Constant Field Values

Contents

• org.proteinshader.*

org.proteinshader.*

org.proteinshader.graphics.Cylinder

public static final int	MIN_CAP_TILING	3
public static final int	MIN_SLICES	3
public static final int	MIN_STACKS	1

org.proteinshader.graphics.FrenetFrames

public static final double	AXIS_RADIUS	0.05
public static final int	FRAMES_PER_SEGMENT	11
public static final double	MAJOR_AXIS_SCALE	1.5
public static final double	MAJOR_SPHERE_RADIUS	0.3
public static final int	MAJOR_SPHERE_TILING	30
public static final double	MINOR_AXIS_SCALE	0.5
public static final double	MINOR_SPHERE_RADIUS	0.0375
public static final int	MINOR_SPHERE_TILING	10
public static final int	SLICES	10
public static final float	SPECULAR_EXP	20.0f
public static final int	STACKS	1
public static final double	TIP_FRACTION	0.2
public static final double	TIP_RADIUS	0.08

org.proteinshader.graphics.Ribbon

public static final double	ALPHA_HEIGHT	4.0
public static final float	ALPHA_S_COORD_END	1.0f
public static final float	ALPHA_S_COORD_START	0.0f
public static final int	ALPHA_STACKS	10
public static final float	ALPHA_THIN_SIDE_S_MAX	0.125f
public static final float	ALPHA_THIN_SIDE_S_MIN	0.0f
public static final double	ALPHA_WIDTH	0.5
public static final double	BETA_HEIGHT	4.0
public static final float	BETA_S_COORD_END	1.0f
public static final float	BETA_S_COORD_START	0.0f
public static final int	BETA_STACKS	10
public static final float	BETA_THIN_SIDE_S_MAX	0.125f
public static final float	BETA_THIN_SIDE_S_MIN	0.0f
public static final double	BETA_WIDTH	0.5
public static final double	LOOP_HEIGHT	1.0
public static final float	LOOP_S_COORD_END	0.75f
public static final float	LOOP_S_COORD_START	0.25f
public static final int	LOOP_STACKS	10
public static final float	LOOP_THIN_SIDE_S_MAX	0.125f
public static final float	LOOP_THIN_SIDE_S_MIN	0.0f
public static final double	LOOP_WIDTH	0.25

org.proteinshader.graphics.Shape

public static final double	HALF_PI	1.57079632679489
public static final double	PI	3.14159265358979
public static final double	TWO_PI	6.28318530717958

org.proteinshader.graphics.Silhouette

public static final boolean

DEFAULT

true

org.proteinshader.graphics.Sphere

public static final int

MIN_TILING

3

org.proteinshader.graphics.Tube

public static final double	ALPHA_RADIUS	1.5
public static final int	ALPHA_SLICES	20
public static final int	ALPHA_STACKS	10
public static final double	BETA_RADIUS	1.5
public static final int	BETA_SLICES	20
public static final int	BETA_STACKS	10
public static final double	LOOP_RADIUS	0.75
public static final int	LOOP_SLICES	10
public static final int	LOOP_STACKS	10
public static final float	S_MAX	2.0f
public static final float	S_MIN	0.0f

org.proteinshader.graphics.adapter.StructureToGraphics

public static final boolean

AUTO_TILING

true

org.proteinshader.graphics.displaylists.CylinderReferences

public static final double	COEFFICIENT	29.059
public static final int	DEFAULT_CAP_TILING	5
public static final double	DEFAULT_HEIGHT	1.0
public static final double	DEFAULT_RADIUS	0.15
public static final int	DEFAULT_SLICES	10
public static final int	DEFAULT_STACKS	1
public static final double	EXPONENT	-0.5267
public static final int	MAX_SLICES	14

org.proteinshader.graphics.displaylists.SphereReferences

public static final double	COEFFICIENT	226.1
public static final double	DEFAULT_RADIUS	1.0
public static final int	DEFAULT_TILING	12
public static final double	EXPONENT	-0.7367
public static final int	MAX_TILING	57

org.proteinshader.graphics.shader.ShaderProgramFactory

public static final String

SHADER_DIRECTORY

"./../shaders/"

org.proteinshader.graphics.textures.TextureFactory

public static final String	BEND_CONFIG	"bend_textures.conf"
public static final String	BEND_DIRECTORY	"./../textures/bend/"
public static final String	HALFTONING_CONFIG	"halftoning_textures.conf"
public static final String	HALFTONING_DIRECTORY	"./../textures/halftoning/"
public static final String	PATTERNS_CONFIG	"patterns_textures.conf"
public static final String	PATTERNS_DIRECTORY	"./../textures/patterns/"

org.proteinshader.graphics.typography.GLF2GlyphSetFactory

public static final int	BYTES_PER_PIXEL	2
public static final int	DATA_TYPE	5121
public static final int	FORMAT	6410

org.proteinshader.graphics.typography.GLF2Header

public static final int	BYTES_PER_PIXEL	2
public static final int	CHAR_INFO_BYTES	24
public static final int	END_INDEX	16
public static final int	HEADER_BYTES	24
public static final int	HEIGHT_INDEX	8
public static final int	START_INDEX	12
public static final int	WIDTH_INDEX	4
public static final int	X1_INDEX	8
public static final int	X2_INDEX	16
public static final int	Y1_INDEX	12
public static final int	Y2_INDEX	20

org.proteinshader.graphics.typography.GlyphSetFactoryFactory

public static final String

FONT_DIRECTORY

"./../fonts/"

org.proteinshader.graphics.typography.TextLabel

public static final int	HEIGHT	32
public static final int	WIDTH	128

org.proteinshader.graphics.typography.TextLabelManager

public static final int	BYTES_PER_PIXEL	2
public static final String	MAP	"textLabelMap"
public static final int	TABLA_RASA_HEIGHT	128
public static final int	TABLA_RASA_WIDTH	64
public static final int	X_OFFSET	15
public static final int	Y_OFFSET	0

org.proteinshader.gui.ProteinShaderGUI

public static final int	BOTTOM_MARGIN	60
public static final int	TOP_MARGIN	30

org.proteinshader.gui.ProteinShaderSplasher

public static final String	IMAGE_FILE	"ProteinShaderLogo.png"
public static final long	MIN_SPLASH_TIME	5000L

org.proteinshader.gui.components.SpringLoadedJFrame

public static final double	DEFAULT_LONG_FACTOR	0.9
public static final double	DEFAULT_SHORT_FACTOR	0.5
public static final int	DELAY	10
public static final double	INCREMENT	0.05
public static final double	MAX_HEIGHT_FACTOR	0.9
public static final double	MAX_WIDTH_FACTOR	0.9
public static final double	MIN_HEIGHT_FACTOR	0.1
public static final double	MIN_WIDTH_FACTOR	0.1

org.proteinshader.gui.components.controlpanel.AntialiasingPanel

public static final String

MENU_NAME

"Antialiasing"

org.proteinshader.gui.components.controlpanel.AtomColorPanel

public static final String

MENU_NAME

"Atom Color"

org.proteinshader.gui.components.controlpanel.AtomScalePanel

public static final String	MENU_NAME	"Atom Scale"
public static final double	SCALE_INCREMENT	0.1
public static final double	SCALE_INIT	1.0
public static final double	SCALE_MAX	10.0
public static final double	SCALE_MIN	0.1

org.proteinshader.gui.components.controlpanel.AtomVisibilityPanel

public static final String

MENU_NAME

"Atom Visibility"

org.proteinshader.gui.components.controlpanel.CartoonColorPanel

public static final String

MENU_NAME

"Cartoon Color"

org.proteinshader.gui.components.controlpanel.CartoonSideChainsPanel

public static final String

MENU_NAME

"Cartoon Side Chains"

org.proteinshader.gui.components.controlpanel.CartoonVisibilityPanel

public static final String

MENU_NAME

"Cartoon Visibility"

org.proteinshader.gui.components.controlpanel.DecorationsPanel

public static final String

MENU_NAME

"Decorations"

org.proteinshader.gui.components.controlpanel.MotionPanel

public static final int	MAX_SPEED	90
public static final String	MENU_NAME	"Motion"
public static final int	MIN_SPEED	-90
public static final int	X_SPEED_INIT	0
public static final int	Y_SPEED_INIT	5

org.proteinshader.gui.components.controlpanel.OptimizePanel

public static final String	MENU_NAME	"Tiling"
public static final int	SPINNER_MAX	100
public static final int	SPINNER_MIN	3

org.proteinshader.gui.components.controlpanel.SelectorPanel

public static final int	DIALOG_HEIGHT	300
public static final int	DIALOG_WIDTH	150

org.proteinshader.gui.components.controlpanel.VisibilityPanel

public static final int

SLIDER_INIT

75

org.proteinshader.gui.components.menubar.AboutBox

public static final int	EXTRA_HEIGHT	90
public static final int	EXTRA_WIDTH	40

org.proteinshader.gui.components.menubar.FileMenu

public static final String	DATA_DIRECTORY	"./../data"
public static final String	IMAGES_DIRECTORY	"./../images"

org.proteinshader.gui.components.menubar.HelpMenu

public static final String	HELP_FILE	"../help/index.html"
public static final String	IMAGE_FILE	"ProteinShaderLogo.png"
public static final String	SOURCEFORGE_WEB_SITE	"http://proteinshader.sourceforge.net"

org.proteinshader.gui.listeners.CanvasMouseListener

public static final int	B1_MASK	16
public static final int	B2_MASK	8
public static final int	B3_MASK	4
public static final int	CAMERA_XY_SCALE	2
public static final int	CAMERA_ZOOM_SCALE	4
public static final int	WHEEL_SCALE_FACTOR	2

org.proteinshader.gui.utils.FileExtensionFilter

public static final String

DEFAULT_EXTENSION

".txt"

org.proteinshader.gui.utils.FpsLabel

public static final String	FONT_DIRECTORY	"./../fonts/"
public static final String	FONT_FILE	"ArialBold18.glf"

org.proteinshader.gui.utils.ImageFileChooser

public static final String

DEFAULT_FILENAME

"canvas"

org.proteinshader.gui.viewing.Camera

public static final double	FOVY	60.0
public static final double	HALF_FOVY	30.0
public static final double	HALF_FOVY_RADIANS	0.5235987755982988
public static final int	MIN_INITIAL_CAMERA_DISTANCE	20

org.proteinshader.gui.viewing.Rotation

public static final double	HALF_PI	1.57079632679489
public static final double	PI	3.14159265358979
public static final double	RADIANS_PER_DEGREE	0.017453292519943278
public static final double	TWO_PI	6.28318530717958

org.proteinshader.math.HermiteDemo

public static final int

SEGMENTS

10

org.proteinshader.math.LocalFrameDemo

public static final int

BANNER_WIDTH

70

org.proteinshader.math.Point3d

public static final String

DECIMAL_FORMAT

"0.000"

org.proteinshader.math.Quaternion

public static final String	DECIMAL_FORMAT	"0.000"
public static final double	MIN_THETA	0.01
public static final double	ONE_DEGREE	0.017453292519943295

org.proteinshader.math.QuaternionDemo

public static final int

BANNER_WIDTH

70

org.proteinshader.math.SlerpDemo

public static final int

BANNER_WIDTH

72

org.proteinshader.math.Vec3d

public static final String

DECIMAL_FORMAT

"0.000"

org.proteinshader.structure.Drawable

public static final float	DEFAULT_ALPHA	1.0f
public static final float	DEFAULT_BLUE	0.0f
public static final float	DEFAULT_GREEN	0.0f
public static final double	DEFAULT_RADIUS	1.0
public static final float	DEFAULT_RED	0.0f
public static final float	DEFAULT_SPECULAR_EXP	20.0f

org.proteinshader.structure.Heterogen

public static final String

HETEROGEN_PREFIX

"HET_"

org.proteinshader.structure.Segment

public static final double

MAX_BEND

0.59

org.proteinshader.structure.Structure

public static final int

SERIAL_NO_CACHE_CAPACITY

2000

org.proteinshader.structure.enums.AtomEnum

public static final double

BALL_SCALE

0.2

org.proteinshader.structure.factory.BetaStrandSegmentFactory

public static final double

HALF_PI

1.5707963267948966

org.proteinshader.structure.factory.SegmentFactory

public static final double	MAX_CA_DISTANCE	4.5
public static final double	SEGMENT_LENGTH	2.6

org.proteinshader.structure.io.PDBLineParser

public static final String	DEFAULT_CHAIN_ID	"A"
public static final String	DEFAULT_MODEL_ID	"1"
public static final int	MIN_CHAR_PER_LINE	80

org.proteinshader.structure.io.PDBStructureReader

public static final int

MIN_CHAR_IN_HEADER

80

org.proteinshader.structure.io.TubeVertices

public static final double	ALPHA_RADIUS	1.5
public static final int	ALPHA_SLICES	20
public static final int	ALPHA_STACKS	10
public static final double	BETA_RADIUS	1.5
public static final int	BETA_SLICES	20
public static final int	BETA_STACKS	10
public static final double	HALF_PI	1.57079632679489
public static final double	LOOP_RADIUS	0.75
public static final int	LOOP_SLICES	10
public static final int	LOOP_STACKS	10
public static final double	PI	3.14159265358979
public static final double	TWO_PI	6.28318530717958

org.proteinshader.structure.io.demos.PDBStructureReaderDemo

public static final String	PATH	"edu/harvard/fas/jrweber/molecular/structure/io/demos/"
public static final String	usageMessage	"USAGE: java -cp . edu/harvard/fas/jrweber/molecular/structure/io/demos/PDBStructureReaderDemo inputFilename outputFilename"

org.proteinshader.structure.io.demos.SegmentDemo

public static final String	PATH	"edu/harvard/fas/jrweber/molecular/structure/io/demos/"
public static final String	usageMessage	"USAGE: java -cp . edu/harvard/fas/jrweber/molecular/structure/io/demos/SegmentDemo inputFilename outputFilename"

org.proteinshader.structure.visitor.BondPredictor

public static final double	DEFAULT_MIN_BOND_LENGTH	0.4
public static final double	DEFAULT_TOLERANCE	0.56

org.proteinshader.structure.visitor.FrenetFrameGeneratorVisitor

public static final double

MAX_CA_DISTANCE

4.5

org.proteinshader.structure.visitor.SFWriterVisitor

public static final int	CHAR_PER_LINE	80
public static final int	INDENTATION_FACTOR	2

org.proteinshader.structure.visitor.demos.ModifierVisitorDemo

public static final String	PATH	"edu/harvard/fas/jrweber/molecular/structure/visitor/demos/"
public static final String	usageMessage	"USAGE: java -cp . edu/harvard/fas/jrweber/molecular/structure/visitor/demos/ModifierVisitorDemo inputFilename outputFilename"

org.proteinshader.structure.visitor.demos.VisitorDemo

public static final String	PATH	"edu/harvard/fas/jrweber/molecular/structure/visitor/demos/"
public static final String	usageMessage	"USAGE: java -cp . edu/harvard/fas/jrweber/molecular/structure/visitor/demos/VisitorDemo filename"