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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer JmolModelAdapter.java,1.1,1.2 JmolViewer.java,1.2,1.3
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From: Michael T H. <mic...@us...> - 2003-08-17 16:48:34
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer
In directory sc8-pr-cvs1:/tmp/cvs-serv25763/src/org/openscience/jmol/viewer
Modified Files:
JmolModelAdapter.java JmolViewer.java
Log Message:
CdkJmolModelAdapter, extensions to JmolModelAdapter, defaults sizes & colors
Index: JmolModelAdapter.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/JmolModelAdapter.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- JmolModelAdapter.java 16 Aug 2003 14:50:44 -0000 1.1
+++ JmolModelAdapter.java 17 Aug 2003 16:48:31 -0000 1.2
@@ -31,11 +31,27 @@
import java.util.Iterator;
public interface JmolModelAdapter {
+ /****************************************************************
+ * the capabilities
+ ****************************************************************/
+ public boolean suppliesAtomicNumber();
+ public boolean suppliesAtomicSymbol();
+ public boolean suppliesAtomTypeName();
+ public boolean suppliesVanderwaalsRadius();
+ public boolean suppliesCovalentRadius();
+ public boolean suppliesAtomColor();
+
+ /*****************************************************************
+ * file related
+ ****************************************************************/
public Object openReader(JmolViewer viewer, String name, Reader reader);
public int getFrameCount(Object clientFile);
public String getModelName(Object clientFile);
+ /****************************************************************
+ * frame related
+ ****************************************************************/
public int getAtomCount(Object clientFile, int frameNumber);
public boolean hasPdbRecords(Object clientFile, int frameNumber);
public AtomIterator getAtomIterator(Object clientFile, int frameNumber);
@@ -47,18 +63,6 @@
public LineIterator getCrystalCellIterator(Object clientFile,
int frameNumber);
- public final static int COLORSCHEME_CPK = 0;
- public final static int COLORSCHEME_CHARGE = 1;
- public final static int COLORSCHEME_MAX = 2;
-
- public int getAtomicNumber(Object clientAtom);
- public String getAtomicSymbol(int atomicNumber, Object clientAtom);
- public String getAtomTypeName(int atomicNumber, Object clientAtom);
- public double getVanderwaalsRadius(int atomicNumber, Object clientAtom);
- public double getCovalentRadius(int atomicNumber, Object clientAtom);
- public Point3d getPoint3d(Object clientAtom);
- public String getPdbAtomRecord(Object clientAtom);
- public Color getColor(int atomicNumber, Object clientAtom, int colorScheme);
// Java 1.1 does not have java.util.Iterator
// and I don't want to use Enumerator
@@ -82,4 +86,495 @@
public abstract Point3d getPoint1();
public abstract Point3d getPoint2();
}
+
+ /****************************************************************
+ * atom properties
+ ****************************************************************/
+ public final static int COLORSCHEME_CPK = 0;
+ public final static int COLORSCHEME_CHARGE = 1;
+ public final static int COLORSCHEME_MAX = 2;
+
+ public int getAtomicNumber(Object clientAtom);
+ public String getAtomicSymbol(Object clientAtom);
+ public String getAtomTypeName(Object clientAtom);
+ public double getVanderwaalsRadius(Object clientAtom);
+ public double getCovalentRadius(Object clientAtom);
+ public Point3d getPoint3d(Object clientAtom);
+ public String getPdbAtomRecord(Object clientAtom);
+ public Color getAtomColor(Object clientAtom, int colorScheme);
+
+ /****************************************************************
+ * these tables are here so that a client can have easy access to them
+ ****************************************************************/
+ public final static String[] atomicSymbols = {
+ "Xx", // 0
+ "H", // 1
+ "He", // 2
+ "Li", // 3
+ "Be", // 4
+ "B", // 5
+ "C", // 6
+ "N", // 7
+ "O", // 8
+ "F", // 9
+ "Ne", // 10
+ "Na", // 11
+ "Mg", // 12
+ "Al", // 13
+ "Si", // 14
+ "P", // 15
+ "S", // 16
+ "Cl", // 17
+ "Ar", // 18
+ "K", // 19
+ "Ca", // 20
+ "Sc", // 21
+ "Ti", // 22
+ "V", // 23
+ "Cr", // 24
+ "Mn", // 25
+ "Fe", // 26
+ "Co", // 27
+ "Ni", // 28
+ "Cu", // 29
+ "Zn", // 30
+ "Ga", // 31
+ "Ge", // 32
+ "As", // 33
+ "Se", // 34
+ "Br", // 35
+ "Kr", // 36
+ "Rb", // 37
+ "Sr", // 38
+ "Y", // 39
+ "Zr", // 40
+ "Nb", // 41
+ "Mo", // 42
+ "Tc", // 43
+ "Ru", // 44
+ "Rh", // 45
+ "Pd", // 46
+ "Ag", // 47
+ "Cd", // 48
+ "In", // 49
+ "Sn", // 50
+ "Sb", // 51
+ "Te", // 52
+ "I", // 53
+ "Xe", // 54
+ "Cs", // 55
+ "Ba", // 56
+ "La", // 57
+ "Ce", // 58
+ "Pr", // 59
+ "Nd", // 60
+ "Pm", // 61
+ "Sm", // 62
+ "Eu", // 63
+ "Gd", // 64
+ "Tb", // 65
+ "Dy", // 66
+ "Ho", // 67
+ "Er", // 68
+ "Tm", // 69
+ "Yb", // 70
+ "Lu", // 71
+ "Hf", // 72
+ "Ta", // 73
+ "W", // 74
+ "Re", // 75
+ "Os", // 76
+ "Ir", // 77
+ "Pt", // 78
+ "Au", // 79
+ "Hg", // 80
+ "Tl", // 81
+ "Pb", // 82
+ "Bi", // 83
+ "Po", // 84
+ "At", // 85
+ "Rn", // 86
+ "Fr", // 87
+ "Ra", // 88
+ "Ac", // 89
+ "Th", // 90
+ "Pa", // 91
+ "U", // 92
+ "Np", // 93
+ "Pu", // 94
+ "Am", // 95
+ "Cm", // 96
+ "Bk", // 97
+ "Cf", // 98
+ "Es", // 99
+ "Fm", // 100
+ "Md", // 101
+ "No", // 102
+ "Lr", // 103
+ "Rf", // 104
+ "Db", // 105
+ "Sg", // 106
+ "Bh", // 107
+ "Hs", // 108
+ "Mt", // 109
+ /*
+ "Ds", // 110
+ "Uuu",// 111
+ "Uub",// 112
+ "Uut",// 113
+ "Uuq",// 114
+ "Uup",// 115
+ "Uuh",// 116
+ "Uus",// 117
+ "Uuo",// 118
+ */
+ };
+ public final static int atomicNumberMax = atomicSymbols.length;
+
+ // vanderwaalsRadius and covalentRadius taken from OpenBabel
+
+ final static float[] vanderwaalsRadii = {
+ 1f, // 0 Xx big enough to see
+ 1.2f, // 1 H
+ 1.4f, // 2 He
+ 1.82f, // 3 Li
+ 1.7f, // 4 Be
+ 2.08f, // 5 B
+ 1.95f, // 6 C
+ 1.85f, // 7 N
+ 1.7f, // 8 O
+ 1.73f, // 9 F
+ 1.54f, // 10 Ne
+ 2.27f, // 11 Na
+ 1.73f, // 12 Mg
+ 2.05f, // 13 Al
+ 2.1f, // 14 Si
+ 2.08f, // 15 P
+ 2f, // 16 S
+ 1.97f, // 17 Cl
+ 1.88f, // 18 Ar
+ 2.75f, // 19 K
+ 1.973f, // 20 Ca
+ 1.7f, // 21 Sc
+ 1.7f, // 22 Ti
+ 1.7f, // 23 V
+ 1.7f, // 24 Cr
+ 1.7f, // 25 Mn
+ 1.7f, // 26 Fe
+ 1.7f, // 27 Co
+ 1.63f, // 28 Ni
+ 1.4f, // 29 Cu
+ 1.39f, // 30 Zn
+ 1.87f, // 31 Ga
+ 1.7f, // 32 Ge
+ 1.85f, // 33 As
+ 1.9f, // 34 Se
+ 2.1f, // 35 Br
+ 2.02f, // 36 Kr
+ 1.7f, // 37 Rb
+ 1.7f, // 38 Sr
+ 1.7f, // 39 Y
+ 1.7f, // 40 Zr
+ 1.7f, // 41 Nb
+ 1.7f, // 42 Mo
+ 1.7f, // 43 Tc
+ 1.7f, // 44 Ru
+ 1.7f, // 45 Rh
+ 1.63f, // 46 Pd
+ 1.72f, // 47 Ag
+ 1.58f, // 48 Cd
+ 1.93f, // 49 In
+ 2.17f, // 50 Sn
+ 2.2f, // 51 Sb
+ 2.06f, // 52 Te
+ 2.15f, // 53 I
+ 2.16f, // 54 Xe
+ 1.7f, // 55 Cs
+ 1.7f, // 56 Ba
+ 1.7f, // 57 La
+ 1.7f, // 58 Ce
+ 1.7f, // 59 Pr
+ 1.7f, // 60 Nd
+ 1.7f, // 61 Pm
+ 1.7f, // 62 Sm
+ 1.7f, // 63 Eu
+ 1.7f, // 64 Gd
+ 1.7f, // 65 Tb
+ 1.7f, // 66 Dy
+ 1.7f, // 67 Ho
+ 1.7f, // 68 Er
+ 1.7f, // 69 Tm
+ 1.7f, // 70 Yb
+ 1.7f, // 71 Lu
+ 1.7f, // 72 Hf
+ 1.7f, // 73 Ta
+ 1.7f, // 74 W
+ 1.7f, // 75 Re
+ 1.7f, // 76 Os
+ 1.7f, // 77 Ir
+ 1.72f, // 78 Pt
+ 1.66f, // 79 Au
+ 1.55f, // 80 Hg
+ 1.96f, // 81 Tl
+ 2.02f, // 82 Pb
+ 1.7f, // 83 Bi
+ 1.7f, // 84 Po
+ 1.7f, // 85 At
+ 1.7f, // 86 Rn
+ 1.7f, // 87 Fr
+ 1.7f, // 88 Ra
+ 1.7f, // 89 Ac
+ 1.7f, // 90 Th
+ 1.7f, // 91 Pa
+ 1.86f, // 92 U
+ 1.7f, // 93 Np
+ 1.7f, // 94 Pu
+ 1.7f, // 95 Am
+ 1.7f, // 96 Cm
+ 1.7f, // 97 Bk
+ 1.7f, // 98 Cf
+ 1.7f, // 99 Es
+ 1.7f, // 100 Fm
+ 1.7f, // 101 Md
+ 1.7f, // 102 No
+ 1.7f, // 103 Lr
+ 1.7f, // 104 Rf
+ 1.7f, // 105 Db
+ 1.7f, // 106 Sg
+ 1.7f, // 107 Bh
+ 1.7f, // 108 Hs
+ 1.7f, // 109 Mt
+ };
+
+ final static float[] covalentRadii = {
+ 1f, // 0 Xx big enough to cause trouble
+ 0.23f, // 1 H
+ 0.93f, // 2 He
+ 0.68f, // 3 Li
+ 0.35f, // 4 Be
+ 0.83f, // 5 B
+ 0.68f, // 6 C
+ 0.68f, // 7 N
+ 0.68f, // 8 O
+ 0.64f, // 9 F
+ 1.12f, // 10 Ne
+ 0.97f, // 11 Na
+ 1.1f, // 12 Mg
+ 1.35f, // 13 Al
+ 1.2f, // 14 Si
+ 0.75f, // 15 P
+ 1.02f, // 16 S
+ 0.99f, // 17 Cl
+ 1.57f, // 18 Ar
+ 1.33f, // 19 K
+ 0.99f, // 20 Ca
+ 1.44f, // 21 Sc
+ 1.47f, // 22 Ti
+ 1.33f, // 23 V
+ 1.35f, // 24 Cr
+ 1.35f, // 25 Mn
+ 1.34f, // 26 Fe
+ 1.33f, // 27 Co
+ 1.5f, // 28 Ni
+ 1.52f, // 29 Cu
+ 1.45f, // 30 Zn
+ 1.22f, // 31 Ga
+ 1.17f, // 32 Ge
+ 1.21f, // 33 As
+ 1.22f, // 34 Se
+ 1.21f, // 35 Br
+ 1.91f, // 36 Kr
+ 1.47f, // 37 Rb
+ 1.12f, // 38 Sr
+ 1.78f, // 39 Y
+ 1.56f, // 40 Zr
+ 1.48f, // 41 Nb
+ 1.47f, // 42 Mo
+ 1.35f, // 43 Tc
+ 1.4f, // 44 Ru
+ 1.45f, // 45 Rh
+ 1.5f, // 46 Pd
+ 1.59f, // 47 Ag
+ 1.69f, // 48 Cd
+ 1.63f, // 49 In
+ 1.46f, // 50 Sn
+ 1.46f, // 51 Sb
+ 1.47f, // 52 Te
+ 1.4f, // 53 I
+ 1.98f, // 54 Xe
+ 1.67f, // 55 Cs
+ 1.34f, // 56 Ba
+ 1.87f, // 57 La
+ 1.83f, // 58 Ce
+ 1.82f, // 59 Pr
+ 1.81f, // 60 Nd
+ 1.8f, // 61 Pm
+ 1.8f, // 62 Sm
+ 1.99f, // 63 Eu
+ 1.79f, // 64 Gd
+ 1.76f, // 65 Tb
+ 1.75f, // 66 Dy
+ 1.74f, // 67 Ho
+ 1.73f, // 68 Er
+ 1.72f, // 69 Tm
+ 1.94f, // 70 Yb
+ 1.72f, // 71 Lu
+ 1.57f, // 72 Hf
+ 1.43f, // 73 Ta
+ 1.37f, // 74 W
+ 1.35f, // 75 Re
+ 1.37f, // 76 Os
+ 1.32f, // 77 Ir
+ 1.5f, // 78 Pt
+ 1.5f, // 79 Au
+ 1.7f, // 80 Hg
+ 1.55f, // 81 Tl
+ 1.54f, // 82 Pb
+ 1.54f, // 83 Bi
+ 1.68f, // 84 Po
+ 1.7f, // 85 At
+ 2.4f, // 86 Rn
+ 2f, // 87 Fr
+ 1.9f, // 88 Ra
+ 1.88f, // 89 Ac
+ 1.79f, // 90 Th
+ 1.61f, // 91 Pa
+ 1.58f, // 92 U
+ 1.55f, // 93 Np
+ 1.53f, // 94 Pu
+ 1.51f, // 95 Am
+ 1.5f, // 96 Cm
+ 1.5f, // 97 Bk
+ 1.5f, // 98 Cf
+ 1.5f, // 99 Es
+ 1.5f, // 100 Fm
+ 1.5f, // 101 Md
+ 1.5f, // 102 No
+ 1.5f, // 103 Lr
+ 1.6f, // 104 Rf
+ 1.6f, // 105 Db
+ 1.6f, // 106 Sg
+ 1.6f, // 107 Bh
+ 1.6f, // 108 Hs
+ 1.6f, // 109 Mt
+ };
+
+ // these colors are the current jmol default colors
+
+ final static Color color190_190_190 = new Color(190, 190, 190);
+ final static Color color165_42_42 = new Color(165, 42, 42);
+ final static Color color255_165_0 = new Color(255, 165, 0);
+
+ Color[] atomColors = {
+ new Color(255,20,147), // Xx 0
+ new Color(250,235,215), // H 1
+ new Color(255,192,203), // He 2
+ new Color(178,34,34), // Li 3
+ new Color(34,139,34), // Be 4
+ Color.green, // B 5
+ new Color(180,180,180), // new Color(112,128,144), // C 6
+ new Color(0,191,255), // N 7
+ Color.red, // O 8
+ new Color(218,165,32), // F 9
+ new Color(255,105,180), // Ne 10
+ Color.blue, // Na 11
+ new Color(34,139,34), // Mg 12
+ color190_190_190, // Al 13
+ new Color(218,165,32), // Si 14
+ color255_165_0, // P 15
+ Color.yellow, // S 16
+ Color.green, // Cl 17
+ new Color(255,192,203), // Ar 18
+ new Color(255,20,147), // K 19
+ new Color(128,128,128), // Ca 20
+ color190_190_190, // Sc 21
+ color190_190_190, // Ti 22
+ color190_190_190, // V 23
+ color190_190_190, // Cr 24
+ color190_190_190, // Mn 25
+ color255_165_0, // Fe 26
+ color165_42_42, // Co 27
+ color165_42_42, // Ni 28
+ color165_42_42, // Cu 29
+ color165_42_42, // Zn 30
+ color165_42_42, // Ga 31
+ new Color(85,107,47), // Ge 32
+ new Color(253,245,230), // As 33
+ new Color(152,251,152), // Se 34
+ color165_42_42, // Br 35
+ new Color(50,205,50), // Kr 36
+ color165_42_42, // Rb 37
+ color190_190_190, // Sr 38
+ color190_190_190, // Y 39
+ color190_190_190, // Zr 40
+ color190_190_190, // Nb 41
+ new Color(255,127,80), // Mo 42
+ color190_190_190, // Tc 43
+ color190_190_190, // Ru 44
+ color190_190_190, // Rh 45
+ color190_190_190, // Pd 46
+ color190_190_190, // Ag 47
+ new Color(255,140,0), // Cd 48
+ color190_190_190, // In 49
+ color190_190_190, // Sn 50
+ color190_190_190, // Sb 51
+ color190_190_190, // Te 52
+ new Color(160,32,240), // I 53
+ new Color(255,105,180), // Xe 54
+ color165_42_42, // Cs 55
+ color190_190_190, // Ba 56
+ color190_190_190, // La 57
+ Color.pink, // 58 Ce
+ Color.pink, // 59 Pr
+ Color.pink, // 60 Nd
+ Color.pink, // 61 Pm
+ Color.pink, // 62 Sm
+ Color.pink, // 63 Eu
+ Color.pink, // 64 Gd
+ Color.pink, // 65 Tb
+ Color.pink, // 66 Dy
+ Color.pink, // 67 Ho
+ Color.pink, // 68 Er
+ Color.pink, // 69 Tm
+ Color.pink, // 70 Yb
+ color190_190_190, // Lu 71
+ color190_190_190, // Hf 72
+ color190_190_190, // Ta 73
+ new Color(64,224,208), // W 74
+ color190_190_190, // Re 75
+ color190_190_190, // Os 76
+ color190_190_190, // Ir 77
+ color190_190_190, // Pt 78
+ new Color(255,215,0), // Au 79
+ color190_190_190, // Hg 80
+ color190_190_190, // Tl 81
+ color190_190_190, // Pb 82
+ new Color(255,181,197), // Bi 83
+ Color.pink, // 84 Po
+ Color.pink, // 85 At
+ Color.pink, // 86 Rn
+ Color.pink, // 87 Fr
+ Color.pink, // 88 Ra
+ Color.pink, // 89 Ac
+ Color.pink, // 90 Th
+ Color.pink, // 91 Pa
+ Color.pink, // 92 U
+ Color.pink, // 93 Np
+ Color.pink, // 94 Pu
+ Color.pink, // 95 Am
+ Color.pink, // 96 Cm
+ Color.pink, // 97 Bk
+ Color.pink, // 98 Cf
+ Color.pink, // 99 Es
+ Color.pink, // 100 Fm
+ Color.pink, // 101 Md
+ Color.pink, // 102 No
+ Color.pink, // 103 Lr
+ Color.pink, // 104 Rf
+ Color.pink, // 105 Db
+ Color.pink, // 106 Sg
+ Color.pink, // 107 Bh
+ Color.pink, // 108 Hs
+ Color.pink, // 109 Mt
+ };
}
Index: JmolViewer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/JmolViewer.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- JmolViewer.java 16 Aug 2003 17:37:14 -0000 1.2
+++ JmolViewer.java 17 Aug 2003 16:48:31 -0000 1.3
@@ -86,13 +86,15 @@
JmolMeasureWatcher jmolMeasureWatcher;
JmolStatusListener jmolStatusListener;
-
+ boolean firePropertyChanges;
public JmolViewer(Component awtComponent,
- JmolModelAdapter jmolModelAdapter) {
+ JmolModelAdapter jmolModelAdapter,
+ boolean firePropertyChanges) {
this.awtComponent = awtComponent;
this.jmolModelAdapter = jmolModelAdapter;
+ this.firePropertyChanges = firePropertyChanges;
strJvmVersion = System.getProperty("java.version");
jvm12orGreater = (strJvmVersion.compareTo("1.2") >= 0);
@@ -103,7 +105,7 @@
selectionManager = new SelectionManager(this);
mouseManager = new MouseManager(awtComponent, this);
fileManager = new FileManager(this);
- modelManager = new ModelManager(this);
+ modelManager = new ModelManager(this, jmolModelAdapter);
repaintManager = new RepaintManager(this);
styleManager = new StyleManager(this);
labelManager = new LabelManager(this);
@@ -895,21 +897,25 @@
}
public void addPropertyChangeListener(PropertyChangeListener pcl) {
- modelManager.addPropertyChangeListener(pcl);
+ if (firePropertyChanges)
+ modelManager.addPropertyChangeListener(pcl);
}
public void addPropertyChangeListener(String prop,
PropertyChangeListener pcl) {
- modelManager.addPropertyChangeListener(prop, pcl);
+ if (firePropertyChanges)
+ modelManager.addPropertyChangeListener(prop, pcl);
}
public void removePropertyChangeListener(PropertyChangeListener pcl) {
- modelManager.removePropertyChangeListener(pcl);
+ if (firePropertyChanges)
+ modelManager.removePropertyChangeListener(pcl);
}
public void removePropertyChangeListener(String prop,
PropertyChangeListener pcl) {
- modelManager.removePropertyChangeListener(prop, pcl);
+ if (firePropertyChanges)
+ modelManager.removePropertyChangeListener(prop, pcl);
}
/****************************************************************
@@ -1639,54 +1645,49 @@
return jmolModelAdapter;
}
- public Object openReader(String name, Reader reader) {
- return jmolModelAdapter.openReader(this, name, reader);
- }
-
public int getFrameCount(Object clientFile) {
- return jmolModelAdapter.getFrameCount(clientFile);
+ return modelManager.getFrameCount(clientFile);
}
public String getModelName(Object clientFile) {
- return jmolModelAdapter.getModelName(clientFile);
+ return modelManager.getModelName(clientFile);
}
public int getAtomicNumber(Object clientAtom) {
- return jmolModelAdapter.getAtomicNumber(clientAtom);
+ return modelManager.getAtomicNumber(clientAtom);
}
public String getAtomicSymbol(int atomicNumber, Object clientAtom) {
- return jmolModelAdapter.getAtomicSymbol(atomicNumber, clientAtom);
+ return modelManager.getAtomicSymbol(atomicNumber, clientAtom);
}
public String getAtomTypeName(int atomicNumber, Object clientAtom) {
- return jmolModelAdapter.getAtomTypeName(atomicNumber, clientAtom);
+ return modelManager.getAtomTypeName(atomicNumber, clientAtom);
}
public double getVanderwaalsRadius(int atomicNumber, Object clientAtom) {
- return jmolModelAdapter.getVanderwaalsRadius(atomicNumber, clientAtom);
+ return modelManager.getVanderwaalsRadius(atomicNumber, clientAtom);
}
public double getCovalentRadius(int atomicNumber, Object clientAtom) {
- return jmolModelAdapter.getCovalentRadius(atomicNumber, clientAtom);
+ return modelManager.getCovalentRadius(atomicNumber, clientAtom);
}
public Point3d getPoint3d(Object clientAtom) {
- return jmolModelAdapter.getPoint3d(clientAtom);
+ return modelManager.getPoint3d(clientAtom);
}
public String getPdbAtomRecord(Object clientAtom) {
- return jmolModelAdapter.getPdbAtomRecord(clientAtom);
+ return modelManager.getPdbAtomRecord(clientAtom);
}
public short getColixAtom(int atomicNumber, Object clientAtom) {
- return Colix.getColix(jmolModelAdapter.getColor(
- atomicNumber, clientAtom, colorManager.modeAtomColorProfile));
+ return Colix.getColix(modelManager.getColorAtom(atomicNumber, clientAtom,
+ colorManager.modeAtomColorProfile));
}
public short getColixAtom(int atomicNumber, Object clientAtom, byte scheme) {
- return Colix.getColix(jmolModelAdapter.getColor(atomicNumber,
- clientAtom,
- scheme));
+ return Colix.getColix(modelManager.getColorAtom(atomicNumber,
+ clientAtom, scheme));
}
}
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