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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel Atom.java,1.12,1.13 Bond.java,1.4,1.5 BondRenderer.java,1.16,1.17 Frame.java,1.20,1.21
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From: Michael T H. <mic...@us...> - 2003-12-06 21:11:56
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1:/tmp/cvs-serv11707/src/org/openscience/jmol/viewer/datamodel
Modified Files:
Atom.java Bond.java BondRenderer.java Frame.java
Log Message:
removed backbone bonding
Index: Atom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Atom.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- Atom.java 6 Dec 2003 12:07:45 -0000 1.12
+++ Atom.java 6 Dec 2003 21:11:53 -0000 1.13
@@ -219,7 +219,7 @@
return 0;
int n = 0;
for (int i = bonds.length; --i >= 0; )
- if ((bonds[i].order & Bond.COVALENT) != 0)
+ if ((bonds[i].order & JmolConstants.BOND_COVALENT) != 0)
++n;
return n;
}
Index: Bond.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Bond.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- Bond.java 27 Nov 2003 18:52:57 -0000 1.4
+++ Bond.java 6 Dec 2003 21:11:53 -0000 1.5
@@ -34,22 +34,6 @@
public class Bond {
/*
- public final static byte COVALENT = 1 << 4;
- public final static byte IONIC = 1 << 5;
- public final static byte HYDROGEN = 1 << 6;
- public final static byte BACKBONE = 1 << 7;
-
- public final static byte SINGLE = 1;
- public final static byte DOUBLE = 2;
- public final static byte TRIPLE = 3;
- public final static byte STEREO_IN = 4;
- public final static byte STEREO_OUT = 5;
- public final static byte AROMATIC = 6;
- public final static byte SULPHUR = 7;
-
- public final static byte COVALENT_MASK = 7;
- */
-
public final static byte COVALENT = 3;
public final static byte STEREO = (1 << 2);
public final static byte STEREO_NEAR = (1 << 2) | 1;
@@ -57,9 +41,9 @@
public final static byte AROMATIC = (1 << 3) | 1;
public final static byte SULFUR = 1 << 4;
public final static byte HYDROGEN = 1 << 5;
- public final static byte BACKBONE = 1 << 6;
public final static byte ALL = (byte)0xFF;
+ */
public Atom atom1;
public Atom atom2;
@@ -77,7 +61,7 @@
this.atom1 = atom1;
this.atom2 = atom2;
if (atom1.atomicNumber == 16 && atom2.atomicNumber == 16)
- order |= SULFUR;
+ order |= JmolConstants.BOND_SULFUR;
this.order = (byte)order;
this.style = style;
this.mar = mar;
@@ -85,23 +69,16 @@
}
public Bond(Atom atom1, Atom atom2, int order, JmolViewer viewer) {
- this(atom1, atom2, order,
- (order == BACKBONE
- ? JmolConstants.STYLE_NONE
- : viewer.getStyleBond()),
+ this(atom1, atom2, order, viewer.getStyleBond(),
viewer.getMarBond(), viewer.getColixBond());
}
public boolean isCovalent() {
- return (order & COVALENT) != 0;
+ return (order & JmolConstants.BOND_COVALENT) != 0;
}
public boolean isStereo() {
- return (order & STEREO) != 0;
- }
-
- public boolean isBackbone() {
- return (order & BACKBONE) != 0;
+ return (order & JmolConstants.BOND_STEREO) != 0;
}
public void deleteAtomReferences() {
Index: BondRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/BondRenderer.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- BondRenderer.java 27 Nov 2003 18:46:34 -0000 1.16
+++ BondRenderer.java 6 Dec 2003 21:11:53 -0000 1.17
@@ -102,33 +102,32 @@
}
bondOrder = getRenderBondOrder(bond.order);
switch(bondOrder) {
- case Bond.BACKBONE:
- bondOrder = 1;
case 1:
case 2:
case 3:
renderCylinder();
break;
- case Bond.STEREO_NEAR:
- case Bond.STEREO_FAR:
+ case JmolConstants.BOND_STEREO_NEAR:
+ case JmolConstants.BOND_STEREO_FAR:
renderTriangle(bond);
break;
- case Bond.HYDROGEN:
+ case JmolConstants.BOND_HYDROGEN:
renderDotted();
}
}
int getRenderBondOrder(int order) {
- if ((order & Bond.SULFUR) != 0)
- order &= ~Bond.SULFUR;
- if ((order & Bond.COVALENT) != 0) {
+ if ((order & JmolConstants.BOND_SULFUR) != 0)
+ order &= ~JmolConstants.BOND_SULFUR;
+ if ((order & JmolConstants.BOND_COVALENT) != 0) {
if (order == 1 ||
!showMultipleBonds ||
modeMultipleBond == JmolConstants.MULTIBOND_NEVER ||
(modeMultipleBond == JmolConstants.MULTIBOND_SMALL &&
- marBond > JmolConstants.marMultipleBondSmallMaximum))
- // there used to be a test here for order == -1 ? why ?
+ marBond > JmolConstants.marMultipleBondSmallMaximum)) {
+ // there used to be a test here for order == -1 ? why ?
return 1;
+ }
}
return order;
}
Index: Frame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Frame.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- Frame.java 6 Dec 2003 12:07:45 -0000 1.20
+++ Frame.java 6 Dec 2003 21:11:53 -0000 1.21
@@ -753,32 +753,6 @@
}
}
iter.release();
-
- // FIXME mth 2003 11 30
- // get this out of here and implement it more like like trace
- // alpha carbon mechanims is not consistent
-
- // Protein backbone bonds
- if (hasPdbRecords) {
- PdbAtom pdbatom = atom.getPdbAtom();
- if (pdbatom != null) {
- char chainThis = pdbatom.getChainID();
- if (chainThis == chainLast) {
- if (pdbatom.getName().equals("CA")) {
- if (atomLastCA != null) {
- bondAtoms(atom, atomLastCA,
- Bond.BACKBONE);
- }
- atomLastCA = atom;
- }
- } else {
- chainLast = chainThis;
- atomLastCA = null;
- }
- } else {
- chainLast = '?';
- }
- }
}
if (showRebondTimes) {
@@ -839,7 +813,7 @@
continue;
if (atom.isBonded(atomNear))
continue;
- addBond(atom.bondMutually(atomNear, Bond.HYDROGEN));
+ addBond(atom.bondMutually(atomNear, JmolConstants.BOND_HYDROGEN));
System.out.println("adding an hbond between " + atom.atomIndex +
" & " + atomNear.atomIndex);
}
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