org.jmol.viewer
Class JmolConstants

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

public final class JmolConstants
extends java.lang.Object


Field Summary
private static java.lang.String allCarbohydrates
           
static int ALPHA_CARBON_VISIBILITY_FLAG
           
static int[] altArgbsCpk
           
static int altElementMax
          length of the altElementSymbols, altElementNames, altElementNumbers arrays
private static java.lang.String[] altElementNames
           
private static short[] altElementNumbers
           
private static java.lang.String[] altElementSymbols
           
static float ANGSTROMS_PER_BOHR
           
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_C2
           
static byte ATOMID_C3_PRIME
           
static byte ATOMID_C4
           
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_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_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 javax.vecmath.Vector3f axisNX
           
static javax.vecmath.Vector3f axisNY
           
static javax.vecmath.Vector3f axisNZ
           
static javax.vecmath.Vector3f axisX
           
static javax.vecmath.Vector3f axisY
           
static javax.vecmath.Vector3f axisZ
           
static int BACKLIT
           
static short BOND_AROMATIC
           
static short BOND_AROMATIC_DOUBLE
           
static short BOND_AROMATIC_MASK
           
static short BOND_AROMATIC_SINGLE
           
static short BOND_COVALENT_DOUBLE
           
static short BOND_COVALENT_MASK
           
static short BOND_COVALENT_QUADRUPLE
           
static short BOND_COVALENT_SINGLE
           
static short BOND_COVALENT_TRIPLE
           
static short BOND_H_CALC
           
static short BOND_H_CALC_MASK
           
static short BOND_H_MINUS_3
           
static short BOND_H_MINUS_4
           
static short BOND_H_NUCLEOTIDE
           
static short BOND_H_PLUS_2
           
static short BOND_H_PLUS_3
           
static short BOND_H_PLUS_4
           
static short BOND_H_PLUS_5
           
static short BOND_H_REGULAR
           
static short BOND_HBOND_SHIFT
           
static short BOND_HYDROGEN_MASK
           
static short BOND_NEW
           
static short BOND_ORDER_ANY
          Extended Bond Definition Types
static short BOND_ORDER_NULL
           
static short BOND_ORDER_UNSPECIFIED
           
static short BOND_PARTIAL_MASK
           
static short BOND_PARTIAL01
           
static short BOND_PARTIAL12
           
static short BOND_PARTIAL23
           
static short BOND_PARTIAL32
           
static short BOND_STEREO_FAR
           
static short BOND_STEREO_MASK
           
static short BOND_STEREO_NEAR
           
static short BOND_SULFUR_MASK
           
private static java.lang.String[] bondOrderNames
           
private static java.lang.String[] bondOrderNumbers
           
private static short[] bondOrderValues
           
(package private) static java.util.BitSet bsAnions
           
(package private) static java.util.BitSet bsCations
           
static int CALLBACK_ANIMFRAME
           
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_SET_MESH_CREATOR
           
static int CALLBACK_SYNC
           
private static java.lang.String[] callbackNames
           
static int CARTOON_VISIBILITY_FLAG
           
private static short[] cationLookupTable
           
static javax.vecmath.Vector3f center
           
static java.lang.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
           
private static java.lang.String[] connectOperationStrings
           
static java.lang.String copyright
           
private static short[] covalentMars
          Default table of covalent Radii stored as a short mar ...
static java.lang.String cvsDate
           
static java.lang.String date
           
static short DEFAULT_BOND_MILLIANGSTROM_RADIUS
           
static float DEFAULT_BOND_RADIUS
           
static float DEFAULT_BOND_TOLERANCE
           
static java.lang.String DEFAULT_FONTFACE
           
static java.lang.String DEFAULT_FONTSTYLE
           
static java.lang.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 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_TRIANGLE
           
private static java.lang.String[] elementNames
           
static int elementNumberMax
          one larger than the last elementNumber, same as elementSymbols.length
private static java.lang.String[] elementSymbols
          The default elementSymbols.
static java.lang.String EMBEDDED_SCRIPT_TAG
           
static java.lang.String EXPORT_DRIVER_LIST
           
static int firstIsotope
          first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
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 java.lang.String group3List
           
static int GROUPID_AMINO_MAX
           
static int GROUPID_PROLINE
           
private static int GROUPID_SOLVENTS
           
private static int GROUPID_SULPHATE
           
private static int GROUPID_WATER
           
private static java.util.Hashtable htElementMap
           
static int INFO_A
           
static int INFO_ALPHA
           
static int INFO_B
           
static int INFO_BETA
           
static int INFO_C
           
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 java.lang.String LOAD_ATOM_DATA_TYPES
           
static short madMultipleBondSmallMaximum
           
static int MAXIMUM_AUTO_BOND_COUNT
           
static int MEASURE_DEFAULT_FONTSIZE
           
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
           
private static java.lang.String naturalIsotopes
           
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_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 java.lang.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 int PICKING_CENTER
           
static int PICKING_DRAW
           
static int PICKING_IDENT
           
static int PICKING_LABEL
           
static int PICKING_MEASURE
           
static int PICKING_MEASURE_ANGLE
           
static int PICKING_MEASURE_DISTANCE
           
static int PICKING_MEASURE_TORSION
           
static int PICKING_NAVIGATE
           
static int PICKING_OFF
          picking modes
static int PICKING_SELECT_ATOM
           
static int PICKING_SELECT_CHAIN
           
static int PICKING_SELECT_ELEMENT
           
static int PICKING_SELECT_GROUP
           
static int PICKING_SELECT_MODEL
           
static int PICKING_SELECT_MOLECULE
           
static int PICKING_SELECT_SITE
           
static int PICKING_SPIN
           
private static java.lang.String[] pickingModeNames
           
static int PICKINGSTYLE_MEASURE_OFF
           
static int PICKINGSTYLE_MEASURE_ON
           
static int PICKINGSTYLE_SELECT_CHIME
           
static int PICKINGSTYLE_SELECT_DRAG
           
static int PICKINGSTYLE_SELECT_JMOL
          picking styles
static int PICKINGSTYLE_SELECT_PFAAT
           
static int PICKINGSTYLE_SELECT_RASMOL
           
private static java.lang.String[] pickingStyleNames
           
static char[] predefinedGroup1Names
           
static java.lang.String[] predefinedGroup3Names
           
static java.lang.String[] predefinedStatic
           
static java.lang.String[] predefinedVariable
           
static java.lang.String PREVIOUS_MESH_ID
           
static byte PROTEIN_STRUCTURE_DNA
           
static byte PROTEIN_STRUCTURE_HELIX
           
static byte PROTEIN_STRUCTURE_NONE
          Default table of PdbStructure colors
static byte PROTEIN_STRUCTURE_RNA
           
static byte PROTEIN_STRUCTURE_SHEET
           
static byte PROTEIN_STRUCTURE_TURN
           
static java.lang.String[] proteinStructureNames
           
private static int[] quantumShellIDs
           
private static java.lang.String[] quantumShellTags
           
static java.lang.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_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_TRACE
           
static int SHAPE_UCCAGE
           
static int SHAPE_VECTORS
           
static java.lang.String[] shapeClassBases
           
static int[] shapeToks
           
static int SHELL_D_CARTESIAN
           
static int SHELL_D_SPHERICAL
           
static int SHELL_F_CARTESIAN
           
static int SHELL_F_SPHERICAL
           
static int SHELL_L
           
static int SHELL_P
           
static int SHELL_S
           
static int SHELL_SP
           
private static java.lang.String[][] shellOrder
           
static java.lang.String[] specialAtomNames
           
(package private) static int STEREO_CUSTOM
           
(package private) static int STEREO_DOUBLE
           
(package private) static int STEREO_NONE
           
(package private) static int STEREO_REDBLUE
           
(package private) static int STEREO_REDCYAN
           
(package private) static int STEREO_REDGREEN
           
(package private) static int STEREO_UNKNOWN
           
private static java.lang.String[] stereoModes
           
static javax.vecmath.Vector3f[] unitAxisVectors
           
static short[] vanderwaalsMars
          Default table of van der Waals Radii.
static int VDW_BABEL
           
static int VDW_JMOL
           
static int VDW_RASMOL
           
static int VDW_USER
           
(package private) static java.lang.String[] vdwLabels
           
static java.lang.String version
           
static int XY_ZTOP
           
 
Constructor Summary
JmolConstants()
           
 
Method Summary
static int altElementIndexFromNumber(int atomicAndIsotopeNumber)
           
static java.lang.String altElementNameFromIndex(int i)
           
static short altElementNumberFromIndex(int i)
           
static java.lang.String altElementSymbolFromIndex(int i)
           
static java.lang.String altIsotopeSymbolFromIndex(int i)
           
static java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)
           
static boolean checkCarbohydrate(java.lang.String group3)
           
static int connectOperationFromString(java.lang.String connectOperationString)
           
static java.lang.String connectOperationName(int i)
           
static java.lang.String elementNameFromNumber(int elementNumber)
           
static short elementNumberFromSymbol(java.lang.String elementSymbol)
           
static java.lang.String elementSymbolFromNumber(int elementNumber)
           
static int getArgbHbondType(short order)
           
static short getBondingMar(int atomicNumber, int charge)
           
static short getBondingMar(int atomicNumber, int charge, short[] table)
           
(package private) static short getBondOrderFromFloat(float fOrder)
           
(package private) static short getBondOrderFromString(java.lang.String bondOrderString)
           
static java.lang.String getBondOrderNameFromOrder(short order)
           
static java.lang.String getBondOrderNumberFromOrder(short order)
          used for formatting labels and in the connect PARTIAL command
static int getCallbackId(java.lang.String callbackName)
           
static java.lang.String getCallbackName(int i)
           
static java.lang.String getDrawTypeName(int drawType)
           
private static java.lang.String getGroup3List()
           
static byte getPaletteID(java.lang.String paletteName)
           
static java.lang.String getPaletteName(byte pid)
           
static int getPartialBondDotted(int order)
           
static short getPartialBondOrder(int order)
           
(package private) static short getPartialBondOrderFromInteger(int bondOrderInteger)
          reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
static int getPickingMode(java.lang.String str)
           
static java.lang.String getPickingModeName(int pickingMode)
           
static int getPickingStyle(java.lang.String str)
           
static java.lang.String getPickingStyleName(int pickingStyle)
           
static java.lang.String getProteinStructureName(int itype)
           
static java.lang.String getQuantumShellTag(int shell)
           
static int getQuantumShellTagID(java.lang.String tag)
           
static int getQuantumShellTagIDSpherical(java.lang.String tag)
           
static java.lang.String getQuantumSubshellTag(int shell, int subshell)
           
static int getQuantumSubshellTagID(int shell, java.lang.String tag)
           
static java.lang.String getShapeClassName(int shapeID)
           
static int getShapeVisibilityFlag(int shapeID)
           
static java.lang.String[] getShellOrder(int i)
           
(package private) static int getStereoMode(java.lang.String id)
           
(package private) static java.lang.String getStereoModeName(int mode)
           
static int getVanderwaalsMar(int i, int scale)
           
static int getVdwType(java.lang.String label)
           
static boolean isHetero(java.lang.String group3)
           
static boolean isNaturalIsotope(java.lang.String isotopeSymbol)
           
static boolean isPaletteVariable(byte pid)
           
static boolean isShapeSecondary(int i)
           
(package private) static int modelValue(java.lang.String strDecimal)
           
static byte pidOf(java.lang.Object value)
           
(package private) 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 java.lang.String copyright
See Also:
Constant Field Values

version

public static final java.lang.String version

cvsDate

public static final java.lang.String cvsDate
See Also:
Constant Field Values

date

public static final java.lang.String date

officialRelease

public static final boolean officialRelease
See Also:
Constant Field Values

CLASSBASE_OPTIONS

public static final java.lang.String CLASSBASE_OPTIONS
See Also:
Constant Field Values

DEFAULT_HELP_PATH

public static final java.lang.String DEFAULT_HELP_PATH
See Also:
Constant Field Values

EMBEDDED_SCRIPT_TAG

public static final java.lang.String EMBEDDED_SCRIPT_TAG
See Also:
Constant Field Values

SCRIPT_EDITOR_IGNORE

public static final java.lang.String SCRIPT_EDITOR_IGNORE
See Also:
Constant Field Values

CALLBACK_ANIMFRAME

public static final int CALLBACK_ANIMFRAME
See Also:
Constant Field Values

CALLBACK_ECHO

public static final int CALLBACK_ECHO
See Also:
Constant Field Values

CALLBACK_ERROR

public static final int CALLBACK_ERROR
See Also:
Constant Field Values

CALLBACK_EVAL

public static final int CALLBACK_EVAL
See Also:
Constant Field Values

CALLBACK_HOVER

public static final int CALLBACK_HOVER
See Also:
Constant Field Values

CALLBACK_LOADSTRUCT

public static final int CALLBACK_LOADSTRUCT
See Also:
Constant Field Values

CALLBACK_MEASURE

public static final int CALLBACK_MEASURE
See Also:
Constant Field Values

CALLBACK_MESSAGE

public static final int CALLBACK_MESSAGE
See Also:
Constant Field Values

CALLBACK_MINIMIZATION

public static final int CALLBACK_MINIMIZATION
See Also:
Constant Field Values

CALLBACK_PICK

public static final int CALLBACK_PICK
See Also:
Constant Field Values

CALLBACK_RESIZE

public static final int CALLBACK_RESIZE
See Also:
Constant Field Values

CALLBACK_SCRIPT

public static final int CALLBACK_SCRIPT
See Also:
Constant Field Values

CALLBACK_SYNC

public static final int CALLBACK_SYNC
See Also:
Constant Field Values

CALLBACK_COUNT

public static final int CALLBACK_COUNT
See Also:
Constant Field Values

CALLBACK_SET_MESH_CREATOR

public static final int CALLBACK_SET_MESH_CREATOR
See Also:
Constant Field Values

callbackNames

private static final java.lang.String[] callbackNames

INFO_A

public static final int INFO_A
See Also:
Constant Field Values

INFO_B

public static final int INFO_B
See Also:
Constant Field Values

INFO_C

public static final int INFO_C
See Also:
Constant Field Values

INFO_ALPHA

public static final int INFO_ALPHA
See Also:
Constant Field Values

INFO_BETA

public static final int INFO_BETA
See Also:
Constant Field Values

INFO_GAMMA

public static final int INFO_GAMMA
See Also:
Constant Field Values

JMOL_DATA_RAMACHANDRAN

public static final int JMOL_DATA_RAMACHANDRAN
See Also:
Constant Field Values

JMOL_DATA_QUATERNION

public static final int JMOL_DATA_QUATERNION
See Also:
Constant Field Values

JMOL_DATA_OTHER

public static final int JMOL_DATA_OTHER
See Also:
Constant Field Values

EXPORT_DRIVER_LIST

public static final java.lang.String EXPORT_DRIVER_LIST
See Also:
Constant Field Values

DRAW_MULTIPLE

public static final int DRAW_MULTIPLE
See Also:
Constant Field Values

DRAW_NONE

public static final int DRAW_NONE
See Also:
Constant Field Values

DRAW_POINT

public static final int DRAW_POINT
See Also:
Constant Field Values

DRAW_LINE

public static final int DRAW_LINE
See Also:
Constant Field Values

DRAW_TRIANGLE

public static final int DRAW_TRIANGLE
See Also:
Constant Field Values

DRAW_PLANE

public static final int DRAW_PLANE
See Also:
Constant Field Values

DRAW_CYLINDER

public static final int DRAW_CYLINDER
See Also:
Constant Field Values

DRAW_ARROW

public static final int DRAW_ARROW
See Also:
Constant Field Values

DRAW_CIRCLE

public static final int DRAW_CIRCLE
See Also:
Constant Field Values

DRAW_CURVE

public static final int DRAW_CURVE
See Also:
Constant Field Values

DRAW_CIRCULARPLANE

public static final int DRAW_CIRCULARPLANE
See Also:
Constant Field Values

DRAW_ARC

public static final int DRAW_ARC
See Also:
Constant Field Values

DRAW_LINE_SEGMENT

public static final int DRAW_LINE_SEGMENT
See Also:
Constant Field Values

center

public static final javax.vecmath.Vector3f center

axisX

public static final javax.vecmath.Vector3f axisX

axisY

public static final javax.vecmath.Vector3f axisY

axisZ

public static final javax.vecmath.Vector3f axisZ

axisNX

public static final javax.vecmath.Vector3f axisNX

axisNY

public static final javax.vecmath.Vector3f axisNY

axisNZ

public static final javax.vecmath.Vector3f axisNZ

unitAxisVectors

public static final javax.vecmath.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_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

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

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

connectOperationStrings

private static final java.lang.String[] connectOperationStrings

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

PICKING_OFF

public static final int PICKING_OFF
picking modes

See Also:
Constant Field Values

PICKING_IDENT

public static final int PICKING_IDENT
See Also:
Constant Field Values

PICKING_LABEL

public static final int PICKING_LABEL
See Also:
Constant Field Values

PICKING_CENTER

public static final int PICKING_CENTER
See Also:
Constant Field Values

PICKING_DRAW

public static final int PICKING_DRAW
See Also:
Constant Field Values

PICKING_SPIN

public static final int PICKING_SPIN
See Also:
Constant Field Values

PICKING_SELECT_ATOM

public static final int PICKING_SELECT_ATOM
See Also:
Constant Field Values

PICKING_SELECT_GROUP

public static final int PICKING_SELECT_GROUP
See Also:
Constant Field Values

PICKING_SELECT_CHAIN

public static final int PICKING_SELECT_CHAIN
See Also:
Constant Field Values

PICKING_SELECT_MOLECULE

public static final int PICKING_SELECT_MOLECULE
See Also:
Constant Field Values

PICKING_SELECT_SITE

public static final int PICKING_SELECT_SITE
See Also:
Constant Field Values

PICKING_SELECT_MODEL

public static final int PICKING_SELECT_MODEL
See Also:
Constant Field Values

PICKING_SELECT_ELEMENT

public static final int PICKING_SELECT_ELEMENT
See Also:
Constant Field Values

PICKING_MEASURE

public static final int PICKING_MEASURE
See Also:
Constant Field Values

PICKING_MEASURE_DISTANCE

public static final int PICKING_MEASURE_DISTANCE
See Also:
Constant Field Values

PICKING_MEASURE_ANGLE

public static final int PICKING_MEASURE_ANGLE
See Also:
Constant Field Values

PICKING_MEASURE_TORSION

public static final int PICKING_MEASURE_TORSION
See Also:
Constant Field Values

PICKING_NAVIGATE

public static final int PICKING_NAVIGATE
See Also:
Constant Field Values

pickingModeNames

private static final java.lang.String[] pickingModeNames

PICKINGSTYLE_SELECT_JMOL

public static final int PICKINGSTYLE_SELECT_JMOL
picking styles

See Also:
Constant Field Values

PICKINGSTYLE_SELECT_CHIME

public static final int PICKINGSTYLE_SELECT_CHIME
See Also:
Constant Field Values

PICKINGSTYLE_SELECT_RASMOL

public static final int PICKINGSTYLE_SELECT_RASMOL
See Also:
Constant Field Values

PICKINGSTYLE_SELECT_PFAAT

public static final int PICKINGSTYLE_SELECT_PFAAT
See Also:
Constant Field Values

PICKINGSTYLE_SELECT_DRAG

public static final int PICKINGSTYLE_SELECT_DRAG
See Also:
Constant Field Values

PICKINGSTYLE_MEASURE_ON

public static final int PICKINGSTYLE_MEASURE_ON
See Also:
Constant Field Values

PICKINGSTYLE_MEASURE_OFF

public static final int PICKINGSTYLE_MEASURE_OFF
See Also:
Constant Field Values

pickingStyleNames

private static final java.lang.String[] pickingStyleNames

BOND_ORDER_ANY

public static final short BOND_ORDER_ANY
Extended Bond Definition Types

See Also:
Constant Field Values

BOND_ORDER_NULL

public static final short BOND_ORDER_NULL
See Also:
Constant Field Values

BOND_HBOND_SHIFT

public static final short BOND_HBOND_SHIFT
See Also:
Constant Field Values

BOND_NEW

public static final short BOND_NEW
See Also:
Constant Field Values

BOND_HYDROGEN_MASK

public static final short BOND_HYDROGEN_MASK
See Also:
Constant Field Values

BOND_H_REGULAR

public static final short BOND_H_REGULAR
See Also:
Constant Field Values

BOND_H_CALC_MASK

public static final short BOND_H_CALC_MASK
See Also:
Constant Field Values

BOND_H_CALC

public static final short BOND_H_CALC
See Also:
Constant Field Values

BOND_H_PLUS_2

public static final short BOND_H_PLUS_2
See Also:
Constant Field Values

BOND_H_PLUS_3

public static final short BOND_H_PLUS_3
See Also:
Constant Field Values

BOND_H_PLUS_4

public static final short BOND_H_PLUS_4
See Also:
Constant Field Values

BOND_H_PLUS_5

public static final short BOND_H_PLUS_5
See Also:
Constant Field Values

BOND_H_MINUS_3

public static final short BOND_H_MINUS_3
See Also:
Constant Field Values

BOND_H_MINUS_4

public static final short BOND_H_MINUS_4
See Also:
Constant Field Values

BOND_H_NUCLEOTIDE

public static final short BOND_H_NUCLEOTIDE
See Also:
Constant Field Values

argbsHbondType

public static final int[] argbsHbondType

BOND_STEREO_MASK

public static final short BOND_STEREO_MASK
See Also:
Constant Field Values

BOND_STEREO_NEAR

public static final short BOND_STEREO_NEAR
See Also:
Constant Field Values

BOND_STEREO_FAR

public static final short BOND_STEREO_FAR
See Also:
Constant Field Values

BOND_AROMATIC_MASK

public static final short BOND_AROMATIC_MASK
See Also:
Constant Field Values

BOND_AROMATIC_SINGLE

public static final short BOND_AROMATIC_SINGLE
See Also:
Constant Field Values

BOND_AROMATIC_DOUBLE

public static final short BOND_AROMATIC_DOUBLE
See Also:
Constant Field Values

BOND_AROMATIC

public static final short BOND_AROMATIC
See Also:
Constant Field Values

BOND_SULFUR_MASK

public static final short BOND_SULFUR_MASK
See Also:
Constant Field Values

BOND_PARTIAL_MASK

public static final short BOND_PARTIAL_MASK
See Also:
Constant Field Values

BOND_PARTIAL01

public static final short BOND_PARTIAL01
See Also:
Constant Field Values

BOND_PARTIAL12

public static final short BOND_PARTIAL12
See Also:
Constant Field Values

BOND_PARTIAL23

public static final short BOND_PARTIAL23
See Also:
Constant Field Values

BOND_PARTIAL32

public static final short BOND_PARTIAL32
See Also:
Constant Field Values

BOND_COVALENT_MASK

public static final short BOND_COVALENT_MASK
See Also:
Constant Field Values

BOND_COVALENT_SINGLE

public static final short BOND_COVALENT_SINGLE
See Also:
Constant Field Values

BOND_COVALENT_DOUBLE

public static final short BOND_COVALENT_DOUBLE
See Also:
Constant Field Values

BOND_COVALENT_TRIPLE

public static final short BOND_COVALENT_TRIPLE
See Also:
Constant Field Values

BOND_COVALENT_QUADRUPLE

public static final short BOND_COVALENT_QUADRUPLE
See Also:
Constant Field Values

BOND_ORDER_UNSPECIFIED

public static final short BOND_ORDER_UNSPECIFIED
See Also:
Constant Field Values

bondOrderNames

private static final java.lang.String[] bondOrderNames

bondOrderNumbers

private static final java.lang.String[] bondOrderNumbers

bondOrderValues

private static final short[] 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

elementSymbols

private static final java.lang.String[] elementSymbols
The default elementSymbols. Presumably the only entry which may cause confusion is element 0, whose symbol we have defined as "Xx".


elementNumberMax

public static final int elementNumberMax
one larger than the last elementNumber, same as elementSymbols.length


htElementMap

private static java.util.Hashtable htElementMap

elementNames

private static final java.lang.String[] elementNames

naturalIsotopes

private static final java.lang.String naturalIsotopes
See Also:
Constant Field Values

altElementNumbers

private static final short[] altElementNumbers

altElementSymbols

private static final java.lang.String[] altElementSymbols

altElementNames

private static final java.lang.String[] altElementNames

altArgbsCpk

public static final int[] altArgbsCpk

firstIsotope

public static final int firstIsotope
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays

See Also:
Constant Field Values

altElementMax

public static final int altElementMax
length of the altElementSymbols, altElementNames, altElementNumbers arrays


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_USER

public static final int VDW_USER
See Also:
Constant Field Values

vdwLabels

static final java.lang.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.

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 java.util.BitSet bsCations

bsAnions

static java.util.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

paletteNames

private static final java.lang.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_NONE

public static final byte PROTEIN_STRUCTURE_NONE
Default table of PdbStructure colors

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

proteinStructureNames

public static final java.lang.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

public static final java.lang.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_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_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_N1

public static final byte ATOMID_N1
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Constant Field Values

ATOMID_C2

public static final byte ATOMID_C2
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Constant Field Values

ATOMID_N3

public static final byte ATOMID_N3
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Constant Field Values

ATOMID_C4

public static final byte ATOMID_C4
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Constant Field Values

ATOMID_C5

public static final byte ATOMID_C5
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Constant Field Values

ATOMID_C6

public static final byte ATOMID_C6
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Constant Field Values

ATOMID_O2

public static final byte ATOMID_O2
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Constant Field Values

ATOMID_N7

public static final byte ATOMID_N7
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Constant Field Values

ATOMID_C8

public static final byte ATOMID_C8
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Constant Field Values

ATOMID_N9

public static final byte ATOMID_N9
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Constant Field Values

ATOMID_N4

public static final byte ATOMID_N4
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Constant Field Values

ATOMID_N2

public static final byte ATOMID_N2
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Constant Field Values

ATOMID_N6

public static final byte ATOMID_N6
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Constant Field Values

ATOMID_C5M

public static final byte ATOMID_C5M
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Constant Field Values

ATOMID_O6

public static final byte ATOMID_O6
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Constant Field Values

ATOMID_O4

public static final byte ATOMID_O4
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Constant Field Values

ATOMID_S4

public static final byte ATOMID_S4
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Constant Field Values

ATOMID_C7

public static final byte ATOMID_C7
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Constant Field Values

ATOMID_BACKBONE_MIN

private static final int ATOMID_BACKBONE_MIN
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Constant Field Values

ATOMID_TERMINATING_OXT

public static final byte ATOMID_TERMINATING_OXT
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Constant Field Values

ATOMID_H5T_TERMINUS

public static final byte ATOMID_H5T_TERMINUS
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Constant Field Values

ATOMID_O5T_TERMINUS

public static final byte ATOMID_O5T_TERMINUS
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Constant Field Values

ATOMID_O1P

public static final byte ATOMID_O1P
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Constant Field Values

ATOMID_OP1

public static final byte ATOMID_OP1
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Constant Field Values

ATOMID_O2P

public static final byte ATOMID_O2P
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Constant Field Values

ATOMID_OP2

public static final byte ATOMID_OP2
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Constant Field Values

ATOMID_O2_PRIME

public static final byte ATOMID_O2_PRIME
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Constant Field Values

ATOMID_H3T_TERMINUS

public static final byte ATOMID_H3T_TERMINUS
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Constant Field Values

ATOMID_HO3_PRIME

public static final byte ATOMID_HO3_PRIME
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Constant Field Values

ATOMID_HO5_PRIME

public static final byte ATOMID_HO5_PRIME
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Constant Field Values

GROUPID_PROLINE

public static final int GROUPID_PROLINE
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Constant Field Values

GROUPID_AMINO_MAX

public static final int GROUPID_AMINO_MAX
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Constant Field Values

GROUPID_WATER

private static final int GROUPID_WATER
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Constant Field Values

GROUPID_SOLVENTS

private static final int GROUPID_SOLVENTS
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Constant Field Values

GROUPID_SULPHATE

private static final int GROUPID_SULPHATE
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Constant Field Values

predefinedGroup3Names

public static final java.lang.String[] predefinedGroup3Names

argbsShapely

public static final int[] argbsShapely

allCarbohydrates

private static final java.lang.String allCarbohydrates
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Constant Field Values

group3List

public static final java.lang.String group3List

group3Count

public static final int group3Count

predefinedGroup1Names

public static final char[] predefinedGroup1Names

predefinedVariable

public static java.lang.String[] predefinedVariable

predefinedStatic

public static java.lang.String[] predefinedStatic

DEFAULT_FONTFACE

public static final java.lang.String DEFAULT_FONTFACE
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Constant Field Values

DEFAULT_FONTSTYLE

public static final java.lang.String DEFAULT_FONTSTYLE
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Constant Field Values

LABEL_MINIMUM_FONTSIZE

public static final int LABEL_MINIMUM_FONTSIZE
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Constant Field Values

LABEL_MAXIMUM_FONTSIZE

public static final int LABEL_MAXIMUM_FONTSIZE
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Constant Field Values

LABEL_DEFAULT_FONTSIZE

public static final int LABEL_DEFAULT_FONTSIZE
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Constant Field Values

LABEL_DEFAULT_X_OFFSET

public static final int LABEL_DEFAULT_X_OFFSET
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Constant Field Values

LABEL_DEFAULT_Y_OFFSET

public static final int LABEL_DEFAULT_Y_OFFSET
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Constant Field Values

MEASURE_DEFAULT_FONTSIZE

public static final int MEASURE_DEFAULT_FONTSIZE
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Constant Field Values

AXES_DEFAULT_FONTSIZE

public static final int AXES_DEFAULT_FONTSIZE
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Constant Field Values

SHAPE_BALLS

public static final int SHAPE_BALLS
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Constant Field Values

SHAPE_STICKS

public static final int SHAPE_STICKS
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Constant Field Values

SHAPE_HSTICKS

public static final int SHAPE_HSTICKS
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Constant Field Values

SHAPE_SSSTICKS

public static final int SHAPE_SSSTICKS
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Constant Field Values

SHAPE_LABELS

public static final int SHAPE_LABELS
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Constant Field Values

SHAPE_MEASURES

public static final int SHAPE_MEASURES
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Constant Field Values

SHAPE_DOTS

public static final int SHAPE_DOTS
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Constant Field Values

SHAPE_STARS

public static final int SHAPE_STARS
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Constant Field Values

SHAPE_HALOS

public static final int SHAPE_HALOS
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Constant Field Values

SHAPE_MIN_SECONDARY

public static final int SHAPE_MIN_SECONDARY
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Constant Field Values

SHAPE_BACKBONE

public static final int SHAPE_BACKBONE
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Constant Field Values

SHAPE_TRACE

public static final int SHAPE_TRACE
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Constant Field Values

SHAPE_CARTOON

public static final int SHAPE_CARTOON
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Constant Field Values

SHAPE_STRANDS

public static final int SHAPE_STRANDS
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Constant Field Values

SHAPE_MESHRIBBON

public static final int SHAPE_MESHRIBBON
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Constant Field Values

SHAPE_RIBBONS

public static final int SHAPE_RIBBONS
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Constant Field Values

SHAPE_ROCKETS

public static final int SHAPE_ROCKETS
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Constant Field Values

SHAPE_MAX_SECONDARY

public static final int SHAPE_MAX_SECONDARY
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Constant Field Values

SHAPE_MIN_SPECIAL

public static final int SHAPE_MIN_SPECIAL
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Constant Field Values

SHAPE_DIPOLES

public static final int SHAPE_DIPOLES
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Constant Field Values

SHAPE_VECTORS

public static final int SHAPE_VECTORS
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Constant Field Values

SHAPE_GEOSURFACE

public static final int SHAPE_GEOSURFACE
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Constant Field Values

SHAPE_ELLIPSOIDS

public static final int SHAPE_ELLIPSOIDS
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Constant Field Values

SHAPE_MAX_SIZE_ZERO_ON_RESTRICT

public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
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Constant Field Values

SHAPE_POLYHEDRA

public static final int SHAPE_POLYHEDRA
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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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Constant Field Values

SHAPE_MAX_SPECIAL

public static final int SHAPE_MAX_SPECIAL
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Constant Field Values

SHAPE_MIN_SURFACE

public static final int SHAPE_MIN_SURFACE
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Constant Field Values

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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Constant Field Values

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_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 java.lang.String[] shapeClassBases

shapeToks

public static final int[] shapeToks

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 java.lang.String PREVIOUS_MESH_ID
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Constant Field Values

CARTOON_VISIBILITY_FLAG

public static final int CARTOON_VISIBILITY_FLAG

ALPHA_CARBON_VISIBILITY_FLAG

public static final int ALPHA_CARBON_VISIBILITY_FLAG

STEREO_UNKNOWN

static final int STEREO_UNKNOWN
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Constant Field Values

STEREO_NONE

static final int STEREO_NONE
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Constant Field Values

STEREO_DOUBLE

static final int STEREO_DOUBLE
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Constant Field Values

STEREO_REDCYAN

static final int STEREO_REDCYAN
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Constant Field Values

STEREO_REDBLUE

static final int STEREO_REDBLUE
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Constant Field Values

STEREO_REDGREEN

static final int STEREO_REDGREEN
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Constant Field Values

STEREO_CUSTOM

static final int STEREO_CUSTOM
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Constant Field Values

stereoModes

private static final java.lang.String[] stereoModes

shellOrder

private static final java.lang.String[][] shellOrder

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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Constant Field Values

SHELL_SP

public static final int SHELL_SP
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Constant Field Values

SHELL_L

public static final int SHELL_L
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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_D_SPHERICAL

public static final int SHELL_D_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_F_SPHERICAL

public static final int SHELL_F_SPHERICAL
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Constant Field Values

quantumShellTags

private static final java.lang.String[] quantumShellTags

quantumShellIDs

private static final int[] quantumShellIDs

LOAD_ATOM_DATA_TYPES

public static final java.lang.String LOAD_ATOM_DATA_TYPES
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Constant Field Values
Constructor Detail

JmolConstants

public JmolConstants()
Method Detail

getCallbackName

public static java.lang.String getCallbackName(int i)

getCallbackId

public static int getCallbackId(java.lang.String callbackName)

getDrawTypeName

public static java.lang.String getDrawTypeName(int drawType)

connectOperationFromString

public static int connectOperationFromString(java.lang.String connectOperationString)

connectOperationName

public static java.lang.String connectOperationName(int i)

getPickingModeName

public static final java.lang.String getPickingModeName(int pickingMode)

getPickingMode

public static final int getPickingMode(java.lang.String str)

getPickingStyleName

public static final java.lang.String getPickingStyleName(int pickingStyle)

getPickingStyle

public static final int getPickingStyle(java.lang.String str)

getArgbHbondType

public static int getArgbHbondType(short order)

getBondOrderFromString

static final short getBondOrderFromString(java.lang.String bondOrderString)

getPartialBondOrderFromInteger

static final short 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

getPartialBondOrder

public static final short getPartialBondOrder(int order)

getPartialBondDotted

public static final int getPartialBondDotted(int order)

getBondOrderFromFloat

static final short getBondOrderFromFloat(float fOrder)

getBondOrderNameFromOrder

public static final java.lang.String getBondOrderNameFromOrder(short order)

getBondOrderNumberFromOrder

public static final java.lang.String getBondOrderNumberFromOrder(short order)
used for formatting labels and in the connect PARTIAL command

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

elementNumberFromSymbol

public static final short elementNumberFromSymbol(java.lang.String elementSymbol)
Parameters:
elementSymbol - First char must be upper case, second char accepts upper or lower case
Returns:
elementNumber = atomicNumber + IsotopeNumber*128

elementSymbolFromNumber

public static final java.lang.String elementSymbolFromNumber(int elementNumber)
Parameters:
elementNumber - may be atomicNumber + isotopeNumber*128
Returns:
elementSymbol

elementNameFromNumber

public static final java.lang.String elementNameFromNumber(int elementNumber)
Parameters:
elementNumber - may be atomicNumber + isotopeNumber*128
Returns:
elementName

altElementNameFromIndex

public static final java.lang.String altElementNameFromIndex(int i)
Parameters:
i - index into altElementNames
Returns:
elementName

altElementNumberFromIndex

public static final short altElementNumberFromIndex(int i)
Parameters:
i - index into altElementNumbers
Returns:
elementNumber (may be atomicNumber + isotopeNumber*128)

altElementSymbolFromIndex

public static final java.lang.String altElementSymbolFromIndex(int i)
Parameters:
i - index into altElementSymbols
Returns:
elementSymbol

altIsotopeSymbolFromIndex

public static final java.lang.String altIsotopeSymbolFromIndex(int i)
Parameters:
i - index into altElementSymbols
Returns:
2H

altElementIndexFromNumber

public static final int altElementIndexFromNumber(int atomicAndIsotopeNumber)
Parameters:
atomicAndIsotopeNumber - (may be atomicNumber + isotopeNumber*128)
Returns:
index into altElementNumbers

isNaturalIsotope

public static final boolean isNaturalIsotope(java.lang.String isotopeSymbol)

getVdwType

public static int getVdwType(java.lang.String label)

getVanderwaalsMar

public static int getVanderwaalsMar(int i,
                                    int scale)

getBondingMar

public static short getBondingMar(int atomicNumber,
                                  int charge)

getBondingMar

public static short getBondingMar(int atomicNumber,
                                  int charge,
                                  short[] table)

pidOf

public static byte pidOf(java.lang.Object value)

isPaletteVariable

public static boolean isPaletteVariable(byte pid)

getPaletteID

public static final byte getPaletteID(java.lang.String paletteName)

getPaletteName

public static final java.lang.String getPaletteName(byte pid)

getProteinStructureName

public static final java.lang.String getProteinStructureName(int itype)

checkCarbohydrate

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

getGroup3List

private static final java.lang.String getGroup3List()

isHetero

public static final boolean isHetero(java.lang.String group3)

isShapeSecondary

public static final boolean isShapeSecondary(int i)

shapeTokenIndex

static final int shapeTokenIndex(int tok)

getShapeClassName

public static final java.lang.String getShapeClassName(int shapeID)

getShapeVisibilityFlag

public static final int getShapeVisibilityFlag(int shapeID)

getStereoMode

static int getStereoMode(java.lang.String id)

getStereoModeName

static java.lang.String getStereoModeName(int mode)

getShellOrder

public static final java.lang.String[] getShellOrder(int i)

getQuantumShellTagID

public static final int getQuantumShellTagID(java.lang.String tag)

getQuantumShellTagIDSpherical

public static final int getQuantumShellTagIDSpherical(java.lang.String tag)

getQuantumShellTag

public static final java.lang.String getQuantumShellTag(int shell)

canonicalizeQuantumSubshellTag

public static final java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)

getQuantumSubshellTagID

public static final int getQuantumSubshellTagID(int shell,
                                                java.lang.String tag)

getQuantumSubshellTag

public static final java.lang.String getQuantumSubshellTag(int shell,
                                                           int subshell)

modelValue

static int modelValue(java.lang.String strDecimal)