+ } else {
+ bsTest.set(i);
+ }
}
+ // now test non-O atoms
+ for (int i = bsTest.nextSetBit(0); i >= 0; i = bsTest.nextSetBit(i + 1)) {
+ bond = bo[i];
+ if (!assignAromaticDouble(bond))
+ assignAromaticSingle(bond);
+ }
// all done: do the actual assignments and clear arrays.
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsBonds.nextSetBit(i + 1))) {
bond = bo[i];
@@ -642,10 +653,11 @@
case 6: // C
return (nAtoms == 4);
case 7: // N
+ return (atom.group.getNitrogenAtom() == atom || nAtoms == 3 &&
atom.getFormalCharge() < 1);
case 8: // O
- return (nAtoms == 10 - n && atom.getFormalCharge() < 1);
+ return (atom.group.getCarbonylOxygenAtom() != atom && nAtoms == 2 &&
atom.getFormalCharge() < 1);
case 16: // S
- return (nAtoms == 18 - n && atom.getFormalCharge() < 1);
+ return (atom.group.groupID == JC.GROUPID_CYSTEINE || nAtoms == 2 &&
atom.getFormalCharge() < 1);
}
return false;
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-09-29 21:53:26 UTC
(rev 20800)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-10-01 06:12:01 UTC
(rev 20801)
@@ -2404,6 +2404,7 @@
Atom atomB = null;
char altloc = '\0';
short newOrder = (short) (order | Edge.BOND_NEW);
+ boolean isAromatic = ((order & Edge.BOND_AROMATIC_MASK) != 0);
try {
for (int i = bsA.nextSetBit(0); i >= 0; i = bsA.nextSetBit(i + 1)) {
if (isBonds) {
@@ -2434,7 +2435,11 @@
if ((bondAB == null ? idOrModifyOnly : createOnly)
|| checkDistance
&& !isInRange(atomA, atomB, minD, maxD, minDIsFrac, maxDIsFrac,
- isFractional))
+ isFractional)
+ || isAromatic
+ && (atomA.getElementNumber() == 1 ||
atomA.getCovalentBondCount() > 3
+ || atomB.getElementNumber() == 1 ||
atomB.getCovalentBondCount() > 3)
+ )
continue;
if (bondAB == null) {
bsBonds.set(bondAtoms(atomA, atomB, order, mad, bsBonds, energy,
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-09-29 21:53:26 UTC
(rev 20800)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-10-01 06:12:01 UTC
(rev 20801)
@@ -643,10 +643,21 @@
eval.report(GT.i(GT._("{0} hydrogen bonds"), Math.abs(n)));
return;
case T.hydrogen:
- bs1 = (slen == 2 ? null : atomExpressionAt(2));
+ boolean andBond = (tokAt(2) == T.on);
+ if (andBond)
+ eval.iToken++;
+ bs1 = (slen == (andBond ? 3 : 2) ? null : atomExpressionAt(andBond ? 3
: 2));
eval.checkLast(eval.iToken);
- if (!chk)
+ if (!chk) {
vwr.addHydrogens(bs1, false, false);
+ if (andBond) {
+ if (bs1 == null)
+ bs1 = vwr.bsA();
+ vwr.makeConnections(0.1f, 1e8f, Edge.BOND_AROMATIC,
+ T.modify, bs1, bs1, null, false, false, 0);
+ vwr.ms.assignAromaticBondsBs(true, null);
+ }
+ }
return;
case T.partialcharge:
eval.iToken = 1;
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2015-09-29 21:53:26 UTC (rev
20800)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2015-10-01 06:12:01 UTC (rev
20801)
@@ -620,7 +620,8 @@
// structure related
//
"@alpha _a=2", // rasmol doc says "approximately *.CA" - whatever?
- "@backbone
protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)",
+ "@bbone0 protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)",
// may or may not include H
+ "@backbone back_bone | _H && connected(single, bbone0)",
"@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12",
"@sidechain (protein,nucleic) & !backbone",
"@base nucleic & !backbone",
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-29 21:53:26 UTC
(rev 20800)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-01 06:12:01 UTC
(rev 20801)
@@ -65,18 +65,27 @@
bug fix: draw ramachandran broken
+JmolVersion="14.3.16_2015.09.30"
+new feature: calculate hydrogen TRUE
+ -- calculates hydrogen and multiple bonding
+
+bug fix: calculate aromatic should not touch atoms with 4 groups or H atoms
+bug fix: calculate hydrogen should consider backbone N sp2.
+
JmolVersion="14.3.16_2015.09.29"
note: I am using "map" for "associative array" now
new feature: mapOfMaps.array(k)
- -- generates an array of maps from a map of maps by storing all map keys
under key k
+ -- generates an array of maps from a map of maps by
+ storing all top-level map keys under key k in lower-level map
-- reversed by another .array(k)
-- causes a script exception if mapOfMaps is not a map of maps
new feature: arrayOfMaps.array(k)
- -- generates a map of maps from an array of maps by retrieving each map's key
k as the key for that map
+ -- generates a map of maps from an array of maps by
+ removing each map's key k and using that as the key for that map value
-- reversed by another .array(k)
-- causes a script exception if arrayOfMaps is not an array of maps or key k
is not present in all maps
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