org.jmol.viewer
Class JmolConstants

java.lang.Object
  extended by org.jmol.viewer.JmolConstants

public final class JmolConstants
extends Object


Field Summary
private static String allCarbohydrates
           
static String allowedQuaternionFrames
           
static int ALPHA_CARBON_VISIBILITY_FLAG
           
static int[] altArgbsCpk
           
static float ANGSTROMS_PER_BOHR
           
static int ANIMATION_LOOP
           
static int ANIMATION_ONCE
           
static int ANIMATION_PALINDROME
           
private static short[] anionLookupTable
           
static int[] argbsAmino
           
static int[] argbsChainAtom
          some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
static int[] argbsChainHetero
           
static int[] argbsCpk
          Default table of CPK atom colors.
static int[] argbsCpkRasmol
           
static int[] argbsFormalCharge
           
static int argbShapelyBackbone
           
static int argbShapelyDefault
           
static int argbShapelySpecial
           
static int[] argbsHbondType
           
static int[] argbsIsosurfaceNegative
           
static int[] argbsIsosurfacePositive
           
static int[] argbsRoygbScale
           
static int[] argbsRwbScale
           
static int[] argbsShapely
           
static int[] argbsStructure
          In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
static int ATOM_IN_FRAME
           
static int ATOM_SLABBED
           
static byte ATOMID_ALPHA_CARBON
           
static int ATOMID_ALPHA_ONLY_MASK
           
static byte ATOMID_AMINO_NITROGEN
           
private static int ATOMID_BACKBONE_MIN
           
static byte ATOMID_C1_PRIME
           
static byte ATOMID_C2
           
static byte ATOMID_C3_PRIME
           
static byte ATOMID_C4
           
static byte ATOMID_C4_PRIME
           
static byte ATOMID_C5
           
static byte ATOMID_C5M
           
static byte ATOMID_C6
           
static byte ATOMID_C7
           
static byte ATOMID_C8
           
static byte ATOMID_CARBONYL_CARBON
           
static byte ATOMID_CARBONYL_OD1
           
static byte ATOMID_CARBONYL_OD2
           
static byte ATOMID_CARBONYL_OE1
           
static byte ATOMID_CARBONYL_OE2
           
static byte ATOMID_CARBONYL_OXYGEN
           
static int ATOMID_DISTINGUISHING_ATOM_MAX
           
static byte ATOMID_H3T_TERMINUS
           
static byte ATOMID_H5T_TERMINUS
           
static byte ATOMID_HO3_PRIME
           
static byte ATOMID_HO5_PRIME
           
static int ATOMID_MAX
           
static byte ATOMID_N1
           
static byte ATOMID_N2
           
static byte ATOMID_N3
           
static byte ATOMID_N4
           
static byte ATOMID_N6
           
static byte ATOMID_N7
           
static byte ATOMID_N9
           
static int ATOMID_NUCLEIC_MASK
           
static byte ATOMID_NUCLEIC_PHOSPHORUS
           
static byte ATOMID_O1
           
static byte ATOMID_O1P
           
static byte ATOMID_O2
           
static byte ATOMID_O2_PRIME
           
static byte ATOMID_O2P
           
static byte ATOMID_O3_PRIME
           
static byte ATOMID_O4
           
static byte ATOMID_O5_PRIME
           
static byte ATOMID_O5T_TERMINUS
           
static byte ATOMID_O6
           
static byte ATOMID_OP1
           
static byte ATOMID_OP2
           
static int ATOMID_PHOSPHORUS_ONLY_MASK
           
static int ATOMID_PROTEIN_MASK
           
static byte ATOMID_S4
           
static byte ATOMID_SG
           
static byte ATOMID_TERMINATING_OXT
           
static int AXES_DEFAULT_FONTSIZE
           
static int AXES_MODE_BOUNDBOX
          axes modes
static int AXES_MODE_MOLECULAR
           
static int AXES_MODE_UNITCELL
           
static Vector3f axisNX
           
static Vector3f axisNY
           
static Vector3f axisNZ
           
static Vector3f axisX
           
static Vector3f axisY
           
static Vector3f axisZ
           
static int BACKBONE_VISIBILITY_FLAG
           
static int BACKLIT
           
private static String[] bondOrderNames
           
private static String[] bondOrderNumbers
           
private static int[] bondOrderValues
           
(package private) static BitSet bsAnions
           
(package private) static BitSet bsCations
           
static int CALLBACK_ANIMFRAME
           
static int CALLBACK_CLICK
           
static int CALLBACK_COUNT
           
static int CALLBACK_ECHO
           
static int CALLBACK_ERROR
           
static int CALLBACK_EVAL
           
static int CALLBACK_HOVER
           
static int CALLBACK_LOADSTRUCT
           
static int CALLBACK_MEASURE
           
static int CALLBACK_MESSAGE
           
static int CALLBACK_MINIMIZATION
           
static int CALLBACK_PICK
           
static int CALLBACK_RESIZE
           
static int CALLBACK_SCRIPT
           
static int CALLBACK_SYNC
           
private static String[] callbackNames
           
static int CARTOON_VISIBILITY_FLAG
           
private static short[] cationLookupTable
           
static Vector3f center
           
static String CLASSBASE_OPTIONS
           
static int CONNECT_AUTO_BOND
           
static int CONNECT_CREATE_ONLY
           
static int CONNECT_DELETE_BONDS
           
static int CONNECT_IDENTIFY_ONLY
           
static int CONNECT_MODIFY_ONLY
           
static int CONNECT_MODIFY_OR_CREATE
           
static String copyright
           
private static short[] covalentMars
          Default table of covalent Radii stored as a short mar ...
static String cvsDate
           
static String date
           
static short DEFAULT_BOND_MILLIANGSTROM_RADIUS
           
static float DEFAULT_BOND_RADIUS
           
static float DEFAULT_BOND_TOLERANCE
           
static String DEFAULT_FONTFACE
           
static String DEFAULT_FONTSTYLE
           
static String DEFAULT_HELP_PATH
           
static float DEFAULT_MAX_CONNECT_DISTANCE
           
static float DEFAULT_MIN_BOND_DISTANCE
           
static float DEFAULT_MIN_CONNECT_DISTANCE
           
static int DEFAULT_PERCENT_VDW_ATOM
           
static int DEFAULT_STEREO_DEGREES
           
static float DEFAULT_STRUT_RADIUS
           
static int DRAW_ARC
           
static int DRAW_ARROW
           
static int DRAW_CIRCLE
           
static int DRAW_CIRCULARPLANE
           
static int DRAW_CURVE
           
static int DRAW_CYLINDER
           
static int DRAW_LINE
           
static int DRAW_LINE_SEGMENT
           
static int DRAW_MULTIPLE
           
static int DRAW_NONE
           
static int DRAW_PLANE
           
static int DRAW_POINT
           
static int DRAW_POLYGON
           
static int DRAW_TRIANGLE
           
static String EMBEDDED_SCRIPT_TAG
           
static String EXPORT_DRIVER_LIST
           
static int FILE_STATUS_MODELS_DELETED
           
static int FILE_STATUS_MODELSET_CREATED
           
static int FILE_STATUS_NOT_LOADED
           
static int FILE_STATUS_ZAPPED
           
static short FORMAL_CHARGE_COLIX_BLUE
           
static short FORMAL_CHARGE_COLIX_RED
           
static short FORMAL_CHARGE_COLIX_WHITE
           
static int FORMAL_CHARGE_INDEX_MAX
           
static int FORMAL_CHARGE_INDEX_WHITE
           
static int FORMAL_CHARGE_MAX
           
static int FORMAL_CHARGE_MIN
          ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
static int FORMAL_CHARGE_RANGE_SIZE
           
static int FRONTLIT
           
static int FULLYLIT
           
static int group3Count
           
static String group3List
           
static int GROUPID_AMINO_MAX
           
static int GROUPID_CYSTEINE
           
static int GROUPID_PROLINE
           
private static int GROUPID_SOLVENTS
           
private static int GROUPID_SULPHATE
           
private static int GROUPID_WATER
           
private static Hashtable htSpecialAtoms
           
static int INFO_A
           
static int INFO_ALPHA
           
static int INFO_B
           
static int INFO_BETA
           
static int INFO_C
           
static int INFO_DIMENSIONS
           
static int INFO_GAMMA
           
static int JMOL_DATA_OTHER
           
static int JMOL_DATA_QUATERNION
           
static int JMOL_DATA_RAMACHANDRAN
           
static int LABEL_DEFAULT_FONTSIZE
           
static int LABEL_DEFAULT_X_OFFSET
           
static int LABEL_DEFAULT_Y_OFFSET
           
static int LABEL_MAXIMUM_FONTSIZE
           
static int LABEL_MINIMUM_FONTSIZE
           
static String LOAD_ATOM_DATA_TYPES
           
static short madMultipleBondSmallMaximum
           
static int MAXIMUM_AUTO_BOND_COUNT
           
static int MEASURE_DEFAULT_FONTSIZE
           
static int MINIMIZATION_ATOM_MAX
           
static float MINIMIZE_FIXED_RANGE
           
static String MODELKIT_ZAP_STRING
           
static String MODELKIT_ZAP_TITLE
           
static int MOUSE_DELETE
           
static int MOUSE_MEASURE
           
static int MOUSE_NONE
           
static int MOUSE_PICK
           
static int MOUSE_POPUP_MENU
           
static int MOUSE_ROTATE
           
static int MOUSE_ROTATE_Z
           
static int MOUSE_SLAB_PLANE
           
static int MOUSE_XLATE
           
static int MOUSE_ZOOM
           
static byte MULTIBOND_ALWAYS
           
static byte MULTIBOND_NEVER
           
static byte MULTIBOND_NOTSMALL
           
static byte MULTIBOND_WIREFRAME
           
static boolean officialRelease
           
static byte PALETTE_ALTLOC
           
static byte PALETTE_AMINO
           
static byte PALETTE_CHAIN
           
static byte PALETTE_CPK
           
static byte PALETTE_ENERGY
           
static byte PALETTE_FIXEDTEMP
           
static byte PALETTE_FORMAL_CHARGE
           
static byte PALETTE_GROUP
           
static byte PALETTE_INSERTION
           
static byte PALETTE_JMOL
           
static byte PALETTE_MOLECULE
           
static byte PALETTE_MONOMER
           
static byte PALETTE_NONE
           
static byte PALETTE_PARTIAL_CHARGE
           
static byte PALETTE_POLYMER
           
static byte PALETTE_PROPERTY
           
static byte PALETTE_RASMOL
           
static byte PALETTE_SHAPELY
           
static byte PALETTE_STATIC
           
static byte PALETTE_STRAIGHTNESS
           
static byte PALETTE_STRUCTURE
           
static byte PALETTE_SURFACE
           
static byte PALETTE_TEMP
           
static byte PALETTE_TYPE
           
static byte PALETTE_UNKNOWN
           
static byte PALETTE_VARIABLE
           
static byte PALETTE_VOLATILE
           
private static int paletteCount
           
private static byte[] paletteIDs
           
private static String[] paletteNames
           
static short PARTIAL_CHARGE_COLIX_BLUE
           
static short PARTIAL_CHARGE_COLIX_RED
           
static short PARTIAL_CHARGE_COLIX_WHITE
           
static int PARTIAL_CHARGE_RANGE_SIZE
           
static char[] predefinedGroup1Names
           
static String[] predefinedGroup3Names
           
static String[] predefinedStatic
           
static String[] predefinedVariable
           
static String PREVIOUS_MESH_ID
           
static byte PROTEIN_STRUCTURE_CARBOHYDRATE
           
static byte PROTEIN_STRUCTURE_DNA
           
static byte PROTEIN_STRUCTURE_HELIX
           
static byte PROTEIN_STRUCTURE_HELIX_310
           
static byte PROTEIN_STRUCTURE_HELIX_ALPHA
           
static byte PROTEIN_STRUCTURE_HELIX_PI
           
static byte PROTEIN_STRUCTURE_NONE
           
static byte PROTEIN_STRUCTURE_NOT
          Default table of PdbStructure colors
static byte PROTEIN_STRUCTURE_RNA
           
static byte PROTEIN_STRUCTURE_SHEET
           
static byte PROTEIN_STRUCTURE_TURN
           
private static String[] proteinStructureNames
           
private static int[] quantumShellIDs
           
private static String[] quantumShellTags
           
static float radiansPerDegree
           
static String SCRIPT_EDITOR_IGNORE
           
static int SHAPE_AXES
           
static int SHAPE_BACKBONE
           
static int SHAPE_BALLS
           
static int SHAPE_BBCAGE
           
static int SHAPE_CARTOON
           
static int SHAPE_DIPOLES
           
static int SHAPE_DOTS
           
static int SHAPE_DRAW
           
static int SHAPE_ECHO
           
static int SHAPE_ELLIPSOIDS
           
static int SHAPE_FRANK
           
static int SHAPE_GEOSURFACE
           
static int SHAPE_HALOS
           
static int SHAPE_HOVER
           
static int SHAPE_HSTICKS
           
static int SHAPE_ISOSURFACE
           
static int SHAPE_LABELS
           
static int SHAPE_LCAOCARTOON
           
static int SHAPE_MAX
           
static int SHAPE_MAX_HAS_ID
           
static int SHAPE_MAX_MESH_COLLECTION
           
static int SHAPE_MAX_SECONDARY
           
static int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
           
static int SHAPE_MAX_SPECIAL
           
static int SHAPE_MAX_SURFACE
           
static int SHAPE_MEASURES
           
static int SHAPE_MESHRIBBON
           
static int SHAPE_MIN_HAS_ID
           
static int SHAPE_MIN_MESH_COLLECTION
           
static int SHAPE_MIN_SECONDARY
           
static int SHAPE_MIN_SPECIAL
           
static int SHAPE_MIN_SURFACE
           
static int SHAPE_MO
           
static int SHAPE_PLOT3D
           
static int SHAPE_PMESH
           
static int SHAPE_POLYHEDRA
           
static int SHAPE_RIBBONS
           
static int SHAPE_ROCKETS
           
static int SHAPE_SSSTICKS
           
static int SHAPE_STARS
           
static int SHAPE_STICKS
           
static int SHAPE_STRANDS
           
static int SHAPE_STRUTS
           
static int SHAPE_TRACE
           
static int SHAPE_UCCAGE
           
static int SHAPE_VECTORS
           
static String[] shapeClassBases
           
static int SHELL_D_CARTESIAN
           
static int SHELL_D_SPHERICAL
           
static int SHELL_F_CARTESIAN
           
static int SHELL_F_SPHERICAL
           
static int SHELL_G_CARTESIAN
           
static int SHELL_G_SPHERICAL
           
static int SHELL_H_CARTESIAN
           
static int SHELL_H_SPHERICAL
           
static int SHELL_L
           
static int SHELL_P
           
static int SHELL_S
           
static int SHELL_SP
           
private static String[][] shellOrder
           
private static String[] specialAtomNames
           
static int STEREO_CUSTOM
           
static int STEREO_DOUBLE
           
static int STEREO_NONE
           
static int STEREO_REDBLUE
           
static int STEREO_REDCYAN
           
static int STEREO_REDGREEN
           
static int STEREO_UNKNOWN
           
private static String[] stereoModes
           
static String SUPPORTED_BASES
           
static String SUPPORTED_BASIS_FUNCTIONS
           
static Vector3f[] unitAxisVectors
           
static short[] vanderwaalsMars
          Default table of van der Waals Radii.
static int VDW_AUTO
           
static int VDW_AUTO_BABEL
           
static int VDW_AUTO_JMOL
           
static int VDW_AUTO_RASMOL
           
static int VDW_BABEL
           
static int VDW_BABEL21
           
static int VDW_JMOL
           
static int VDW_NOJMOL
           
static int VDW_RASMOL
           
static int VDW_UNKNOWN
           
static int VDW_USER
           
(package private) static String[] vdwLabels
           
static String version
           
static int XY_ZTOP
           
 
Constructor Summary
JmolConstants()
           
 
Method Summary
static boolean checkCarbohydrate(String group3)
           
static String embedScript(String s)
           
static int getArgbHbondType(int order)
           
static float getBondingRadiusFloat(int atomicNumber, int charge)
           
private static float getBondingRadiusFloat(int atomicNumber, int charge, short[] table)
           
static int getBondOrderFromFloat(float fOrder)
           
static int getBondOrderFromString(String bondOrderString)
           
static String getBondOrderNameFromOrder(int order)
           
static String getBondOrderNumberFromOrder(int order)
          used for formatting labels and in the connect PARTIAL command
static int getCallbackId(String callbackName)
           
static String getCallbackName(int i)
           
static String getCmlOrder(int order)
           
static int getCovalentBondOrder(int order)
           
static String getDrawTypeName(int drawType)
           
private static String getGroup3List()
           
static byte getPaletteID(String paletteName)
           
static String getPaletteName(byte pid)
           
static int getPartialBondDotted(int order)
           
static int getPartialBondOrder(int order)
           
static int getPartialBondOrderFromInteger(int bondOrderInteger)
          reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
static String getProteinStructureName(int itype, boolean isGeneric)
           
static byte getProteinStructureType(String type)
           
static String getQuantumShellTag(int shell)
           
static int getQuantumShellTagID(String tag)
           
static int getQuantumShellTagIDSpherical(String tag)
           
static String getShapeClassName(int shapeID)
           
static int getShapeVisibilityFlag(int shapeID)
           
static String[] getShellOrder(int i)
           
static String getSpecialAtomName(int atomID)
           
static int getStereoMode(String id)
           
(package private) static String getStereoModeName(int mode)
           
static int getVanderwaalsMar(int i, int iType)
           
static String getVdwLabel(int i)
           
static int getVdwType(String label)
           
static boolean isHetero(String group3)
           
static boolean isPaletteVariable(byte pid)
           
static boolean isShapeSecondary(int i)
           
static byte lookupSpecialAtomID(String atomName)
           
static int modelValue(String strDecimal)
           
static byte pidOf(Object value)
           
static int shapeTokenIndex(int tok)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

copyright

public static final String copyright
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Constant Field Values

version

public static final String version

cvsDate

public static final String cvsDate
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Constant Field Values

date

public static final String date

officialRelease

public static final boolean officialRelease
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Constant Field Values

CLASSBASE_OPTIONS

public static final String CLASSBASE_OPTIONS
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DEFAULT_HELP_PATH

public static final String DEFAULT_HELP_PATH
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EMBEDDED_SCRIPT_TAG

public static final String EMBEDDED_SCRIPT_TAG
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SCRIPT_EDITOR_IGNORE

public static final String SCRIPT_EDITOR_IGNORE
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CALLBACK_ANIMFRAME

public static final int CALLBACK_ANIMFRAME
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CALLBACK_ECHO

public static final int CALLBACK_ECHO
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CALLBACK_ERROR

public static final int CALLBACK_ERROR
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CALLBACK_EVAL

public static final int CALLBACK_EVAL
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CALLBACK_HOVER

public static final int CALLBACK_HOVER
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CALLBACK_LOADSTRUCT

public static final int CALLBACK_LOADSTRUCT
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CALLBACK_MEASURE

public static final int CALLBACK_MEASURE
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CALLBACK_MESSAGE

public static final int CALLBACK_MESSAGE
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CALLBACK_MINIMIZATION

public static final int CALLBACK_MINIMIZATION
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CALLBACK_PICK

public static final int CALLBACK_PICK
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CALLBACK_RESIZE

public static final int CALLBACK_RESIZE
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CALLBACK_SCRIPT

public static final int CALLBACK_SCRIPT
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CALLBACK_SYNC

public static final int CALLBACK_SYNC
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CALLBACK_CLICK

public static final int CALLBACK_CLICK
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CALLBACK_COUNT

public static final int CALLBACK_COUNT
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FILE_STATUS_NOT_LOADED

public static final int FILE_STATUS_NOT_LOADED
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FILE_STATUS_ZAPPED

public static final int FILE_STATUS_ZAPPED
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FILE_STATUS_MODELSET_CREATED

public static final int FILE_STATUS_MODELSET_CREATED
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FILE_STATUS_MODELS_DELETED

public static final int FILE_STATUS_MODELS_DELETED
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callbackNames

private static final String[] callbackNames

INFO_A

public static final int INFO_A
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INFO_B

public static final int INFO_B
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INFO_C

public static final int INFO_C
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INFO_ALPHA

public static final int INFO_ALPHA
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INFO_BETA

public static final int INFO_BETA
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INFO_GAMMA

public static final int INFO_GAMMA
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INFO_DIMENSIONS

public static final int INFO_DIMENSIONS
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JMOL_DATA_OTHER

public static final int JMOL_DATA_OTHER
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JMOL_DATA_RAMACHANDRAN

public static final int JMOL_DATA_RAMACHANDRAN
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JMOL_DATA_QUATERNION

public static final int JMOL_DATA_QUATERNION
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allowedQuaternionFrames

public static final String allowedQuaternionFrames
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EXPORT_DRIVER_LIST

public static final String EXPORT_DRIVER_LIST
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DRAW_MULTIPLE

public static final int DRAW_MULTIPLE
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DRAW_NONE

public static final int DRAW_NONE
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DRAW_POINT

public static final int DRAW_POINT
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DRAW_LINE

public static final int DRAW_LINE
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DRAW_TRIANGLE

public static final int DRAW_TRIANGLE
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DRAW_PLANE

public static final int DRAW_PLANE
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DRAW_CYLINDER

public static final int DRAW_CYLINDER
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DRAW_ARROW

public static final int DRAW_ARROW
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DRAW_CIRCLE

public static final int DRAW_CIRCLE
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DRAW_CURVE

public static final int DRAW_CURVE
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DRAW_CIRCULARPLANE

public static final int DRAW_CIRCULARPLANE
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DRAW_ARC

public static final int DRAW_ARC
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DRAW_LINE_SEGMENT

public static final int DRAW_LINE_SEGMENT
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DRAW_POLYGON

public static final int DRAW_POLYGON
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Constant Field Values

center

public static final Vector3f center

axisX

public static final Vector3f axisX

axisY

public static final Vector3f axisY

axisZ

public static final Vector3f axisZ

axisNX

public static final Vector3f axisNX

axisNY

public static final Vector3f axisNY

axisNZ

public static final Vector3f axisNZ

unitAxisVectors

public static final Vector3f[] unitAxisVectors

XY_ZTOP

public static final int XY_ZTOP
See Also:
Constant Field Values

DEFAULT_PERCENT_VDW_ATOM

public static final int DEFAULT_PERCENT_VDW_ATOM
See Also:
Constant Field Values

DEFAULT_BOND_RADIUS

public static final float DEFAULT_BOND_RADIUS
See Also:
Constant Field Values

DEFAULT_BOND_MILLIANGSTROM_RADIUS

public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS
See Also:
Constant Field Values

DEFAULT_STRUT_RADIUS

public static final float DEFAULT_STRUT_RADIUS
See Also:
Constant Field Values

DEFAULT_BOND_TOLERANCE

public static final float DEFAULT_BOND_TOLERANCE
See Also:
Constant Field Values

DEFAULT_MIN_BOND_DISTANCE

public static final float DEFAULT_MIN_BOND_DISTANCE
See Also:
Constant Field Values

DEFAULT_MAX_CONNECT_DISTANCE

public static final float DEFAULT_MAX_CONNECT_DISTANCE
See Also:
Constant Field Values

DEFAULT_MIN_CONNECT_DISTANCE

public static final float DEFAULT_MIN_CONNECT_DISTANCE
See Also:
Constant Field Values

MINIMIZATION_ATOM_MAX

public static final int MINIMIZATION_ATOM_MAX
See Also:
Constant Field Values

MINIMIZE_FIXED_RANGE

public static final float MINIMIZE_FIXED_RANGE
See Also:
Constant Field Values

CONNECT_DELETE_BONDS

public static final int CONNECT_DELETE_BONDS
See Also:
Constant Field Values

CONNECT_MODIFY_ONLY

public static final int CONNECT_MODIFY_ONLY
See Also:
Constant Field Values

CONNECT_CREATE_ONLY

public static final int CONNECT_CREATE_ONLY
See Also:
Constant Field Values

CONNECT_MODIFY_OR_CREATE

public static final int CONNECT_MODIFY_OR_CREATE
See Also:
Constant Field Values

CONNECT_AUTO_BOND

public static final int CONNECT_AUTO_BOND
See Also:
Constant Field Values

CONNECT_IDENTIFY_ONLY

public static final int CONNECT_IDENTIFY_ONLY
See Also:
Constant Field Values

MOUSE_NONE

public static final int MOUSE_NONE
See Also:
Constant Field Values

MOUSE_ROTATE

public static final int MOUSE_ROTATE
See Also:
Constant Field Values

MOUSE_ZOOM

public static final int MOUSE_ZOOM
See Also:
Constant Field Values

MOUSE_XLATE

public static final int MOUSE_XLATE
See Also:
Constant Field Values

MOUSE_PICK

public static final int MOUSE_PICK
See Also:
Constant Field Values

MOUSE_DELETE

public static final int MOUSE_DELETE
See Also:
Constant Field Values

MOUSE_MEASURE

public static final int MOUSE_MEASURE
See Also:
Constant Field Values

MOUSE_ROTATE_Z

public static final int MOUSE_ROTATE_Z
See Also:
Constant Field Values

MOUSE_SLAB_PLANE

public static final int MOUSE_SLAB_PLANE
See Also:
Constant Field Values

MOUSE_POPUP_MENU

public static final int MOUSE_POPUP_MENU
See Also:
Constant Field Values

MULTIBOND_NEVER

public static final byte MULTIBOND_NEVER
See Also:
Constant Field Values

MULTIBOND_WIREFRAME

public static final byte MULTIBOND_WIREFRAME
See Also:
Constant Field Values

MULTIBOND_NOTSMALL

public static final byte MULTIBOND_NOTSMALL
See Also:
Constant Field Values

MULTIBOND_ALWAYS

public static final byte MULTIBOND_ALWAYS
See Also:
Constant Field Values

madMultipleBondSmallMaximum

public static final short madMultipleBondSmallMaximum
See Also:
Constant Field Values

AXES_MODE_BOUNDBOX

public static final int AXES_MODE_BOUNDBOX
axes modes

See Also:
Constant Field Values

AXES_MODE_MOLECULAR

public static final int AXES_MODE_MOLECULAR
See Also:
Constant Field Values

AXES_MODE_UNITCELL

public static final int AXES_MODE_UNITCELL
See Also:
Constant Field Values

argbsHbondType

public static final int[] argbsHbondType

bondOrderNames

private static final String[] bondOrderNames

bondOrderNumbers

private static final String[] bondOrderNumbers

bondOrderValues

private static final int[] bondOrderValues

ANGSTROMS_PER_BOHR

public static final float ANGSTROMS_PER_BOHR
See Also:
Constant Field Values

FRONTLIT

public static final int FRONTLIT
See Also:
Constant Field Values

BACKLIT

public static final int BACKLIT
See Also:
Constant Field Values

FULLYLIT

public static final int FULLYLIT
See Also:
Constant Field Values

altArgbsCpk

public static final int[] altArgbsCpk

VDW_UNKNOWN

public static final int VDW_UNKNOWN
See Also:
Constant Field Values

VDW_JMOL

public static final int VDW_JMOL
See Also:
Constant Field Values

VDW_BABEL

public static final int VDW_BABEL
See Also:
Constant Field Values

VDW_RASMOL

public static final int VDW_RASMOL
See Also:
Constant Field Values

VDW_BABEL21

public static final int VDW_BABEL21
See Also:
Constant Field Values

VDW_AUTO_JMOL

public static final int VDW_AUTO_JMOL
See Also:
Constant Field Values

VDW_AUTO_BABEL

public static final int VDW_AUTO_BABEL
See Also:
Constant Field Values

VDW_AUTO_RASMOL

public static final int VDW_AUTO_RASMOL
See Also:
Constant Field Values

VDW_NOJMOL

public static final int VDW_NOJMOL
See Also:
Constant Field Values

VDW_AUTO

public static final int VDW_AUTO
See Also:
Constant Field Values

VDW_USER

public static final int VDW_USER
See Also:
Constant Field Values

vdwLabels

static final String[] vdwLabels

vanderwaalsMars

public static final short[] vanderwaalsMars
Default table of van der Waals Radii. values are stored as MAR -- Milli Angstrom Radius Used for spacefill rendering of atoms. Values taken from OpenBabel. Note that AUTO_JMOL, AUTO_BABEL, and AUTO_RASMOL are 4, 5, and 6, respectively, so their mod will be JMOL, BABEL, and RASMOL. AUTO is 8, so will default to Jmol

See Also:
openbabel.sourceforge.net, vdw_comparison.xls

covalentMars

private static final short[] covalentMars
Default table of covalent Radii stored as a short mar ... Milli Angstrom Radius Values taken from OpenBabel.

See Also:
openbabel.sourceforge.net

FORMAL_CHARGE_MIN

public static final int FORMAL_CHARGE_MIN
ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7. This data is from Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143 (scanned for Jmol by Phillip Barak, Jan 2004) Reorganized from two separate arrays 9/2006 by Bob Hanson, who thought it was just too hard to look these up and, if necessary, add or modify. At the same time, the table was split into cations and anions for easier retrieval. O- and N+ removed 9/2008 - BH. The problem is that the formal charge is used to determine bonding radius. But these formal charges are different than the charges used in compilation of HCP data (which is crystal ionic radii). Specifically, because O- and N+ are very common in organic compounds, I have removed their radii from the table FOR OUR PURPOSES HERE. I suppose there are some ionic compounds that have O- and N+ as isolated ions, but what they would be I have no clue. Better to be safe and go with somewhat more reasonable values. Argh. Changed for Jmol 11.6.RC15

See Also:
Constant Field Values

FORMAL_CHARGE_MAX

public static final int FORMAL_CHARGE_MAX
See Also:
Constant Field Values

cationLookupTable

private static final short[] cationLookupTable

anionLookupTable

private static final short[] anionLookupTable

bsCations

static BitSet bsCations

bsAnions

static BitSet bsAnions

MAXIMUM_AUTO_BOND_COUNT

public static final int MAXIMUM_AUTO_BOND_COUNT
See Also:
Constant Field Values

PALETTE_VOLATILE

public static final byte PALETTE_VOLATILE
See Also:
Constant Field Values

PALETTE_STATIC

public static final byte PALETTE_STATIC
See Also:
Constant Field Values

PALETTE_UNKNOWN

public static final byte PALETTE_UNKNOWN
See Also:
Constant Field Values

PALETTE_NONE

public static final byte PALETTE_NONE
See Also:
Constant Field Values

PALETTE_CPK

public static final byte PALETTE_CPK
See Also:
Constant Field Values

PALETTE_PARTIAL_CHARGE

public static final byte PALETTE_PARTIAL_CHARGE
See Also:
Constant Field Values

PALETTE_FORMAL_CHARGE

public static final byte PALETTE_FORMAL_CHARGE
See Also:
Constant Field Values

PALETTE_TEMP

public static final byte PALETTE_TEMP
See Also:
Constant Field Values

PALETTE_FIXEDTEMP

public static final byte PALETTE_FIXEDTEMP
See Also:
Constant Field Values

PALETTE_SURFACE

public static final byte PALETTE_SURFACE
See Also:
Constant Field Values

PALETTE_STRUCTURE

public static final byte PALETTE_STRUCTURE
See Also:
Constant Field Values

PALETTE_AMINO

public static final byte PALETTE_AMINO
See Also:
Constant Field Values

PALETTE_SHAPELY

public static final byte PALETTE_SHAPELY
See Also:
Constant Field Values

PALETTE_CHAIN

public static final byte PALETTE_CHAIN
See Also:
Constant Field Values

PALETTE_GROUP

public static final byte PALETTE_GROUP
See Also:
Constant Field Values

PALETTE_MONOMER

public static final byte PALETTE_MONOMER
See Also:
Constant Field Values

PALETTE_MOLECULE

public static final byte PALETTE_MOLECULE
See Also:
Constant Field Values

PALETTE_ALTLOC

public static final byte PALETTE_ALTLOC
See Also:
Constant Field Values

PALETTE_INSERTION

public static final byte PALETTE_INSERTION
See Also:
Constant Field Values

PALETTE_JMOL

public static final byte PALETTE_JMOL
See Also:
Constant Field Values

PALETTE_RASMOL

public static final byte PALETTE_RASMOL
See Also:
Constant Field Values

PALETTE_TYPE

public static final byte PALETTE_TYPE
See Also:
Constant Field Values

PALETTE_ENERGY

public static final byte PALETTE_ENERGY
See Also:
Constant Field Values

PALETTE_PROPERTY

public static final byte PALETTE_PROPERTY
See Also:
Constant Field Values

PALETTE_VARIABLE

public static final byte PALETTE_VARIABLE
See Also:
Constant Field Values

PALETTE_STRAIGHTNESS

public static final byte PALETTE_STRAIGHTNESS
See Also:
Constant Field Values

PALETTE_POLYMER

public static final byte PALETTE_POLYMER
See Also:
Constant Field Values

paletteNames

private static final String[] paletteNames

paletteIDs

private static final byte[] paletteIDs

paletteCount

private static final int paletteCount

argbsCpk

public static final int[] argbsCpk
Default table of CPK atom colors. ghemical colors with a few proposed modifications


argbsCpkRasmol

public static final int[] argbsCpkRasmol

PROTEIN_STRUCTURE_NOT

public static final byte PROTEIN_STRUCTURE_NOT
Default table of PdbStructure colors

See Also:
Constant Field Values

PROTEIN_STRUCTURE_NONE

public static final byte PROTEIN_STRUCTURE_NONE
See Also:
Constant Field Values

PROTEIN_STRUCTURE_TURN

public static final byte PROTEIN_STRUCTURE_TURN
See Also:
Constant Field Values

PROTEIN_STRUCTURE_SHEET

public static final byte PROTEIN_STRUCTURE_SHEET
See Also:
Constant Field Values

PROTEIN_STRUCTURE_HELIX

public static final byte PROTEIN_STRUCTURE_HELIX
See Also:
Constant Field Values

PROTEIN_STRUCTURE_DNA

public static final byte PROTEIN_STRUCTURE_DNA
See Also:
Constant Field Values

PROTEIN_STRUCTURE_RNA

public static final byte PROTEIN_STRUCTURE_RNA
See Also:
Constant Field Values

PROTEIN_STRUCTURE_CARBOHYDRATE

public static final byte PROTEIN_STRUCTURE_CARBOHYDRATE
See Also:
Constant Field Values

PROTEIN_STRUCTURE_HELIX_310

public static final byte PROTEIN_STRUCTURE_HELIX_310
See Also:
Constant Field Values

PROTEIN_STRUCTURE_HELIX_ALPHA

public static final byte PROTEIN_STRUCTURE_HELIX_ALPHA
See Also:
Constant Field Values

PROTEIN_STRUCTURE_HELIX_PI

public static final byte PROTEIN_STRUCTURE_HELIX_PI
See Also:
Constant Field Values

proteinStructureNames

private static final String[] proteinStructureNames

argbsStructure

public static final int[] argbsStructure
In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure. Structure Decimal RGB Hex RGB Alpha helices red-magenta [255,0,128] FF 00 80 * Beta strands yellow [255,200,0] FF C8 00 * Turns pale blue [96,128,255] 60 80 FF Other white [255,255,255] FF FF FF Values given in the 1994 RasMol 2.5 Quick Reference Card ([240,0,128] and [255,255,0]) are not correct for RasMol 2.6-beta-2a. This correction was made above on Dec 5, 1998.


argbsAmino

public static final int[] argbsAmino

argbShapelyBackbone

public static final int argbShapelyBackbone
See Also:
Constant Field Values

argbShapelySpecial

public static final int argbShapelySpecial
See Also:
Constant Field Values

argbShapelyDefault

public static final int argbShapelyDefault
See Also:
Constant Field Values

argbsChainAtom

public static final int[] argbsChainAtom
some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off


argbsChainHetero

public static final int[] argbsChainHetero

FORMAL_CHARGE_COLIX_RED

public static final short FORMAL_CHARGE_COLIX_RED

FORMAL_CHARGE_COLIX_WHITE

public static final short FORMAL_CHARGE_COLIX_WHITE

FORMAL_CHARGE_COLIX_BLUE

public static final short FORMAL_CHARGE_COLIX_BLUE

FORMAL_CHARGE_RANGE_SIZE

public static final int FORMAL_CHARGE_RANGE_SIZE
See Also:
Constant Field Values

argbsFormalCharge

public static final int[] argbsFormalCharge

FORMAL_CHARGE_INDEX_WHITE

public static final int FORMAL_CHARGE_INDEX_WHITE
See Also:
Constant Field Values

FORMAL_CHARGE_INDEX_MAX

public static final int FORMAL_CHARGE_INDEX_MAX

PARTIAL_CHARGE_COLIX_RED

public static final short PARTIAL_CHARGE_COLIX_RED

PARTIAL_CHARGE_COLIX_WHITE

public static final short PARTIAL_CHARGE_COLIX_WHITE

PARTIAL_CHARGE_COLIX_BLUE

public static final short PARTIAL_CHARGE_COLIX_BLUE

PARTIAL_CHARGE_RANGE_SIZE

public static final int PARTIAL_CHARGE_RANGE_SIZE
See Also:
Constant Field Values

argbsRwbScale

public static final int[] argbsRwbScale

argbsRoygbScale

public static final int[] argbsRoygbScale

argbsIsosurfacePositive

public static final int[] argbsIsosurfacePositive

argbsIsosurfaceNegative

public static final int[] argbsIsosurfaceNegative

specialAtomNames

private static final String[] specialAtomNames

ATOMID_MAX

public static final int ATOMID_MAX

ATOMID_AMINO_NITROGEN

public static final byte ATOMID_AMINO_NITROGEN
See Also:
Constant Field Values

ATOMID_ALPHA_CARBON

public static final byte ATOMID_ALPHA_CARBON
See Also:
Constant Field Values

ATOMID_CARBONYL_CARBON

public static final byte ATOMID_CARBONYL_CARBON
See Also:
Constant Field Values

ATOMID_CARBONYL_OXYGEN

public static final byte ATOMID_CARBONYL_OXYGEN
See Also:
Constant Field Values

ATOMID_O1

public static final byte ATOMID_O1
See Also:
Constant Field Values

ATOMID_ALPHA_ONLY_MASK

public static final int ATOMID_ALPHA_ONLY_MASK
See Also:
Constant Field Values

ATOMID_PROTEIN_MASK

public static final int ATOMID_PROTEIN_MASK
See Also:
Constant Field Values

ATOMID_O5_PRIME

public static final byte ATOMID_O5_PRIME
See Also:
Constant Field Values

ATOMID_C4_PRIME

public static final byte ATOMID_C4_PRIME
See Also:
Constant Field Values

ATOMID_C3_PRIME

public static final byte ATOMID_C3_PRIME
See Also:
Constant Field Values

ATOMID_O3_PRIME

public static final byte ATOMID_O3_PRIME
See Also:
Constant Field Values

ATOMID_C1_PRIME

public static final byte ATOMID_C1_PRIME
See Also:
Constant Field Values

ATOMID_NUCLEIC_MASK

public static final int ATOMID_NUCLEIC_MASK
See Also:
Constant Field Values

ATOMID_NUCLEIC_PHOSPHORUS

public static final byte ATOMID_NUCLEIC_PHOSPHORUS
See Also:
Constant Field Values

ATOMID_PHOSPHORUS_ONLY_MASK

public static final int ATOMID_PHOSPHORUS_ONLY_MASK
See Also:
Constant Field Values

ATOMID_DISTINGUISHING_ATOM_MAX

public static final int ATOMID_DISTINGUISHING_ATOM_MAX
See Also:
Constant Field Values

ATOMID_CARBONYL_OD1

public static final byte ATOMID_CARBONYL_OD1
See Also:
Constant Field Values

ATOMID_CARBONYL_OD2

public static final byte ATOMID_CARBONYL_OD2
See Also:
Constant Field Values

ATOMID_CARBONYL_OE1

public static final byte ATOMID_CARBONYL_OE1
See Also:
Constant Field Values

ATOMID_CARBONYL_OE2

public static final byte ATOMID_CARBONYL_OE2
See Also:
Constant Field Values

ATOMID_SG

public static final byte ATOMID_SG
See Also:
Constant Field Values

ATOMID_N1

public static final byte ATOMID_N1
See Also:
Constant Field Values

ATOMID_C2

public static final byte ATOMID_C2
See Also:
Constant Field Values

ATOMID_N3

public static final byte ATOMID_N3
See Also:
Constant Field Values

ATOMID_C4

public static final byte ATOMID_C4
See Also:
Constant Field Values

ATOMID_C5

public static final byte ATOMID_C5
See Also:
Constant Field Values

ATOMID_C6

public static final byte ATOMID_C6
See Also:
Constant Field Values

ATOMID_O2

public static final byte ATOMID_O2
See Also:
Constant Field Values

ATOMID_N7

public static final byte ATOMID_N7
See Also:
Constant Field Values

ATOMID_C8

public static final byte ATOMID_C8
See Also:
Constant Field Values

ATOMID_N9

public static final byte ATOMID_N9
See Also:
Constant Field Values

ATOMID_N4

public static final byte ATOMID_N4
See Also:
Constant Field Values

ATOMID_N2

public static final byte ATOMID_N2
See Also:
Constant Field Values

ATOMID_N6

public static final byte ATOMID_N6
See Also:
Constant Field Values

ATOMID_C5M

public static final byte ATOMID_C5M
See Also:
Constant Field Values

ATOMID_O6

public static final byte ATOMID_O6
See Also:
Constant Field Values

ATOMID_O4

public static final byte ATOMID_O4
See Also:
Constant Field Values

ATOMID_S4

public static final byte ATOMID_S4
See Also:
Constant Field Values

ATOMID_C7

public static final byte ATOMID_C7
See Also:
Constant Field Values

ATOMID_BACKBONE_MIN

private static final int ATOMID_BACKBONE_MIN
See Also:
Constant Field Values

ATOMID_TERMINATING_OXT

public static final byte ATOMID_TERMINATING_OXT
See Also:
Constant Field Values

ATOMID_H5T_TERMINUS

public static final byte ATOMID_H5T_TERMINUS
See Also:
Constant Field Values

ATOMID_O5T_TERMINUS

public static final byte ATOMID_O5T_TERMINUS
See Also:
Constant Field Values

ATOMID_O1P

public static final byte ATOMID_O1P
See Also:
Constant Field Values

ATOMID_OP1

public static final byte ATOMID_OP1
See Also:
Constant Field Values

ATOMID_O2P

public static final byte ATOMID_O2P
See Also:
Constant Field Values

ATOMID_OP2

public static final byte ATOMID_OP2
See Also:
Constant Field Values

ATOMID_O2_PRIME

public static final byte ATOMID_O2_PRIME
See Also:
Constant Field Values

ATOMID_H3T_TERMINUS

public static final byte ATOMID_H3T_TERMINUS
See Also:
Constant Field Values

ATOMID_HO3_PRIME

public static final byte ATOMID_HO3_PRIME
See Also:
Constant Field Values

ATOMID_HO5_PRIME

public static final byte ATOMID_HO5_PRIME
See Also:
Constant Field Values

htSpecialAtoms

private static Hashtable htSpecialAtoms

GROUPID_CYSTEINE

public static final int GROUPID_CYSTEINE
See Also:
Constant Field Values

GROUPID_PROLINE

public static final int GROUPID_PROLINE
See Also:
Constant Field Values

GROUPID_AMINO_MAX

public static final int GROUPID_AMINO_MAX
See Also:
Constant Field Values

GROUPID_WATER

private static final int GROUPID_WATER
See Also:
Constant Field Values

GROUPID_SOLVENTS

private static final int GROUPID_SOLVENTS
See Also:
Constant Field Values

GROUPID_SULPHATE

private static final int GROUPID_SULPHATE
See Also:
Constant Field Values

predefinedGroup3Names

public static final String[] predefinedGroup3Names

argbsShapely

public static final int[] argbsShapely

allCarbohydrates

private static final String allCarbohydrates
See Also:
Constant Field Values

group3List

public static final String group3List

group3Count

public static final int group3Count

predefinedGroup1Names

public static final char[] predefinedGroup1Names

predefinedVariable

public static String[] predefinedVariable

predefinedStatic

public static String[] predefinedStatic

MODELKIT_ZAP_STRING

public static final String MODELKIT_ZAP_STRING
See Also:
Constant Field Values

MODELKIT_ZAP_TITLE

public static final String MODELKIT_ZAP_TITLE
See Also:
Constant Field Values

DEFAULT_FONTFACE

public static final String DEFAULT_FONTFACE
See Also:
Constant Field Values

DEFAULT_FONTSTYLE

public static final String DEFAULT_FONTSTYLE
See Also:
Constant Field Values

LABEL_MINIMUM_FONTSIZE

public static final int LABEL_MINIMUM_FONTSIZE
See Also:
Constant Field Values

LABEL_MAXIMUM_FONTSIZE

public static final int LABEL_MAXIMUM_FONTSIZE
See Also:
Constant Field Values

LABEL_DEFAULT_FONTSIZE

public static final int LABEL_DEFAULT_FONTSIZE
See Also:
Constant Field Values

LABEL_DEFAULT_X_OFFSET

public static final int LABEL_DEFAULT_X_OFFSET
See Also:
Constant Field Values

LABEL_DEFAULT_Y_OFFSET

public static final int LABEL_DEFAULT_Y_OFFSET
See Also:
Constant Field Values

MEASURE_DEFAULT_FONTSIZE

public static final int MEASURE_DEFAULT_FONTSIZE
See Also:
Constant Field Values

AXES_DEFAULT_FONTSIZE

public static final int AXES_DEFAULT_FONTSIZE
See Also:
Constant Field Values

SHAPE_BALLS

public static final int SHAPE_BALLS
See Also:
Constant Field Values

SHAPE_STICKS

public static final int SHAPE_STICKS
See Also:
Constant Field Values

SHAPE_HSTICKS

public static final int SHAPE_HSTICKS
See Also:
Constant Field Values

SHAPE_SSSTICKS

public static final int SHAPE_SSSTICKS
See Also:
Constant Field Values

SHAPE_STRUTS

public static final int SHAPE_STRUTS
See Also:
Constant Field Values

SHAPE_LABELS

public static final int SHAPE_LABELS
See Also:
Constant Field Values

SHAPE_MEASURES

public static final int SHAPE_MEASURES
See Also:
Constant Field Values

SHAPE_STARS

public static final int SHAPE_STARS
See Also:
Constant Field Values

SHAPE_HALOS

public static final int SHAPE_HALOS
See Also:
Constant Field Values

SHAPE_MIN_SECONDARY

public static final int SHAPE_MIN_SECONDARY
See Also:
Constant Field Values

SHAPE_BACKBONE

public static final int SHAPE_BACKBONE
See Also:
Constant Field Values

SHAPE_TRACE

public static final int SHAPE_TRACE
See Also:
Constant Field Values

SHAPE_CARTOON

public static final int SHAPE_CARTOON
See Also:
Constant Field Values

SHAPE_STRANDS

public static final int SHAPE_STRANDS
See Also:
Constant Field Values

SHAPE_MESHRIBBON

public static final int SHAPE_MESHRIBBON
See Also:
Constant Field Values

SHAPE_RIBBONS

public static final int SHAPE_RIBBONS
See Also:
Constant Field Values

SHAPE_ROCKETS

public static final int SHAPE_ROCKETS
See Also:
Constant Field Values

SHAPE_MAX_SECONDARY

public static final int SHAPE_MAX_SECONDARY
See Also:
Constant Field Values

SHAPE_MIN_SPECIAL

public static final int SHAPE_MIN_SPECIAL
See Also:
Constant Field Values

SHAPE_DOTS

public static final int SHAPE_DOTS
See Also:
Constant Field Values

SHAPE_DIPOLES

public static final int SHAPE_DIPOLES
See Also:
Constant Field Values

SHAPE_VECTORS

public static final int SHAPE_VECTORS
See Also:
Constant Field Values

SHAPE_GEOSURFACE

public static final int SHAPE_GEOSURFACE
See Also:
Constant Field Values

SHAPE_ELLIPSOIDS

public static final int SHAPE_ELLIPSOIDS
See Also:
Constant Field Values

SHAPE_MAX_SIZE_ZERO_ON_RESTRICT

public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
See Also:
Constant Field Values

SHAPE_POLYHEDRA

public static final int SHAPE_POLYHEDRA
See Also:
Constant Field Values

SHAPE_MIN_HAS_ID

public static final int SHAPE_MIN_HAS_ID
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Constant Field Values

SHAPE_MIN_MESH_COLLECTION

public static final int SHAPE_MIN_MESH_COLLECTION
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Constant Field Values

SHAPE_DRAW

public static final int SHAPE_DRAW
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SHAPE_MAX_SPECIAL

public static final int SHAPE_MAX_SPECIAL
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SHAPE_MIN_SURFACE

public static final int SHAPE_MIN_SURFACE
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SHAPE_ISOSURFACE

public static final int SHAPE_ISOSURFACE
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Constant Field Values

SHAPE_LCAOCARTOON

public static final int SHAPE_LCAOCARTOON
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SHAPE_MO

public static final int SHAPE_MO
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Constant Field Values

SHAPE_PMESH

public static final int SHAPE_PMESH
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Constant Field Values

SHAPE_PLOT3D

public static final int SHAPE_PLOT3D
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Constant Field Values

SHAPE_MAX_SURFACE

public static final int SHAPE_MAX_SURFACE
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Constant Field Values

SHAPE_MAX_MESH_COLLECTION

public static final int SHAPE_MAX_MESH_COLLECTION
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Constant Field Values

SHAPE_ECHO

public static final int SHAPE_ECHO
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Constant Field Values

SHAPE_MAX_HAS_ID

public static final int SHAPE_MAX_HAS_ID
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Constant Field Values

SHAPE_AXES

public static final int SHAPE_AXES
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Constant Field Values

SHAPE_BBCAGE

public static final int SHAPE_BBCAGE
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Constant Field Values

SHAPE_UCCAGE

public static final int SHAPE_UCCAGE
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Constant Field Values

SHAPE_HOVER

public static final int SHAPE_HOVER
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Constant Field Values

SHAPE_FRANK

public static final int SHAPE_FRANK
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Constant Field Values

SHAPE_MAX

public static final int SHAPE_MAX
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Constant Field Values

shapeClassBases

public static final String[] shapeClassBases

ATOM_IN_FRAME

public static final int ATOM_IN_FRAME
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Constant Field Values

ATOM_SLABBED

public static final int ATOM_SLABBED
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Constant Field Values

PREVIOUS_MESH_ID

public static final String PREVIOUS_MESH_ID
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Constant Field Values

CARTOON_VISIBILITY_FLAG

public static final int CARTOON_VISIBILITY_FLAG

BACKBONE_VISIBILITY_FLAG

public static final int BACKBONE_VISIBILITY_FLAG

ALPHA_CARBON_VISIBILITY_FLAG

public static final int ALPHA_CARBON_VISIBILITY_FLAG

DEFAULT_STEREO_DEGREES

public static final int DEFAULT_STEREO_DEGREES
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Constant Field Values

STEREO_UNKNOWN

public static final int STEREO_UNKNOWN
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STEREO_NONE

public static final int STEREO_NONE
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STEREO_DOUBLE

public static final int STEREO_DOUBLE
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STEREO_REDCYAN

public static final int STEREO_REDCYAN
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STEREO_REDBLUE

public static final int STEREO_REDBLUE
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STEREO_REDGREEN

public static final int STEREO_REDGREEN
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STEREO_CUSTOM

public static final int STEREO_CUSTOM
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stereoModes

private static final String[] stereoModes

SHELL_S

public static final int SHELL_S
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Constant Field Values

SHELL_P

public static final int SHELL_P
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SHELL_SP

public static final int SHELL_SP
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SHELL_L

public static final int SHELL_L
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SHELL_D_SPHERICAL

public static final int SHELL_D_SPHERICAL
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Constant Field Values

SHELL_D_CARTESIAN

public static final int SHELL_D_CARTESIAN
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Constant Field Values

SHELL_F_SPHERICAL

public static final int SHELL_F_SPHERICAL
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Constant Field Values

SHELL_F_CARTESIAN

public static final int SHELL_F_CARTESIAN
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Constant Field Values

SHELL_G_SPHERICAL

public static final int SHELL_G_SPHERICAL
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Constant Field Values

SHELL_G_CARTESIAN

public static final int SHELL_G_CARTESIAN
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Constant Field Values

SHELL_H_SPHERICAL

public static final int SHELL_H_SPHERICAL
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Constant Field Values

SHELL_H_CARTESIAN

public static final int SHELL_H_CARTESIAN
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Constant Field Values

SUPPORTED_BASIS_FUNCTIONS

public static final String SUPPORTED_BASIS_FUNCTIONS
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Constant Field Values

quantumShellTags

private static final String[] quantumShellTags

quantumShellIDs

private static final int[] quantumShellIDs

SUPPORTED_BASES

public static final String SUPPORTED_BASES
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Constant Field Values

shellOrder

private static final String[][] shellOrder

LOAD_ATOM_DATA_TYPES

public static final String LOAD_ATOM_DATA_TYPES
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Constant Field Values

ANIMATION_ONCE

public static final int ANIMATION_ONCE
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Constant Field Values

ANIMATION_LOOP

public static final int ANIMATION_LOOP
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Constant Field Values

ANIMATION_PALINDROME

public static final int ANIMATION_PALINDROME
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Constant Field Values

radiansPerDegree

public static final float radiansPerDegree
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Constant Field Values
Constructor Detail

JmolConstants

public JmolConstants()
Method Detail

embedScript

public static String embedScript(String s)

getCallbackName

public static String getCallbackName(int i)

getCallbackId

public static int getCallbackId(String callbackName)

getDrawTypeName

public static String getDrawTypeName(int drawType)

getArgbHbondType

public static int getArgbHbondType(int order)

getBondOrderFromString

public static final int getBondOrderFromString(String bondOrderString)

getPartialBondOrderFromInteger

public static final int getPartialBondOrderFromInteger(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)

Parameters:
bondOrderInteger -
Returns:
Bond order partial mask

getCovalentBondOrder

public static final int getCovalentBondOrder(int order)

getPartialBondOrder

public static final int getPartialBondOrder(int order)

getPartialBondDotted

public static final int getPartialBondDotted(int order)

getBondOrderFromFloat

public static final int getBondOrderFromFloat(float fOrder)

getBondOrderNameFromOrder

public static final String getBondOrderNameFromOrder(int order)

getCmlOrder

public static String getCmlOrder(int order)

getBondOrderNumberFromOrder

public static final String getBondOrderNumberFromOrder(int order)
used for formatting labels and in the connect PARTIAL command

Parameters:
order -
Returns:
a string representation to preserve float n.m

getVdwLabel

public static String getVdwLabel(int i)

getVdwType

public static int getVdwType(String label)

getVanderwaalsMar

public static int getVanderwaalsMar(int i,
                                    int iType)

getBondingRadiusFloat

public static float getBondingRadiusFloat(int atomicNumber,
                                          int charge)

getBondingRadiusFloat

private static float getBondingRadiusFloat(int atomicNumber,
                                           int charge,
                                           short[] table)

pidOf

public static byte pidOf(Object value)

isPaletteVariable

public static boolean isPaletteVariable(byte pid)

getPaletteID

public static final byte getPaletteID(String paletteName)

getPaletteName

public static final String getPaletteName(byte pid)

getProteinStructureName

public static final String getProteinStructureName(int itype,
                                                   boolean isGeneric)

getProteinStructureType

public static final byte getProteinStructureType(String type)

getSpecialAtomName

public static final String getSpecialAtomName(int atomID)

lookupSpecialAtomID

public static byte lookupSpecialAtomID(String atomName)

checkCarbohydrate

public static final boolean checkCarbohydrate(String group3)
Parameters:
group3 - a potential group3 name
Returns:
whether this is a carbohydrate from the list

getGroup3List

private static final String getGroup3List()

isHetero

public static final boolean isHetero(String group3)

isShapeSecondary

public static final boolean isShapeSecondary(int i)

shapeTokenIndex

public static final int shapeTokenIndex(int tok)

getShapeClassName

public static final String getShapeClassName(int shapeID)

getShapeVisibilityFlag

public static final int getShapeVisibilityFlag(int shapeID)

getStereoMode

public static int getStereoMode(String id)

getStereoModeName

static String getStereoModeName(int mode)

getShellOrder

public static final String[] getShellOrder(int i)

getQuantumShellTagID

public static final int getQuantumShellTagID(String tag)

getQuantumShellTagIDSpherical

public static final int getQuantumShellTagIDSpherical(String tag)

getQuantumShellTag

public static final String getQuantumShellTag(int shell)

modelValue

public static int modelValue(String strDecimal)