MarvinSpace Developer's Guide

SurfaceColoring

Code examples of typical usages

  1. Built-in CPK coloring
    SurfaceColoring sc = new SurfaceColoring(molecules, surface, precision);
    sc.doColoring(SurfaceColoring.BUILT_IN_CPK_MAPPING);
  2. Built-in residue coloring
    SurfaceColoring sc = new SurfaceColoring(molecules, surface, precision);
    sc.doColoring(SurfaceColoring.BUILT_IN_RESIDUE_MAPPING);
  3. Built-in chain coloring
    SurfaceColoring sc = new SurfaceColoring(molecules, surface, precision);
    sc.doColoring(SurfaceColoring.BUILT_IN_CHAIN_MAPPING);
  4. Coloring by parametrized built-in electrostaic potential property and built-in colors
    SurfaceColoring sc = new SurfaceColoring( molecules, surface, precision );
    sc.setEnrtyRadiusMode( SurfaceColoring.RADIUS_VDW_EXTENDED );
    surfaceColoring.setAtomRadiusExtension( 1 );
    sc.setPropertyValueDecreasement( SurfaceColoring.DECREASE_RECIPROCAL_SQUARE );
    sc.setReciprocalConstant( 8.854 );
    sc.setWeightMode( SurfaceColoring.SUM_OF_VALUES );
    sc.setBuiltInColorMapperMethod(SurfaceColoring.COLOR_MAPPER_RED_AND_BLUE);
    sc.setPropertyMethod( MoleculeIterators.AtomPropertyInterface.class.getMethod( "getPartialAtomCharge", new Class[] {int.class} ) );
    sc.doColoring();
  5. Coloring by custom atom property (of built-in MoleculeIterators.AtomPropertyInterface class) and built-in rainbow colors
    SurfaceColoring sc = new SurfaceColoring(molecules, surface, precision);
    sc.setWeightMode( SurfaceColoring.DISTANCE_WEIGHTED );
    sc.setPropertyMethod( MoleculeIterators.AtomPropertyInterface.class.getMethod( "getType", new Class[] {int.class} ) );
    sc.setBuiltInColorMapperMethod( SurfaceColoring.COLOR_MAPPER_RAINBOW );
    sc.doColoring();
  6. Coloring by custom atom property and parametrized colors
    SurfaceColoring sc = new SurfaceColoring(molecules, surface, precision);
    sc.setWeightMode( SurfaceColoring.DISTANCE_WEIGHTED );
    sc.setPropertyMethod( MoleculeIterators.AtomPropertyInterface.class.getMethod( "getType", new Class[] {int.class} ) );
    sc.setHomogeneousPaletteColors( new byte[][] {Colors.lightgray, Colors.yellow} );
    sc.doColoring();
  7. Coloring by custom property and custom colors
    chemaxon.marvin.space.util.Palette palette = new chemaxon.marvin.space.util.Palette(0, 16);
    palette.clear();
    palette.putColor( Colors.lightgray );
    palette.putColor( Colors.yellow );
    SurfaceColoring sc = new SurfaceColoring(molecules, surface, precision);
    sc.setWeightMode( SurfaceColoring.DISTANCE_WEIGHTED );
    sc.setPropertyMethod( MoleculeIterators.AtomPropertyInterface.class.getMethod( "getType", new Class[] {int.class} ) );
    sc.setPropertyColorMapperMethod( chemaxon.marvin.space.util.Palette.class.getMethod("getByteColor", new Class[] {double.class}) );
    sc.setPropertyColorObject(palette);
    sc.doColoring();
  8. Coloring by custom values of a custom object and built-in coloring:
    SurfaceColoring sc = new SurfaceColoring( molecules, surface, precision );
    sc.setPropertyObject( myGrid );
    sc.setPropertyMethod( MyGrid.class.getMethod( "getLinearWeightedValue", new Class[] {float.class, float.class, float.class} ) );
    sc.setBuiltInColorMapperMethod( SurfaceColoring.COLOR_MAPPER_RAINBOW );
    sc.doColoring();

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