From: Miguel <mic...@us...> - 2004-05-18 21:11:26
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11350/src/org/openscience/jmol/viewer Modified Files: JmolConstants.java JmolViewer.java Log Message: infrastructure for color hbonds type Index: JmolConstants.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/JmolConstants.java,v retrieving revision 1.112 retrieving revision 1.113 diff -u -r1.112 -r1.113 --- JmolConstants.java 18 May 2004 18:22:22 -0000 1.112 +++ JmolConstants.java 18 May 2004 21:11:13 -0000 1.113 @@ -96,15 +96,38 @@ * Extended Bond Definition Types * */ - public final static byte BOND_COVALENT = 3; - public final static byte BOND_AROMATIC_MASK = (1 << 2); - public final static byte BOND_AROMATIC = (1 << 2) | 1; - public final static byte BOND_STEREO_MASK = (3 << 3); - public final static byte BOND_STEREO_NEAR = (1 << 3) | 1; - public final static byte BOND_STEREO_FAR = (2 << 3) | 2; - public final static byte BOND_SULFUR_MASK = (1 << 5); - public final static byte BOND_HYDROGEN = (1 << 6); - public final static byte BOND_ALL_MASK = (byte)0xFF; + public final static short BOND_COVALENT = 3; + public final static short BOND_AROMATIC_MASK = (1 << 2); + public final static short BOND_AROMATIC = (1 << 2) | 1; + public final static short BOND_STEREO_MASK = (3 << 3); + public final static short BOND_STEREO_NEAR = (1 << 3) | 1; + public final static short BOND_STEREO_FAR = (2 << 3) | 2; + public final static short BOND_SULFUR_MASK = (1 << 5); + public final static short BOND_HBOND_SHIFT = 6; + public final static short BOND_HYDROGEN_MASK = (0x0F << BOND_HBOND_SHIFT); + public final static short BOND_H_REGULAR = (1 << BOND_HBOND_SHIFT); + public final static short BOND_H_PLUS_2 = (2 << BOND_HBOND_SHIFT); + public final static short BOND_H_PLUS_3 = (3 << BOND_HBOND_SHIFT); + public final static short BOND_H_PLUS_4 = (4 << BOND_HBOND_SHIFT); + public final static short BOND_H_PLUS_5 = (5 << BOND_HBOND_SHIFT); + public final static short BOND_H_MINUS_3 = (6 << BOND_HBOND_SHIFT); + public final static short BOND_H_MINUS_4 = (7 << BOND_HBOND_SHIFT); + public final static short BOND_H_NUCLEOTIDE = (8 << BOND_HBOND_SHIFT); + + public final static short BOND_ALL_MASK = (short)0xFFFF; + + public final static int[] argbsHbondType = + { + 0xFFFF69B4, // unused - pink + 0xFFFFFF00, // regular yellow + 0xFFFFFFFF, // +2 white + 0xFFFF00FF, // +3 magenta + 0xFFFF0000, // +4 red + 0xFFFFA500, // +5 orange + 0xFF00FFFF, // -3 cyan + 0xFF00FF00, // -4 green + 0xFFFF8080, // nucleotide + }; /** * The default elementSymbols. Presumably the only entry which may cause Index: JmolViewer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/JmolViewer.java,v retrieving revision 1.174 retrieving revision 1.175 diff -u -r1.174 -r1.175 --- JmolViewer.java 14 May 2004 14:40:40 -0000 1.174 +++ JmolViewer.java 18 May 2004 21:11:13 -0000 1.175 @@ -762,6 +762,10 @@ return colorManager.getColixAtomPalette(atom, palette); } + public short getColixHbondType(short order) { + return colorManager.getColixHbondType(order); + } + public short getColixAxes() { return colorManager.colixAxes; } @@ -1454,7 +1458,7 @@ } public short getColixBond(int order) { - if (order == JmolConstants.BOND_HYDROGEN) + if ((order & JmolConstants.BOND_HYDROGEN_MASK) != 0) return colorManager.colixHbond; if ((order & JmolConstants.BOND_SULFUR_MASK) != 0) return colorManager.colixSsbond; @@ -1471,6 +1475,10 @@ setShapeProperty(JmolConstants.SHAPE_STICKS, "hbondColor", color); } + public void setColorHbondType() { + setShapeProperty(JmolConstants.SHAPE_STICKS, "hbondColor", "type"); + } + public void setSsbondsBackbone(boolean ssbondsBackbone) { styleManager.setSsbondsBackbone(ssbondsBackbone); } @@ -2094,7 +2102,7 @@ return modelManager.getBondRadius(i); } - public byte getBondOrder(int i) { + public short getBondOrder(int i) { return modelManager.getBondOrder(i); } |