SurfaceColoring (JChem Base API documentation (c) 1998-2020 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.space.SurfaceColoring

@PublicAPI
public class SurfaceColoring
extends java.lang.Object

SurfaceColoring is an easy-to-use tool to map different properties as colors onto surfaces.
Examples of typical usages:

 
      Mapping simple float values from a property grid (for example Gaussian Cube grid) to a surface.

      
      SurfaceColoring sc = new SurfaceColoring(surface);

      sc.setPropertyObject(myGrid);

      sc.setPropertyMethod(myGrid.getClass().getMethod("get",
              new Class[] {float.class, float.class, float.class} ));

      sc.addColors( blue, cyan, green, yellow, red );

      
      Mapping own atom properties.

      
      SurfaceColoring sc = new SurfaceColoring(molecules, surface);

      sc.setPropertyMethod( myMolecule.getClass().getMethod("getAtomType", new Class[] {int.class}) );

          // it has to have 1 int argument

          // it will be called through getAtomProperty() of MoleculeInterface:

          // ((MoleculeInterface)molecules.get(i)).getAtomProperty().getAtomType(atomIndex);

      sc.setPropertyColorMapperMethod( getMethod( "getAtomColor", new Class[] {float.class} ) );
      
      
 

 See also SurfaceColoringInUse.html for more examples.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ATOM_PROPERTY_MAPPING` Coloring by mapping atom based property values to the surface.
`static int`	`BUILT_IN_CHAIN_MAPPING` Coloring by built-in chain colors.
`static int`	`BUILT_IN_CPK_MAPPING` Coloring by built-in cpk colors.
`static int`	`BUILT_IN_RAINBOW_MAPPING` Coloring by built-in rainbow colors.
`static int`	`BUILT_IN_RESIDUE_MAPPING` Coloring by built-in residue colors.
`static int`	`BUILT_IN_SECONDARY_STRUCTURE_MAPPING` Coloring by built-in secondary structure colors.
`static int`	`COLOR_MAPPER_BLUE_TO_GREEN` Built-in blue-cyan-green palette will be used.
`static int`	`COLOR_MAPPER_BLUE_TO_RED` Built-in blue-lightgray-red palette will be used.
`static int`	`COLOR_MAPPER_FIRE` Built-in "fire" palette will be used.
`static int`	`COLOR_MAPPER_GREEN_TO_BLUE` Built-in green-cyan-blue palette will be used.
`static int`	`COLOR_MAPPER_RAINBOW` Built-in rainbow palette will be used.
`static int`	`COLOR_MAPPER_RED_TO_BLUE` Built-in red-lightgray-blue palette will be used.
`static int`	`COLOR_MAPPER_REVERSE_RAINBOW` Built-in reverse rainbow palette will be used.
`static int`	`DECREASE_LINEAR` The property values will decrease when getting farther from the atom center.
`static int`	`DECREASE_RECIPROCAL_SQUARE` The property values will decrease when getting farther from the atom center.
`static int`	`DECREASE_SQUARE` The property values will decrease when getting farther from the atom center.
`static int`	`DISTANCE_CONSTANT` Is the distance measured from the atom center extended by a constant value.
`static int`	`DISTANCE_FROM_VDW` In case of distance weighted property mapping is the distance measured from the atom center extended by the van der Waals radius.
`static int`	`DISTANCE_FROM_VDW_EXTENDED` Is the distance measured from the atom center extended by the van der Waals radius plus a constant, typically the probe radius.
`static int`	`DISTANCE_WEIGHTED` Will all affecting properties be mapped onto the surface weighted by atom distances.
`static int`	`GRID_MAPPING` Coloring by mapping values form a grid to the surface.
`static int`	`MEAN_VALUE` Will the mean of the affecting properties be mapped onto the surface.
`static int`	`NEAREST_VALUE` Will only the property of the nearest atom be mapped onto the surface.
`static int`	`NO_DECREASE` The property values will not decrease when getting farther from the atom center.
`static int`	`RADIUS_CONSTANT` Is the atom property range a fix value
`static int`	`RADIUS_VDW` Is the atom property range the van der Waals radius
`static int`	`RADIUS_VDW_EXTENDED` Is the atom property range the van der Waals radius plus a fix value (for example the probe radius)
`static int`	`SUM_OF_VALUES` Will the sum of the affecting properties be mapped onto the surface.

Constructor Summary

Constructors
Constructor and Description
`SurfaceColoring(java.util.ArrayList molecules, SurfaceComponent surface)` The given surface of the given molecules is to be colored after the parametrization.
`SurfaceColoring(java.util.ArrayList molecules, SurfaceComponent surface, float step)` The given surface of the given molecules is to be colored after the parametrization.
`SurfaceColoring(SurfaceComponent surface)` The given surface is to be colored after the parametrization.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`changeColorMapperColors(int mode)` Switches to another built-in color palette and leaves minimum, maximum and cutoff values unchanged.
`void`	`doColoring()` This function has to be called after proper parametrization of the `SurfaceColoring` object in case of custom properties.
`void`	`doColoring(int mappingMode)` This function has to be called after proper parametrization of the `SurfaceColoring` object in case of built-in properties.
`protected void`	`finalize()`
`static byte[][]`	`getBuiltInPalette(int paletteId)` Returns the colors of a built-in palette.
`static byte[][]`	`getBuiltInPalette(java.lang.Object paletteId)` Returns the colors of a built-in palette.
`static java.lang.String[]`	`getBuiltInPalettes()` Returns the string identifiers of the built-in palettes.
`double`	`getMaximumValue()` Returns the greatest property value of the surface vertices.
`double`	`getMinimumValue()` Returns the lowest property value of the surface vertices.
`void`	`reset()` Resets all parameters to the default.
`void`	`setAtomRadiusExtension(float r)` In case of {#RADIUS_VDW_EXTENDED} mode the extension can be set.
`void`	`setBuiltInColorMapperMethod(int mode)` Selection of built-in color palettes through their identifier.
`void`	`setBuiltInColorMapperMethod(int mode, boolean twoPolePalette)` Selection of built-in color palettes through their identifier.
`void`	`setConstantAtomRadius(float r)` In case of {#RADIUS_CONSTANT} mode the constant radius can be set.
`void`	`setConstantDistanceRadius(float r)` In case of distance weighted property values constant radius can be set.
`void`	`setDistanceRadiusExtension(float r)` In case of distance weighted property values radius extension can be set.
`void`	`setDistanceRadiusMode(int pvs)` In case of distance weighted property values the distance computation can be set differently from the property radius but in the same way.
`void`	`setEnrtyRadiusMode(int pvs)` Atom properties will effect surface vertices being closer than a certain radius.
`void`	`setHomogeneousPaletteColors(byte[][] colorArray)` This is an easy way to create a homogenous palette and use it as a color mapper.
`void`	`setLowerCutoffValue(double v)` Cutoff values can be set to the built-in two pole palettes.
`void`	`setMaximumValue(double v)` Sets the greatest property value of the surface vertices considered.
`void`	`setMinimumValue(double v)` Sets the lowest property value of the surface vertices considered.
`void`	`setProgressBar(chemaxon.marvin.space.ProgressBarInterface progressBar)`
`void`	`setPropertyColorMapperMethod(java.lang.reflect.Method m)` Colors will be got by this method.
`void`	`setPropertyColorMapperRange(double min, double max)` Sets the range of the built-in palette.
`void`	`setPropertyColorObject(java.lang.Object o)` Colors will be got from this object.
`void`	`setPropertyMethod(java.lang.reflect.Method m)` Atom properties will be got by this method.
`void`	`setPropertyObject(java.lang.Object o, int mappingMode)` Atom properties will be get from this object.
`void`	`setPropertyValueDecreasement(int pvd)` Atom property values can decrease when getting farhter from the atom center.
`void`	`setReciprocalConstant(double c)` Atom property values will decrease by (1.0/(4PIc)) * (v/(d*d)).
`void`	`setSmoothColoringToCutoffValues(boolean b)` See `Palette.smoothColorToCutoffValues(boolean)`.
`void`	`setSurface(SurfaceComponent surface)` Sets the surface for coloring.
`void`	`setUpperCutoffValue(double v)` Cutoff values can be set to the built-in two pole palettes.
`void`	`setWeightMode(int mode)` Way of handling values when multiple atoms have effect on one surface vertex.
`void`	`updateColors()` Useful fast updating method when the atom properties have not changed, but there is a change in the way of coloring.

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - RADIUS_VDW
```
public static final int RADIUS_VDW
```
    Is the atom property range the van der Waals radius
    
    See Also:
    
    Constant Field Values
  - RADIUS_VDW_EXTENDED
```
public static final int RADIUS_VDW_EXTENDED
```
    Is the atom property range the van der Waals radius plus a fix value (for example the probe radius)
    
    See Also:
    
    Constant Field Values
  - RADIUS_CONSTANT
```
public static final int RADIUS_CONSTANT
```
    Is the atom property range a fix value
    
    See Also:
    
    Constant Field Values
  - NEAREST_VALUE
```
public static final int NEAREST_VALUE
```
    Will only the property of the nearest atom be mapped onto the surface.
    
    See Also:
    
    Constant Field Values
  - SUM_OF_VALUES
```
public static final int SUM_OF_VALUES
```
    Will the sum of the affecting properties be mapped onto the surface.
    
    See Also:
    
    Constant Field Values
  - MEAN_VALUE
```
public static final int MEAN_VALUE
```
    Will the mean of the affecting properties be mapped onto the surface.
    
    See Also:
    
    Constant Field Values
  - DISTANCE_WEIGHTED
```
public static final int DISTANCE_WEIGHTED
```
    Will all affecting properties be mapped onto the surface weighted by atom distances.
    
    See Also:
    
    Constant Field Values
  - DISTANCE_FROM_VDW
```
public static final int DISTANCE_FROM_VDW
```
    In case of distance weighted property mapping is the distance measured from the atom center extended by the van der Waals radius. Example:
    A surface vertex is affected by 2 atoms, a hydrogen and a carbon. The vertex lies exactly where the two atom spheres intersect. Thus it is nearer to the H, but the 2 atoms have to effect equally. If the distance is computed as the distance from the van der Walls radius, it will be 0 to both atoms getting equal weight properly.
    
    See Also:
    
    Constant Field Values
  - DISTANCE_FROM_VDW_EXTENDED
```
public static final int DISTANCE_FROM_VDW_EXTENDED
```
    Is the distance measured from the atom center extended by the van der Waals radius plus a constant, typically the probe radius.
    
    See Also:
    
    Constant Field Values
  - DISTANCE_CONSTANT
```
public static final int DISTANCE_CONSTANT
```
    Is the distance measured from the atom center extended by a constant value.
    
    See Also:
    
    Constant Field Values
  - BUILT_IN_CPK_MAPPING
```
public static final int BUILT_IN_CPK_MAPPING
```
    Coloring by built-in cpk colors.
    
    See Also:
    
    Constant Field Values
  - BUILT_IN_RESIDUE_MAPPING
```
public static final int BUILT_IN_RESIDUE_MAPPING
```
    Coloring by built-in residue colors.
    
    See Also:
    
    Constant Field Values
  - BUILT_IN_CHAIN_MAPPING
```
public static final int BUILT_IN_CHAIN_MAPPING
```
    Coloring by built-in chain colors.
    
    See Also:
    
    Constant Field Values
  - BUILT_IN_SECONDARY_STRUCTURE_MAPPING
```
public static final int BUILT_IN_SECONDARY_STRUCTURE_MAPPING
```
    Coloring by built-in secondary structure colors.
    
    See Also:
    
    Constant Field Values
  - BUILT_IN_RAINBOW_MAPPING
```
public static final int BUILT_IN_RAINBOW_MAPPING
```
    Coloring by built-in rainbow colors.
    
    See Also:
    
    Constant Field Values
  - ATOM_PROPERTY_MAPPING
```
public static final int ATOM_PROPERTY_MAPPING
```
    Coloring by mapping atom based property values to the surface.
    
    See Also:
    
    Constant Field Values
  - GRID_MAPPING
```
public static final int GRID_MAPPING
```
    Coloring by mapping values form a grid to the surface.
    
    See Also:
    
    Constant Field Values
  - NO_DECREASE
```
public static final int NO_DECREASE
```
    The property values will not decrease when getting farther from the atom center.
    
    See Also:
    
    Constant Field Values
  - DECREASE_LINEAR
```
public static final int DECREASE_LINEAR
```
    The property values will decrease when getting farther from the atom center.
    
    See Also:
    
    Constant Field Values
  - DECREASE_SQUARE
```
public static final int DECREASE_SQUARE
```
    The property values will decrease when getting farther from the atom center.
    
    See Also:
    
    Constant Field Values
  - DECREASE_RECIPROCAL_SQUARE
```
public static final int DECREASE_RECIPROCAL_SQUARE
```
    The property values will decrease when getting farther from the atom center.
    
    See Also:
    
    Constant Field Values
  - COLOR_MAPPER_RAINBOW
```
public static final int COLOR_MAPPER_RAINBOW
```
    Built-in rainbow palette will be used.
    
    See Also:
    
    Constant Field Values
  - COLOR_MAPPER_REVERSE_RAINBOW
```
public static final int COLOR_MAPPER_REVERSE_RAINBOW
```
    Built-in reverse rainbow palette will be used.
    
    See Also:
    
    Constant Field Values
  - COLOR_MAPPER_RED_TO_BLUE
```
public static final int COLOR_MAPPER_RED_TO_BLUE
```
    Built-in red-lightgray-blue palette will be used.
    
    See Also:
    
    Constant Field Values
  - COLOR_MAPPER_BLUE_TO_RED
```
public static final int COLOR_MAPPER_BLUE_TO_RED
```
    Built-in blue-lightgray-red palette will be used.
    
    See Also:
    
    Constant Field Values
  - COLOR_MAPPER_GREEN_TO_BLUE
```
public static final int COLOR_MAPPER_GREEN_TO_BLUE
```
    Built-in green-cyan-blue palette will be used.
    
    See Also:
    
    Constant Field Values
  - COLOR_MAPPER_BLUE_TO_GREEN
```
public static final int COLOR_MAPPER_BLUE_TO_GREEN
```
    Built-in blue-cyan-green palette will be used.
    
    See Also:
    
    Constant Field Values
  - COLOR_MAPPER_FIRE
```
public static final int COLOR_MAPPER_FIRE
```
    Built-in "fire" palette will be used.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SurfaceColoring
```
public SurfaceColoring(SurfaceComponent surface)
```
    The given surface is to be colored after the parametrization.
    
    Parameters:
    
    surface - surface to be colored
  - SurfaceColoring
```
public SurfaceColoring(java.util.ArrayList molecules,
                       SurfaceComponent surface)
```
    The given surface of the given molecules is to be colored after the parametrization.
    
    Parameters:
    
    molecules - set of MoleculeInterfaces
    
    surface - surface to be colored
  - SurfaceColoring
```
public SurfaceColoring(java.util.ArrayList molecules,
                       SurfaceComponent surface,
                       float step)
```
    The given surface of the given molecules is to be colored after the parametrization.
    
    Parameters:
    
    molecules - set of MoleculeInterfaces
    
    surface - surface to be colored
    
    step - precision value, it is an approximate value of distances between surface vertices
- Method Detail
  - finalize
```
protected void finalize()
                 throws java.lang.Throwable
```
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.Throwable
  - setProgressBar
```
public void setProgressBar(chemaxon.marvin.space.ProgressBarInterface progressBar)
```
  - setSurface
```
public void setSurface(SurfaceComponent surface)
```
    Sets the surface for coloring. This is useful when the surface has been changed, but the grid and molecules are the same, especially in case of isosurfaces.
    
    Parameters:
    
    surface -
  - reset
```
public void reset()
```
    Resets all parameters to the default. Useful when coloring the same surface multiple times by different parameters.
  - setPropertyObject
```
public void setPropertyObject(java.lang.Object o,
                              int mappingMode)
```
    Atom properties will be get from this object. Typically it can be a grid.
    
    Parameters:
    
    o - object that has the property method
    
    mappingMode - either GRID_MAPPING or ATOM_PROPERTY_MAPPING indicating {int} or {float, float, float} arguments to the property method
  - setPropertyMethod
```
public void setPropertyMethod(java.lang.reflect.Method m)
                       throws java.lang.Exception
```
    Atom properties will be got by this method. The method will get atom type or atom index or x-y-z values as argument, depending the mapping mode was a built-in mapping or ATOM_PROPERTY_MAPPING or GRID_MAPPING. By default the parameter will be atom type. It has to return a property value.
    
    Parameters:
    
    m - custom method that computes the atom properties
    
    Throws:
    
    java.lang.Exception - in case of illegal method or illegal arguments
  - setBuiltInColorMapperMethod
```
public void setBuiltInColorMapperMethod(int mode)
                                 throws java.lang.Exception
```
    Selection of built-in color palettes through their identifier.
    
    Parameters:
    
    mode - See {#COLOR_MAPPER_RAINBOW}, {#COLOR_MAPPER_RED_AND_BLUE}.
    
    Throws:
    
    java.lang.Exception
  - setBuiltInColorMapperMethod
```
public void setBuiltInColorMapperMethod(int mode,
                                        boolean twoPolePalette)
                                 throws java.lang.Exception
```
    Selection of built-in color palettes through their identifier.
    
    Parameters:
    
    mode - See {#COLOR_MAPPER_RAINBOW}, {#COLOR_MAPPER_RED_AND_BLUE}. "param twoPolePalette if the palette should handle negative and positive values separately
    
    Throws:
    
    java.lang.Exception
  - changeColorMapperColors
```
public void changeColorMapperColors(int mode)
```
    Switches to another built-in color palette and leaves minimum, maximum and cutoff values unchanged.
    
    Parameters:
    
    mode - internal id of the newly set color palette
  - setPropertyColorMapperRange
```
public void setPropertyColorMapperRange(double min,
                                        double max)
```
    Sets the range of the built-in palette.
    
    Parameters:
    
    min - Sets the minimum value the palette assignes color to.
    
    max - Sets the maximum value the palette assignes color to.
  - setPropertyColorMapperMethod
```
public void setPropertyColorMapperMethod(java.lang.reflect.Method m)
                                  throws java.lang.Exception
```
    Colors will be got by this method. The method will get atom properties as an argument and has to return byte[] colors.
    
    Parameters:
    
    m - custom method that returns a color to an atom property
    
    Throws:
    
    java.lang.Exception - in case of illegal method or illegal arguments
  - setPropertyColorObject
```
public void setPropertyColorObject(java.lang.Object o)
```
    Colors will be got from this object. Typically it can be a custom pelette.
    
    Parameters:
    
    o - object that has the color mapper method
  - doColoring
```
public void doColoring()
                throws java.lang.Exception
```
    This function has to be called after proper parametrization of the SurfaceColoring object in case of custom properties.
    
    Throws:
    
    java.lang.Exception
  - doColoring
```
public void doColoring(int mappingMode)
                throws java.lang.Exception
```
    This function has to be called after proper parametrization of the SurfaceColoring object in case of built-in properties.
    
    Parameters:
    
    mappingMode - identifier of the built-in method, see {#BUILT_IN_CPK_MAPPING}, {#BUILT_IN_RESIDUE_MAPPING}, {#BUILT_IN_CHAIN_MAPPING}
    
    Throws:
    
    java.lang.Exception
  - setEnrtyRadiusMode
```
public void setEnrtyRadiusMode(int pvs)
```
    Atom properties will effect surface vertices being closer than a certain radius. The mode of getting this radius can be set here, namely van der Waals radius of the atoms, van der Waals radius plus a constant value (e.g. probe radius), or a constant radius.
    
    Parameters:
    
    pvs - See {#RADIUS_VDW}, {#RADIUS_VDW_EXTENDED}, {#RADIUS_CONSTANT}.
  - setAtomRadiusExtension
```
public void setAtomRadiusExtension(float r)
```
    In case of {#RADIUS_VDW_EXTENDED} mode the extension can be set.
    
    Parameters:
    
    r - radius extension in angstroms
  - setConstantAtomRadius
```
public void setConstantAtomRadius(float r)
```
    In case of {#RADIUS_CONSTANT} mode the constant radius can be set.
    
    Parameters:
    
    r - radius in angstroms
  - setDistanceRadiusMode
```
public void setDistanceRadiusMode(int pvs)
```
    In case of distance weighted property values the distance computation can be set differently from the property radius but in the same way. Example: "I would like to set 1.0 weight if the distance of the surface vertex and the atom center is the van der Waals radius, though the atom still has effect farther from the atom center."
    
    Parameters:
    
    pvs - mode as distance is computed, see {#DISTANCE_FROM_VDW}, {#DISTANCE_FROM_VDW_EXTENDED}, {#DISTANCE_CONSTANT}.
  - setDistanceRadiusExtension
```
public void setDistanceRadiusExtension(float r)
```
    In case of distance weighted property values radius extension can be set.
    
    Parameters:
    
    r - distance radius extension in angstroms
  - setConstantDistanceRadius
```
public void setConstantDistanceRadius(float r)
```
    In case of distance weighted property values constant radius can be set.
    
    Parameters:
    
    r - constant distance radius in angstroms
  - setPropertyValueDecreasement
```
public void setPropertyValueDecreasement(int pvd)
```
    Atom property values can decrease when getting farhter from the atom center. The way of decreasement can be set here.
    
    Parameters:
    
    pvd - See {#NO_DECREASE}, {#DECREASE_LINEAR}, {#DECREASE_SQUARE}, {#DECREASE_RECIPROCAL_SQUARE}.
  - setReciprocalConstant
```
public void setReciprocalConstant(double c)
```
    Atom property values will decrease by (1.0/(4*PI*c)) * (v/(d*d)).
    
    Parameters:
    
    c -
  - setWeightMode
```
public void setWeightMode(int mode)
```
    Way of handling values when multiple atoms have effect on one surface vertex.
    
    Parameters:
    
    mode - See {#NEAREST_VALUE}, {#SUM_OF_VALUES}, {#MEAN_VALUE}, {#DISTANCE_WEIGHTED}.
  - setHomogeneousPaletteColors
```
public void setHomogeneousPaletteColors(byte[][] colorArray)
```
    This is an easy way to create a homogenous palette and use it as a color mapper. There is no need to call {#setPropertyColorMapperMethod()} or {#setPropertyColorObject()}.
    
    Parameters:
    
    colorArray - array of byte[] colors.
  - getBuiltInPalettes
```
public static java.lang.String[] getBuiltInPalettes()
```
    Returns the string identifiers of the built-in palettes.
    
    Returns:
    
    array of palette names
  - getBuiltInPalette
```
public static byte[][] getBuiltInPalette(int paletteId)
```
    Returns the colors of a built-in palette. See {#COLOR_MAPPER_RAINBOW}, {#COLOR_MAPPER_RED_AND_BLUE}, etc.
    
    Parameters:
    
    paletteId - int identifier of a built-in palette
    
    Returns:
    
    array of the rgb colors represented as byte arrays
  - getBuiltInPalette
```
public static byte[][] getBuiltInPalette(java.lang.Object paletteId)
```
    Returns the colors of a built-in palette.
    
    Parameters:
    
    paletteId - string identifier of a built-in palette
    
    Returns:
    
    array of the rgb colors represented as byte arrays
  - getMinimumValue
```
public double getMinimumValue()
```
    Returns the lowest property value of the surface vertices.
    
    Returns:
    
    minimum weighted value
  - getMaximumValue
```
public double getMaximumValue()
```
    Returns the greatest property value of the surface vertices.
    
    Returns:
    
    maximum weighted value
  - setMinimumValue
```
public void setMinimumValue(double v)
```
    Sets the lowest property value of the surface vertices considered.
    
    Parameters:
    
    v - minimum weighted value
  - setMaximumValue
```
public void setMaximumValue(double v)
```
    Sets the greatest property value of the surface vertices considered.
    
    Parameters:
    
    v - maximum weighted value
  - setLowerCutoffValue
```
public void setLowerCutoffValue(double v)
```
    Cutoff values can be set to the built-in two pole palettes. Values greater than the lower cutoff value and lesser than the upper cutoff value are uniformly colored.
    
    Parameters:
    
    v - lower cutoff value
  - setUpperCutoffValue
```
public void setUpperCutoffValue(double v)
```
    Cutoff values can be set to the built-in two pole palettes. Values greater than the lower cutoff value and lesser than the upper cutoff value are uniformly colored.
    
    Parameters:
    
    v - upper cutoff value
  - setSmoothColoringToCutoffValues
```
public void setSmoothColoringToCutoffValues(boolean b)
```
    See Palette.smoothColorToCutoffValues(boolean).
    
    Parameters:
    
    b -
  - updateColors
```
public void updateColors()
                  throws java.lang.Exception
```
    Useful fast updating method when the atom properties have not changed, but there is a change in the way of coloring. Typically when setting a new palette, setting cutoff values, etc.
    
    Throws:
    
    java.lang.Exception

Class SurfaceColoring

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

RADIUS_VDW

RADIUS_VDW_EXTENDED

RADIUS_CONSTANT

NEAREST_VALUE

SUM_OF_VALUES

MEAN_VALUE

DISTANCE_WEIGHTED

DISTANCE_FROM_VDW

DISTANCE_FROM_VDW_EXTENDED

DISTANCE_CONSTANT

BUILT_IN_CPK_MAPPING

BUILT_IN_RESIDUE_MAPPING

BUILT_IN_CHAIN_MAPPING

BUILT_IN_SECONDARY_STRUCTURE_MAPPING

BUILT_IN_RAINBOW_MAPPING

ATOM_PROPERTY_MAPPING

GRID_MAPPING

NO_DECREASE

DECREASE_LINEAR

DECREASE_SQUARE

DECREASE_RECIPROCAL_SQUARE

COLOR_MAPPER_RAINBOW

COLOR_MAPPER_REVERSE_RAINBOW

COLOR_MAPPER_RED_TO_BLUE

COLOR_MAPPER_BLUE_TO_RED

COLOR_MAPPER_GREEN_TO_BLUE

COLOR_MAPPER_BLUE_TO_GREEN

COLOR_MAPPER_FIRE

Constructor Detail

SurfaceColoring

SurfaceColoring

SurfaceColoring

Method Detail

finalize

setProgressBar

setSurface

reset

setPropertyObject

setPropertyMethod

setBuiltInColorMapperMethod

setBuiltInColorMapperMethod

changeColorMapperColors

setPropertyColorMapperRange

setPropertyColorMapperMethod

setPropertyColorObject

doColoring

doColoring

setEnrtyRadiusMode

setAtomRadiusExtension

setConstantAtomRadius

setDistanceRadiusMode

setDistanceRadiusExtension

setConstantDistanceRadius

setPropertyValueDecreasement

setReciprocalConstant

setWeightMode

setHomogeneousPaletteColors

getBuiltInPalettes

getBuiltInPalette

getBuiltInPalette

getMinimumValue

getMaximumValue

setMinimumValue

setMaximumValue

setLowerCutoffValue

setUpperCutoffValue

setSmoothColoringToCutoffValues

updateColors