Revision: 20804
http://sourceforge.net/p/jmol/code/20804
Author: hansonr
Date: 2015-10-01 13:11:38 +0000 (Thu, 01 Oct 2015)
Log Message:
-----------
JmolVersion="14.3.16_2015.09.30"
new feature: calculate hydrogens TRUE
-- calculates hydrogens and multiple bonding
-- same as
calculate hydrogens
connect aromatic modify
calculate aromatic
-- similar to, but not identical to set pdbAddHydrogens
-- allows reasonable addition of multiple bonds to proteins after loading
bug fix: connect aromatic should not touch H atoms or atoms with 4 or more
covalent bonds
bug fix: calculate hydrogen should consider backbone N sp2
bug fix: {backbone} should include attached H atoms
bug fix: calculate hydrogens should not place H atoms on water
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/Atom.java
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/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-10-01 06:15:23 UTC (rev
20803)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-10-01 13:11:38 UTC (rev
20804)
@@ -444,6 +444,9 @@
valence = (byte) (nBonds < 0 ? 0 : nBonds < 0xEF ? nBonds : 0xEF);
}
+ /**
+ * return the total bond order for this atom
+ */
@Override
public int getValence() {
if (isDeleted())
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-10-01
06:15:23 UTC (rev 20803)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2015-10-01
13:11:38 UTC (rev 20804)
@@ -1236,12 +1236,14 @@
int targetValence = aaRet[0];
int hybridization = aaRet[2];
int nBonds = aaRet[3];
-
+ if (nBonds == 0 && atom.isHetero())
+ continue; // no adding to water
hAtoms[i] = new P3[n];
int hPt = 0;
if (nBonds == 0) {
switch (n) {
case 4:
+ // methane
z.set(0.635f, 0.635f, 0.635f);
pt = P3.newP(z);
pt.add(atom);
@@ -1250,6 +1252,7 @@
vConnect.addLast(atom);
//$FALL-THROUGH$
case 3:
+ // nitrogen
z.set(-0.635f, -0.635f, 0.635f);
pt = P3.newP(z);
pt.add(atom);
@@ -1258,6 +1261,7 @@
vConnect.addLast(atom);
//$FALL-THROUGH$
case 2:
+ // oxygen
z.set(-0.635f, 0.635f, -0.635f);
pt = P3.newP(z);
pt.add(atom);
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-10-01
06:15:23 UTC (rev 20803)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2015-10-01
13:11:38 UTC (rev 20804)
@@ -586,7 +586,7 @@
*/
private boolean assignAromaticSingleForAtom(Atom atom, int notBondIndex) {
Bond[] bonds = atom.bonds;
- if (bonds == null || assignAromaticSingleHetero(atom))
+ if (bonds == null)// || assignAromaticMustBeSingle(atom))
return false;
for (int i = bonds.length; --i >= 0;) {
Bond bond = bonds[i];
@@ -613,7 +613,7 @@
Bond[] bonds = atom.bonds;
if (bonds == null)
return false;
- boolean haveDouble = assignAromaticSingleHetero(atom);
+ boolean haveDouble = false;//assignAromaticMustBeSingle(atom);
int lastBond = -1;
for (int i = bonds.length; --i >= 0;) {
if (bsAromaticDouble.get(bonds[i].index))
@@ -636,7 +636,20 @@
return haveDouble;
}
- private boolean assignAromaticSingleHetero(Atom atom) {
+ protected boolean allowAromaticBond(Bond b) {
+ if (assignAromaticMustBeSingle(b.atom1)
+ || assignAromaticMustBeSingle(b.atom2))
+ return false;
+ switch (b.getCovalentOrder()) {
+ case Edge.BOND_COVALENT_SINGLE:
+ case Edge.BOND_COVALENT_DOUBLE:
+ return b.atom1.getCovalentBondCount() <= 3 &&
b.atom2.getCovalentBondCount() <= 3;
+ default:
+ return false;
+ }
+ }
+
+ private boolean assignAromaticMustBeSingle(Atom atom) {
// only C N O S may be a problematic:
int n = atom.getElementNumber();
switch (n) {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-10-01 06:15:23 UTC
(rev 20803)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-10-01 13:11:38 UTC
(rev 20804)
@@ -2436,9 +2436,7 @@
|| checkDistance
&& !isInRange(atomA, atomB, minD, maxD, minDIsFrac, maxDIsFrac,
isFractional)
- || isAromatic
- && (atomA.getElementNumber() == 1 ||
atomA.getCovalentBondCount() > 3
- || atomB.getElementNumber() == 1 ||
atomB.getCovalentBondCount() > 3)
+ || isAromatic && !allowAromaticBond(bondAB)
)
continue;
if (bondAB == null) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-01 06:15:23 UTC
(rev 20803)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-01 13:11:38 UTC
(rev 20804)
@@ -75,10 +75,13 @@
connect aromatic modify
calculate aromatic
+ -- similar to, but not identical to set pdbAddHydrogens
+ -- allows reasonable addition of multiple bonds to proteins after loading
-bug fix: calculate aromatic should not touch atoms with 4 groups or H atoms
+bug fix: connect aromatic should not touch H atoms or atoms with 4 or more
covalent bonds
bug fix: calculate hydrogen should consider backbone N sp2
bug fix: {backbone} should include attached H atoms
+bug fix: calculate hydrogens should not place H atoms on water
JmolVersion="14.3.16_2015.09.29"
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