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();