org.jmol.viewer

Class JmolConstants

public final class JmolConstants extends Object

Field Summary
static intALPHA_CARBON_VISIBILITY_FLAG
static floatANGSTROMS_PER_BOHR
static byteATOMID_ALPHA_CARBON
static intATOMID_ALPHA_ONLY_MASK
static byteATOMID_AMINO_NITROGEN
static intATOMID_BACKBONE_MIN
static byteATOMID_C2
static byteATOMID_C3_PRIME
static byteATOMID_C4
static byteATOMID_C5
static byteATOMID_C5M
static byteATOMID_C6
static byteATOMID_C7
static byteATOMID_C8
static byteATOMID_CARBONYL_CARBON
static byteATOMID_CARBONYL_OXYGEN
static intATOMID_DISTINGUISHING_ATOM_MAX
static byteATOMID_H3T_TERMINUS
static byteATOMID_H5T_TERMINUS
static byteATOMID_HO3_PRIME
static byteATOMID_HO5_PRIME
static intATOMID_MAX
static byteATOMID_N1
static byteATOMID_N2
static byteATOMID_N3
static byteATOMID_N4
static byteATOMID_N6
static byteATOMID_N7
static byteATOMID_N9
static intATOMID_NUCLEIC_MASK
static byteATOMID_NUCLEIC_PHOSPHORUS
static byteATOMID_O1
static byteATOMID_O1P
static byteATOMID_O2
static byteATOMID_O2P
static byteATOMID_O2_PRIME
static byteATOMID_O3_PRIME
static byteATOMID_O4
static byteATOMID_O5T_TERMINUS
static byteATOMID_O5_PRIME
static byteATOMID_O6
static byteATOMID_OP1
static byteATOMID_OP2
static intATOMID_PHOSPHORUS_ONLY_MASK
static intATOMID_PROTEIN_MASK
static byteATOMID_S4
static byteATOMID_TERMINATING_OXT
static intATOM_IN_MODEL
static intATOM_SLABBED
static intAXES_DEFAULT_FONTSIZE
static intAXES_MODE_BOUNDBOX
axes modes
static intAXES_MODE_MOLECULAR
static intAXES_MODE_UNITCELL
static StringallCarbohydrates
static int[]altArgbsCpk
static intaltElementMax
length of the altElementSymbols, altElementNames, altElementNumbers arrays
static String[]altElementNames
static short[]altElementNumbers
static String[]altElementSymbols
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. ghemical colors with a few proposed modifications
static int[]argbsCpkRasmol
static int[]argbsFormalCharge
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 intargbShapelyBackbone
static intargbShapelyDefault
static intargbShapelySpecial
static String[]bondOrderNames
static String[]bondOrderNumbers
static short[]bondOrderValues
static BitSetbsAnions
static BitSetbsCations
static intBACKLIT
static shortBOND_AROMATIC
static shortBOND_AROMATIC_DOUBLE
static shortBOND_AROMATIC_MASK
static shortBOND_AROMATIC_SINGLE
static shortBOND_COVALENT_DOUBLE
static shortBOND_COVALENT_MASK
static shortBOND_COVALENT_QUADRUPLE
static shortBOND_COVALENT_SINGLE
static shortBOND_COVALENT_TRIPLE
static shortBOND_HBOND_SHIFT
static shortBOND_HYDROGEN_MASK
static shortBOND_H_CALC
static shortBOND_H_CALC_MASK
static shortBOND_H_MINUS_3
static shortBOND_H_MINUS_4
static shortBOND_H_NUCLEOTIDE
static shortBOND_H_PLUS_2
static shortBOND_H_PLUS_3
static shortBOND_H_PLUS_4
static shortBOND_H_PLUS_5
static shortBOND_H_REGULAR
static shortBOND_NEW
static shortBOND_ORDER_ANY
Extended Bond Definition Types
static shortBOND_ORDER_NULL
static shortBOND_ORDER_UNSPECIFIED
static shortBOND_PARTIAL01
static shortBOND_PARTIAL12
static shortBOND_PARTIAL23
static shortBOND_PARTIAL32
static shortBOND_PARTIAL_MASK
static shortBOND_STEREO_FAR
static shortBOND_STEREO_MASK
static shortBOND_STEREO_NEAR
static shortBOND_SULFUR_MASK
static String[]callbackNames
static short[]cationLookupTable
static String[]connectOperationStrings
static Stringcopyright
static short[]covalentMars
Default table of covalent Radii stored as a short mar ...
static StringcvsDate
static intCALLBACK_ANIMFRAME
static intCALLBACK_COUNT
static intCALLBACK_ECHO
static intCALLBACK_EVAL
static intCALLBACK_HOVER
static intCALLBACK_LOADSTRUCT
static intCALLBACK_MEASURE
static intCALLBACK_MESSAGE
static intCALLBACK_MINIMIZATION
static intCALLBACK_PICK
static intCALLBACK_RESIZE
static intCALLBACK_SCRIPT
static intCALLBACK_SYNC
static intCARTOON_VISIBILITY_FLAG
static StringCLASSBASE_OPTIONS
static intCONNECT_AUTO_BOND
static intCONNECT_CREATE_ONLY
static intCONNECT_DELETE_BONDS
static intCONNECT_IDENTIFY_ONLY
static intCONNECT_MODIFY_ONLY
static intCONNECT_MODIFY_OR_CREATE
static Stringdate
static shortDEFAULT_BOND_MILLIANGSTROM_RADIUS
static floatDEFAULT_BOND_RADIUS
static floatDEFAULT_BOND_TOLERANCE
static StringDEFAULT_FONTFACE
static StringDEFAULT_FONTSTYLE
static StringDEFAULT_HELP_PATH
static floatDEFAULT_MAX_CONNECT_DISTANCE
static floatDEFAULT_MIN_BOND_DISTANCE
static floatDEFAULT_MIN_CONNECT_DISTANCE
static intDEFAULT_PERCENT_VDW_ATOM
static intDRAW_ARC
static intDRAW_ARROW
static intDRAW_CIRCLE
static intDRAW_CIRCULARPLANE
static intDRAW_CURVE
static intDRAW_CYLINDER
static intDRAW_LINE
static intDRAW_MULTIPLE
static intDRAW_NONE
static intDRAW_PLANE
static intDRAW_POINT
static intDRAW_TRIANGLE
static String[]elementNames
static intelementNumberMax
one larger than the last elementNumber, same as elementSymbols.length
static String[]elementSymbols
The default elementSymbols.
static StringEMBEDDED_SCRIPT_TAG
static StringEXPORT_DRIVER_LIST
static intfirstIsotope
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
static shortFORMAL_CHARGE_COLIX_BLUE
static shortFORMAL_CHARGE_COLIX_RED
static shortFORMAL_CHARGE_COLIX_WHITE
static intFORMAL_CHARGE_INDEX_MAX
static intFORMAL_CHARGE_INDEX_WHITE
static intFORMAL_CHARGE_MAX
static intFORMAL_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 intFORMAL_CHARGE_RANGE_SIZE
static intFRONTLIT
static intFULLYLIT
static intgroup3Count
static Stringgroup3List
static intGROUPID_AMINO_MAX
static intGROUPID_PROLINE
static intGROUPID_SULPHATE
static intGROUPID_WATER
static HashtablehtElementMap
static intINFO_A
static intINFO_ALPHA
static intINFO_B
static intINFO_BETA
static intINFO_C
static intINFO_GAMMA
static intJMOL_DATA_OTHER
static intJMOL_DATA_QUATERNION
static intJMOL_DATA_RAMACHANDRAN
static intLABEL_DEFAULT_FONTSIZE
static intLABEL_DEFAULT_X_OFFSET
static intLABEL_DEFAULT_Y_OFFSET
static intLABEL_MAXIMUM_FONTSIZE
static intLABEL_MINIMUM_FONTSIZE
static shortmadMultipleBondSmallMaximum
static intMAXIMUM_AUTO_BOND_COUNT
static intMEASURE_DEFAULT_FONTSIZE
static intMOUSE_DELETE
static intMOUSE_MEASURE
static intMOUSE_NONE
static intMOUSE_PICK
static intMOUSE_POPUP_MENU
static intMOUSE_ROTATE
static intMOUSE_ROTATE_Z
static intMOUSE_SLAB_PLANE
static intMOUSE_XLATE
static intMOUSE_ZOOM
static byteMULTIBOND_ALWAYS
static byteMULTIBOND_NEVER
static byteMULTIBOND_NOTSMALL
static byteMULTIBOND_WIREFRAME
static StringnaturalIsotopes
static booleanofficialRelease
static intpaletteCount
static byte[]paletteIDs
static String[]paletteNames
static String[]pickingModeNames
static String[]pickingStyleNames
static char[]predefinedGroup1Names
static String[]predefinedGroup3Names
static String[]predefinedStatic
static String[]predefinedVariable
static String[]proteinStructureNames
static bytePALETTE_ALTLOC
static bytePALETTE_AMINO
static bytePALETTE_CHAIN
static bytePALETTE_CPK
static bytePALETTE_FIXEDTEMP
static bytePALETTE_FORMAL_CHARGE
static bytePALETTE_GROUP
static bytePALETTE_INSERTION
static bytePALETTE_JMOL
static bytePALETTE_MOLECULE
static bytePALETTE_MONOMER
static bytePALETTE_NONE
static bytePALETTE_PARTIAL_CHARGE
static bytePALETTE_PROPERTY
static bytePALETTE_RASMOL
static bytePALETTE_SHAPELY
static bytePALETTE_STATIC
static bytePALETTE_STRAIGHTNESS
static bytePALETTE_STRUCTURE
static bytePALETTE_SURFACE
static bytePALETTE_TEMP
static bytePALETTE_TYPE
static bytePALETTE_UNKNOWN
static bytePALETTE_VARIABLE
static bytePALETTE_VOLATILE
static shortPARTIAL_CHARGE_COLIX_BLUE
static shortPARTIAL_CHARGE_COLIX_RED
static shortPARTIAL_CHARGE_COLIX_WHITE
static intPARTIAL_CHARGE_RANGE_SIZE
static intPICKINGSTYLE_MEASURE_OFF
static intPICKINGSTYLE_MEASURE_ON
static intPICKINGSTYLE_SELECT_CHIME
static intPICKINGSTYLE_SELECT_DRAG
static intPICKINGSTYLE_SELECT_JMOL
picking styles
static intPICKINGSTYLE_SELECT_PFAAT
static intPICKINGSTYLE_SELECT_RASMOL
static intPICKING_CENTER
static intPICKING_DRAW
static intPICKING_IDENT
static intPICKING_LABEL
static intPICKING_MEASURE
static intPICKING_MEASURE_ANGLE
static intPICKING_MEASURE_DISTANCE
static intPICKING_MEASURE_TORSION
static intPICKING_NAVIGATE
static intPICKING_OFF
picking modes
static intPICKING_SELECT_ATOM
static intPICKING_SELECT_CHAIN
static intPICKING_SELECT_DRAG
static intPICKING_SELECT_ELEMENT
static intPICKING_SELECT_GROUP
static intPICKING_SELECT_MOLECULE
static intPICKING_SELECT_SITE
static intPICKING_SPIN
static StringPREVIOUS_MESH_ID
static bytePROTEIN_STRUCTURE_DNA
static bytePROTEIN_STRUCTURE_HELIX
static bytePROTEIN_STRUCTURE_NONE
Default table of PdbStructure colors
static bytePROTEIN_STRUCTURE_RNA
static bytePROTEIN_STRUCTURE_SHEET
static bytePROTEIN_STRUCTURE_TURN
static int[]quantumShellIDs
static String[]quantumShellTags
static String[]shapeClassBases
static int[]shapeToks
static String[][]shellOrder
static String[]specialAtomNames
static intSHAPE_AXES
static intSHAPE_BACKBONE
static intSHAPE_BALLS
static intSHAPE_BBCAGE
static intSHAPE_CARTOON
static intSHAPE_DIPOLES
static intSHAPE_DOTS
static intSHAPE_DRAW
static intSHAPE_ECHO
static intSHAPE_ELLIPSOIDS
static intSHAPE_FRANK
static intSHAPE_GEOSURFACE
static intSHAPE_HALOS
static intSHAPE_HOVER
static intSHAPE_HSTICKS
static intSHAPE_ISOSURFACE
static intSHAPE_LABELS
static intSHAPE_LCAOCARTOON
static intSHAPE_MAX
static intSHAPE_MAX_HAS_ID
static intSHAPE_MAX_MESH_COLLECTION
static intSHAPE_MAX_SECONDARY
static intSHAPE_MAX_SIZE_ZERO_ON_RESTRICT
static intSHAPE_MAX_SPECIAL
static intSHAPE_MAX_SURFACE
static intSHAPE_MEASURES
static intSHAPE_MESHRIBBON
static intSHAPE_MIN_HAS_ID
static intSHAPE_MIN_MESH_COLLECTION
static intSHAPE_MIN_SECONDARY
static intSHAPE_MIN_SPECIAL
static intSHAPE_MIN_SURFACE
static intSHAPE_MO
static intSHAPE_PMESH
static intSHAPE_POLYHEDRA
static intSHAPE_RIBBONS
static intSHAPE_ROCKETS
static intSHAPE_SSSTICKS
static intSHAPE_STARS
static intSHAPE_STICKS
static intSHAPE_STRANDS
static intSHAPE_TRACE
static intSHAPE_UCCAGE
static intSHAPE_VECTORS
static intSHELL_D_CARTESIAN
static intSHELL_D_SPHERICAL
static intSHELL_F_CARTESIAN
static intSHELL_F_SPHERICAL
static intSHELL_L
static intSHELL_P
static intSHELL_S
static intSHELL_SP
static intSTEREO_CUSTOM
static intSTEREO_DOUBLE
static intSTEREO_NONE
static intSTEREO_REDBLUE
static intSTEREO_REDCYAN
static intSTEREO_REDGREEN
static short[]vanderwaalsMars
Default table of van der Waals Radii. values are stored as MAR -- Milli Angstrom Radius Used for spacefill rendering of atoms.
static String[]vdwLabels
static Stringversion
static intVDW_BABEL
static intVDW_JMOL
static intVDW_RASMOL
static intVDW_USER
static intXY_ZTOP
Method Summary
static intaltElementIndexFromNumber(int atomicAndIsotopeNumber)
static StringaltElementNameFromIndex(int i)
static shortaltElementNumberFromIndex(int i)
static StringaltElementSymbolFromIndex(int i)
static StringaltIsotopeSymbolFromIndex(int i)
static StringcanonicalizeQuantumSubshellTag(String tag)
static booleancheckCarbohydrate(String group3)
static intconnectOperationFromString(String connectOperationString)
static StringconnectOperationName(int i)
static StringelementNameFromNumber(int elementNumber)
static shortelementNumberFromSymbol(String elementSymbol)
static StringelementSymbolFromNumber(int elementNumber)
static intgetArgbHbondType(short order)
static shortgetBondingMar(int atomicNumber, int charge)
static shortgetBondingMar(int atomicNumber, int charge, short[] table)
static shortgetBondOrderFromFloat(float fOrder)
static shortgetBondOrderFromString(String bondOrderString)
static StringgetBondOrderNameFromOrder(short order)
static StringgetBondOrderNumberFromOrder(short order)
used for formatting labels and in the connect PARTIAL command
static StringgetCallbackName(int i)
static StringgetDrawTypeName(int drawType)
static StringgetGroup3List()
static bytegetPaletteID(String paletteName)
static StringgetPaletteName(byte pid)
static intgetPartialBondDotted(int order)
static shortgetPartialBondOrder(int order)
static shortgetPartialBondOrderFromInteger(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
static intgetPickingMode(String str)
static StringgetPickingModeName(int pickingMode)
static intgetPickingStyle(String str)
static StringgetPickingStyleName(int pickingStyle)
static StringgetProteinStructureName(int itype)
static StringgetQuantumShellTag(int shell)
static intgetQuantumShellTagID(String tag)
static intgetQuantumShellTagIDSpherical(String tag)
static StringgetQuantumSubshellTag(int shell, int subshell)
static intgetQuantumSubshellTagID(int shell, String tag)
static StringgetShapeClassName(int shapeID)
static intgetShapeVisibilityFlag(int shapeID)
static String[]getShellOrder(int i)
static intgetVanderwaalsMar(int i, int scale)
static intgetVdwType(String label)
static booleanisHetero(String group3)
static booleanisNaturalIsotope(String isotopeSymbol)
static booleanisPaletteVariable(byte pid)
static booleanisShapeSecondary(int i)
static bytepidOf(Object value)
static intshapeTokenIndex(int tok)

Field Detail

ALPHA_CARBON_VISIBILITY_FLAG

public static int ALPHA_CARBON_VISIBILITY_FLAG

ANGSTROMS_PER_BOHR

public static final float ANGSTROMS_PER_BOHR

ATOMID_ALPHA_CARBON

public static final byte ATOMID_ALPHA_CARBON

ATOMID_ALPHA_ONLY_MASK

public static final int ATOMID_ALPHA_ONLY_MASK

ATOMID_AMINO_NITROGEN

public static final byte ATOMID_AMINO_NITROGEN

ATOMID_BACKBONE_MIN

private static final int ATOMID_BACKBONE_MIN

ATOMID_C2

public static final byte ATOMID_C2

ATOMID_C3_PRIME

public static final byte ATOMID_C3_PRIME

ATOMID_C4

public static final byte ATOMID_C4

ATOMID_C5

public static final byte ATOMID_C5

ATOMID_C5M

public static final byte ATOMID_C5M

ATOMID_C6

public static final byte ATOMID_C6

ATOMID_C7

public static final byte ATOMID_C7

ATOMID_C8

public static final byte ATOMID_C8

ATOMID_CARBONYL_CARBON

public static final byte ATOMID_CARBONYL_CARBON

ATOMID_CARBONYL_OXYGEN

public static final byte ATOMID_CARBONYL_OXYGEN

ATOMID_DISTINGUISHING_ATOM_MAX

public static final int ATOMID_DISTINGUISHING_ATOM_MAX

ATOMID_H3T_TERMINUS

public static final byte ATOMID_H3T_TERMINUS

ATOMID_H5T_TERMINUS

public static final byte ATOMID_H5T_TERMINUS

ATOMID_HO3_PRIME

public static final byte ATOMID_HO3_PRIME

ATOMID_HO5_PRIME

public static final byte ATOMID_HO5_PRIME

ATOMID_MAX

public static final int ATOMID_MAX

ATOMID_N1

public static final byte ATOMID_N1

ATOMID_N2

public static final byte ATOMID_N2

ATOMID_N3

public static final byte ATOMID_N3

ATOMID_N4

public static final byte ATOMID_N4

ATOMID_N6

public static final byte ATOMID_N6

ATOMID_N7

public static final byte ATOMID_N7

ATOMID_N9

public static final byte ATOMID_N9

ATOMID_NUCLEIC_MASK

public static final int ATOMID_NUCLEIC_MASK

ATOMID_NUCLEIC_PHOSPHORUS

public static final byte ATOMID_NUCLEIC_PHOSPHORUS

ATOMID_O1

public static final byte ATOMID_O1

ATOMID_O1P

public static final byte ATOMID_O1P

ATOMID_O2

public static final byte ATOMID_O2

ATOMID_O2P

public static final byte ATOMID_O2P

ATOMID_O2_PRIME

public static final byte ATOMID_O2_PRIME

ATOMID_O3_PRIME

public static final byte ATOMID_O3_PRIME

ATOMID_O4

public static final byte ATOMID_O4

ATOMID_O5T_TERMINUS

public static final byte ATOMID_O5T_TERMINUS

ATOMID_O5_PRIME

public static final byte ATOMID_O5_PRIME

ATOMID_O6

public static final byte ATOMID_O6

ATOMID_OP1

public static final byte ATOMID_OP1

ATOMID_OP2

public static final byte ATOMID_OP2

ATOMID_PHOSPHORUS_ONLY_MASK

public static final int ATOMID_PHOSPHORUS_ONLY_MASK

ATOMID_PROTEIN_MASK

public static final int ATOMID_PROTEIN_MASK

ATOMID_S4

public static final byte ATOMID_S4

ATOMID_TERMINATING_OXT

public static final byte ATOMID_TERMINATING_OXT

ATOM_IN_MODEL

public static final int ATOM_IN_MODEL

ATOM_SLABBED

public static final int ATOM_SLABBED

AXES_DEFAULT_FONTSIZE

public static final int AXES_DEFAULT_FONTSIZE

AXES_MODE_BOUNDBOX

public static final int AXES_MODE_BOUNDBOX
axes modes

AXES_MODE_MOLECULAR

public static final int AXES_MODE_MOLECULAR

AXES_MODE_UNITCELL

public static final int AXES_MODE_UNITCELL

allCarbohydrates

private static final String allCarbohydrates

altArgbsCpk

public static final int[] altArgbsCpk

altElementMax

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

altElementNames

private static final String[] altElementNames

altElementNumbers

private static final short[] altElementNumbers

altElementSymbols

private static final String[] altElementSymbols

anionLookupTable

private static final short[] anionLookupTable

argbsAmino

public static final int[] argbsAmino

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

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

argbsFormalCharge

public static final int[] argbsFormalCharge

argbsHbondType

public static final int[] argbsHbondType

argbsIsosurfaceNegative

public static final int[] argbsIsosurfaceNegative

argbsIsosurfacePositive

public static final int[] argbsIsosurfacePositive

argbsRoygbScale

public static final int[] argbsRoygbScale

argbsRwbScale

public static final int[] argbsRwbScale

argbsShapely

public static final int[] argbsShapely

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.

argbShapelyBackbone

public static final int argbShapelyBackbone

argbShapelyDefault

public static final int argbShapelyDefault

argbShapelySpecial

public static final int argbShapelySpecial

bondOrderNames

private static final String[] bondOrderNames

bondOrderNumbers

private static final String[] bondOrderNumbers

bondOrderValues

private static final short[] bondOrderValues

bsAnions

static BitSet bsAnions

bsCations

static BitSet bsCations

BACKLIT

public static final int BACKLIT

BOND_AROMATIC

public static final short BOND_AROMATIC

BOND_AROMATIC_DOUBLE

public static final short BOND_AROMATIC_DOUBLE

BOND_AROMATIC_MASK

public static final short BOND_AROMATIC_MASK

BOND_AROMATIC_SINGLE

public static final short BOND_AROMATIC_SINGLE

BOND_COVALENT_DOUBLE

public static final short BOND_COVALENT_DOUBLE

BOND_COVALENT_MASK

public static final short BOND_COVALENT_MASK

BOND_COVALENT_QUADRUPLE

public static final short BOND_COVALENT_QUADRUPLE

BOND_COVALENT_SINGLE

public static final short BOND_COVALENT_SINGLE

BOND_COVALENT_TRIPLE

public static final short BOND_COVALENT_TRIPLE

BOND_HBOND_SHIFT

public static final short BOND_HBOND_SHIFT

BOND_HYDROGEN_MASK

public static final short BOND_HYDROGEN_MASK

BOND_H_CALC

public static final short BOND_H_CALC

BOND_H_CALC_MASK

public static final short BOND_H_CALC_MASK

BOND_H_MINUS_3

public static final short BOND_H_MINUS_3

BOND_H_MINUS_4

public static final short BOND_H_MINUS_4

BOND_H_NUCLEOTIDE

public static final short BOND_H_NUCLEOTIDE

BOND_H_PLUS_2

public static final short BOND_H_PLUS_2

BOND_H_PLUS_3

public static final short BOND_H_PLUS_3

BOND_H_PLUS_4

public static final short BOND_H_PLUS_4

BOND_H_PLUS_5

public static final short BOND_H_PLUS_5

BOND_H_REGULAR

public static final short BOND_H_REGULAR

BOND_NEW

public static final short BOND_NEW

BOND_ORDER_ANY

public static final short BOND_ORDER_ANY
Extended Bond Definition Types

BOND_ORDER_NULL

public static final short BOND_ORDER_NULL

BOND_ORDER_UNSPECIFIED

public static final short BOND_ORDER_UNSPECIFIED

BOND_PARTIAL01

public static final short BOND_PARTIAL01

BOND_PARTIAL12

public static final short BOND_PARTIAL12

BOND_PARTIAL23

public static final short BOND_PARTIAL23

BOND_PARTIAL32

public static final short BOND_PARTIAL32

BOND_PARTIAL_MASK

public static final short BOND_PARTIAL_MASK

BOND_STEREO_FAR

public static final short BOND_STEREO_FAR

BOND_STEREO_MASK

public static final short BOND_STEREO_MASK

BOND_STEREO_NEAR

public static final short BOND_STEREO_NEAR

BOND_SULFUR_MASK

public static final short BOND_SULFUR_MASK

callbackNames

private static final String[] callbackNames

cationLookupTable

private static final short[] cationLookupTable

connectOperationStrings

private static final String[] connectOperationStrings

copyright

public static final String copyright

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

cvsDate

public static final String cvsDate

CALLBACK_ANIMFRAME

public static final int CALLBACK_ANIMFRAME

CALLBACK_COUNT

public static final int CALLBACK_COUNT

CALLBACK_ECHO

public static final int CALLBACK_ECHO

CALLBACK_EVAL

public static final int CALLBACK_EVAL

CALLBACK_HOVER

public static final int CALLBACK_HOVER

CALLBACK_LOADSTRUCT

public static final int CALLBACK_LOADSTRUCT

CALLBACK_MEASURE

public static final int CALLBACK_MEASURE

CALLBACK_MESSAGE

public static final int CALLBACK_MESSAGE

CALLBACK_MINIMIZATION

public static final int CALLBACK_MINIMIZATION

CALLBACK_PICK

public static final int CALLBACK_PICK

CALLBACK_RESIZE

public static final int CALLBACK_RESIZE

CALLBACK_SCRIPT

public static final int CALLBACK_SCRIPT

CALLBACK_SYNC

public static final int CALLBACK_SYNC

CARTOON_VISIBILITY_FLAG

public static int CARTOON_VISIBILITY_FLAG

CLASSBASE_OPTIONS

public static final String CLASSBASE_OPTIONS

CONNECT_AUTO_BOND

public static final int CONNECT_AUTO_BOND

CONNECT_CREATE_ONLY

public static final int CONNECT_CREATE_ONLY

CONNECT_DELETE_BONDS

public static final int CONNECT_DELETE_BONDS

CONNECT_IDENTIFY_ONLY

public static final int CONNECT_IDENTIFY_ONLY

CONNECT_MODIFY_ONLY

public static final int CONNECT_MODIFY_ONLY

CONNECT_MODIFY_OR_CREATE

public static final int CONNECT_MODIFY_OR_CREATE

date

public static final String date

DEFAULT_BOND_MILLIANGSTROM_RADIUS

public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS

DEFAULT_BOND_RADIUS

public static final float DEFAULT_BOND_RADIUS

DEFAULT_BOND_TOLERANCE

public static final float DEFAULT_BOND_TOLERANCE

DEFAULT_FONTFACE

public static final String DEFAULT_FONTFACE

DEFAULT_FONTSTYLE

public static final String DEFAULT_FONTSTYLE

DEFAULT_HELP_PATH

public static final String DEFAULT_HELP_PATH

DEFAULT_MAX_CONNECT_DISTANCE

public static final float DEFAULT_MAX_CONNECT_DISTANCE

DEFAULT_MIN_BOND_DISTANCE

public static final float DEFAULT_MIN_BOND_DISTANCE

DEFAULT_MIN_CONNECT_DISTANCE

public static final float DEFAULT_MIN_CONNECT_DISTANCE

DEFAULT_PERCENT_VDW_ATOM

public static final int DEFAULT_PERCENT_VDW_ATOM

DRAW_ARC

public static final int DRAW_ARC

DRAW_ARROW

public static final int DRAW_ARROW

DRAW_CIRCLE

public static final int DRAW_CIRCLE

DRAW_CIRCULARPLANE

public static final int DRAW_CIRCULARPLANE

DRAW_CURVE

public static final int DRAW_CURVE

DRAW_CYLINDER

public static final int DRAW_CYLINDER

DRAW_LINE

public static final int DRAW_LINE

DRAW_MULTIPLE

public static final int DRAW_MULTIPLE

DRAW_NONE

public static final int DRAW_NONE

DRAW_PLANE

public static final int DRAW_PLANE

DRAW_POINT

public static final int DRAW_POINT

DRAW_TRIANGLE

public static final int DRAW_TRIANGLE

elementNames

private static final String[] elementNames

elementNumberMax

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

elementSymbols

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

EMBEDDED_SCRIPT_TAG

public static final String EMBEDDED_SCRIPT_TAG

EXPORT_DRIVER_LIST

public static final String EXPORT_DRIVER_LIST

firstIsotope

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

FORMAL_CHARGE_COLIX_BLUE

public static final short FORMAL_CHARGE_COLIX_BLUE

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_INDEX_MAX

public static final int FORMAL_CHARGE_INDEX_MAX

FORMAL_CHARGE_INDEX_WHITE

public static final int FORMAL_CHARGE_INDEX_WHITE

FORMAL_CHARGE_MAX

public static final int FORMAL_CHARGE_MAX

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

FORMAL_CHARGE_RANGE_SIZE

public static final int FORMAL_CHARGE_RANGE_SIZE

FRONTLIT

public static final int FRONTLIT

FULLYLIT

public static final int FULLYLIT

group3Count

public static final int group3Count

group3List

public static final String group3List

GROUPID_AMINO_MAX

public static final int GROUPID_AMINO_MAX

GROUPID_PROLINE

public static final int GROUPID_PROLINE

GROUPID_SULPHATE

private static final int GROUPID_SULPHATE

GROUPID_WATER

private static final int GROUPID_WATER

htElementMap

private static Hashtable htElementMap

INFO_A

public static final int INFO_A

INFO_ALPHA

public static final int INFO_ALPHA

INFO_B

public static final int INFO_B

INFO_BETA

public static final int INFO_BETA

INFO_C

public static final int INFO_C

INFO_GAMMA

public static final int INFO_GAMMA

JMOL_DATA_OTHER

public static final int JMOL_DATA_OTHER

JMOL_DATA_QUATERNION

public static final int JMOL_DATA_QUATERNION

JMOL_DATA_RAMACHANDRAN

public static final int JMOL_DATA_RAMACHANDRAN

LABEL_DEFAULT_FONTSIZE

public static final int LABEL_DEFAULT_FONTSIZE

LABEL_DEFAULT_X_OFFSET

public static final int LABEL_DEFAULT_X_OFFSET

LABEL_DEFAULT_Y_OFFSET

public static final int LABEL_DEFAULT_Y_OFFSET

LABEL_MAXIMUM_FONTSIZE

public static final int LABEL_MAXIMUM_FONTSIZE

LABEL_MINIMUM_FONTSIZE

public static final int LABEL_MINIMUM_FONTSIZE

madMultipleBondSmallMaximum

public static final short madMultipleBondSmallMaximum

MAXIMUM_AUTO_BOND_COUNT

public static final int MAXIMUM_AUTO_BOND_COUNT

MEASURE_DEFAULT_FONTSIZE

public static final int MEASURE_DEFAULT_FONTSIZE

MOUSE_DELETE

public static final int MOUSE_DELETE

MOUSE_MEASURE

public static final int MOUSE_MEASURE

MOUSE_NONE

public static final int MOUSE_NONE

MOUSE_PICK

public static final int MOUSE_PICK

MOUSE_POPUP_MENU

public static final int MOUSE_POPUP_MENU

MOUSE_ROTATE

public static final int MOUSE_ROTATE

MOUSE_ROTATE_Z

public static final int MOUSE_ROTATE_Z

MOUSE_SLAB_PLANE

public static final int MOUSE_SLAB_PLANE

MOUSE_XLATE

public static final int MOUSE_XLATE

MOUSE_ZOOM

public static final int MOUSE_ZOOM

MULTIBOND_ALWAYS

public static final byte MULTIBOND_ALWAYS

MULTIBOND_NEVER

public static final byte MULTIBOND_NEVER

MULTIBOND_NOTSMALL

public static final byte MULTIBOND_NOTSMALL

MULTIBOND_WIREFRAME

public static final byte MULTIBOND_WIREFRAME

naturalIsotopes

private static final String naturalIsotopes

officialRelease

public static final boolean officialRelease

paletteCount

private static final int paletteCount

paletteIDs

private static final byte[] paletteIDs

paletteNames

private static final String[] paletteNames

pickingModeNames

private static final String[] pickingModeNames

pickingStyleNames

private static final String[] pickingStyleNames

predefinedGroup1Names

public static final char[] predefinedGroup1Names

predefinedGroup3Names

public static final String[] predefinedGroup3Names

predefinedStatic

public static String[] predefinedStatic

predefinedVariable

public static String[] predefinedVariable

proteinStructureNames

public static final String[] proteinStructureNames

PALETTE_ALTLOC

public static final byte PALETTE_ALTLOC

PALETTE_AMINO

public static final byte PALETTE_AMINO

PALETTE_CHAIN

public static final byte PALETTE_CHAIN

PALETTE_CPK

public static final byte PALETTE_CPK

PALETTE_FIXEDTEMP

public static final byte PALETTE_FIXEDTEMP

PALETTE_FORMAL_CHARGE

public static final byte PALETTE_FORMAL_CHARGE

PALETTE_GROUP

public static final byte PALETTE_GROUP

PALETTE_INSERTION

public static final byte PALETTE_INSERTION

PALETTE_JMOL

public static final byte PALETTE_JMOL

PALETTE_MOLECULE

public static final byte PALETTE_MOLECULE

PALETTE_MONOMER

public static final byte PALETTE_MONOMER

PALETTE_NONE

public static final byte PALETTE_NONE

PALETTE_PARTIAL_CHARGE

public static final byte PALETTE_PARTIAL_CHARGE

PALETTE_PROPERTY

public static final byte PALETTE_PROPERTY

PALETTE_RASMOL

public static final byte PALETTE_RASMOL

PALETTE_SHAPELY

public static final byte PALETTE_SHAPELY

PALETTE_STATIC

public static final byte PALETTE_STATIC

PALETTE_STRAIGHTNESS

public static final byte PALETTE_STRAIGHTNESS

PALETTE_STRUCTURE

public static final byte PALETTE_STRUCTURE

PALETTE_SURFACE

public static final byte PALETTE_SURFACE

PALETTE_TEMP

public static final byte PALETTE_TEMP

PALETTE_TYPE

public static final byte PALETTE_TYPE

PALETTE_UNKNOWN

public static final byte PALETTE_UNKNOWN

PALETTE_VARIABLE

public static final byte PALETTE_VARIABLE

PALETTE_VOLATILE

public static final byte PALETTE_VOLATILE

PARTIAL_CHARGE_COLIX_BLUE

public static final short PARTIAL_CHARGE_COLIX_BLUE

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_RANGE_SIZE

public static final int PARTIAL_CHARGE_RANGE_SIZE

PICKINGSTYLE_MEASURE_OFF

public static final int PICKINGSTYLE_MEASURE_OFF

PICKINGSTYLE_MEASURE_ON

public static final int PICKINGSTYLE_MEASURE_ON

PICKINGSTYLE_SELECT_CHIME

public static final int PICKINGSTYLE_SELECT_CHIME

PICKINGSTYLE_SELECT_DRAG

public static final int PICKINGSTYLE_SELECT_DRAG

PICKINGSTYLE_SELECT_JMOL

public static final int PICKINGSTYLE_SELECT_JMOL
picking styles

PICKINGSTYLE_SELECT_PFAAT

public static final int PICKINGSTYLE_SELECT_PFAAT

PICKINGSTYLE_SELECT_RASMOL

public static final int PICKINGSTYLE_SELECT_RASMOL

PICKING_CENTER

public static final int PICKING_CENTER

PICKING_DRAW

public static final int PICKING_DRAW

PICKING_IDENT

public static final int PICKING_IDENT

PICKING_LABEL

public static final int PICKING_LABEL

PICKING_MEASURE

public static final int PICKING_MEASURE

PICKING_MEASURE_ANGLE

public static final int PICKING_MEASURE_ANGLE

PICKING_MEASURE_DISTANCE

public static final int PICKING_MEASURE_DISTANCE

PICKING_MEASURE_TORSION

public static final int PICKING_MEASURE_TORSION

PICKING_NAVIGATE

public static final int PICKING_NAVIGATE

PICKING_OFF

public static final int PICKING_OFF
picking modes

PICKING_SELECT_ATOM

public static final int PICKING_SELECT_ATOM

PICKING_SELECT_CHAIN

public static final int PICKING_SELECT_CHAIN

PICKING_SELECT_DRAG

public static final int PICKING_SELECT_DRAG

PICKING_SELECT_ELEMENT

public static final int PICKING_SELECT_ELEMENT

PICKING_SELECT_GROUP

public static final int PICKING_SELECT_GROUP

PICKING_SELECT_MOLECULE

public static final int PICKING_SELECT_MOLECULE

PICKING_SELECT_SITE

public static final int PICKING_SELECT_SITE

PICKING_SPIN

public static final int PICKING_SPIN

PREVIOUS_MESH_ID

public static final String PREVIOUS_MESH_ID

PROTEIN_STRUCTURE_DNA

public static final byte PROTEIN_STRUCTURE_DNA

PROTEIN_STRUCTURE_HELIX

public static final byte PROTEIN_STRUCTURE_HELIX

PROTEIN_STRUCTURE_NONE

public static final byte PROTEIN_STRUCTURE_NONE
Default table of PdbStructure colors

PROTEIN_STRUCTURE_RNA

public static final byte PROTEIN_STRUCTURE_RNA

PROTEIN_STRUCTURE_SHEET

public static final byte PROTEIN_STRUCTURE_SHEET

PROTEIN_STRUCTURE_TURN

public static final byte PROTEIN_STRUCTURE_TURN

quantumShellIDs

private static final int[] quantumShellIDs

quantumShellTags

private static final String[] quantumShellTags

shapeClassBases

public static final String[] shapeClassBases

shapeToks

public static final int[] shapeToks

shellOrder

private static final String[][] shellOrder

specialAtomNames

public static final String[] specialAtomNames

SHAPE_AXES

public static final int SHAPE_AXES

SHAPE_BACKBONE

public static final int SHAPE_BACKBONE

SHAPE_BALLS

public static final int SHAPE_BALLS

SHAPE_BBCAGE

public static final int SHAPE_BBCAGE

SHAPE_CARTOON

public static final int SHAPE_CARTOON

SHAPE_DIPOLES

public static final int SHAPE_DIPOLES

SHAPE_DOTS

public static final int SHAPE_DOTS

SHAPE_DRAW

public static final int SHAPE_DRAW

SHAPE_ECHO

public static final int SHAPE_ECHO

SHAPE_ELLIPSOIDS

public static final int SHAPE_ELLIPSOIDS

SHAPE_FRANK

public static final int SHAPE_FRANK

SHAPE_GEOSURFACE

public static final int SHAPE_GEOSURFACE

SHAPE_HALOS

public static final int SHAPE_HALOS

SHAPE_HOVER

public static final int SHAPE_HOVER

SHAPE_HSTICKS

public static final int SHAPE_HSTICKS

SHAPE_ISOSURFACE

public static final int SHAPE_ISOSURFACE

SHAPE_LABELS

public static final int SHAPE_LABELS

SHAPE_LCAOCARTOON

public static final int SHAPE_LCAOCARTOON

SHAPE_MAX

public static final int SHAPE_MAX

SHAPE_MAX_HAS_ID

public static final int SHAPE_MAX_HAS_ID

SHAPE_MAX_MESH_COLLECTION

public static final int SHAPE_MAX_MESH_COLLECTION

SHAPE_MAX_SECONDARY

public static final int SHAPE_MAX_SECONDARY

SHAPE_MAX_SIZE_ZERO_ON_RESTRICT

public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT

SHAPE_MAX_SPECIAL

public static final int SHAPE_MAX_SPECIAL

SHAPE_MAX_SURFACE

public static final int SHAPE_MAX_SURFACE

SHAPE_MEASURES

public static final int SHAPE_MEASURES

SHAPE_MESHRIBBON

public static final int SHAPE_MESHRIBBON

SHAPE_MIN_HAS_ID

public static final int SHAPE_MIN_HAS_ID

SHAPE_MIN_MESH_COLLECTION

public static final int SHAPE_MIN_MESH_COLLECTION

SHAPE_MIN_SECONDARY

public static final int SHAPE_MIN_SECONDARY

SHAPE_MIN_SPECIAL

public static final int SHAPE_MIN_SPECIAL

SHAPE_MIN_SURFACE

public static final int SHAPE_MIN_SURFACE

SHAPE_MO

public static final int SHAPE_MO

SHAPE_PMESH

public static final int SHAPE_PMESH

SHAPE_POLYHEDRA

public static final int SHAPE_POLYHEDRA

SHAPE_RIBBONS

public static final int SHAPE_RIBBONS

SHAPE_ROCKETS

public static final int SHAPE_ROCKETS

SHAPE_SSSTICKS

public static final int SHAPE_SSSTICKS

SHAPE_STARS

public static final int SHAPE_STARS

SHAPE_STICKS

public static final int SHAPE_STICKS

SHAPE_STRANDS

public static final int SHAPE_STRANDS

SHAPE_TRACE

public static final int SHAPE_TRACE

SHAPE_UCCAGE

public static final int SHAPE_UCCAGE

SHAPE_VECTORS

public static final int SHAPE_VECTORS

SHELL_D_CARTESIAN

public static final int SHELL_D_CARTESIAN

SHELL_D_SPHERICAL

public static final int SHELL_D_SPHERICAL

SHELL_F_CARTESIAN

public static final int SHELL_F_CARTESIAN

SHELL_F_SPHERICAL

public static final int SHELL_F_SPHERICAL

SHELL_L

public static final int SHELL_L

SHELL_P

public static final int SHELL_P

SHELL_S

public static final int SHELL_S

SHELL_SP

public static final int SHELL_SP

STEREO_CUSTOM

public static final int STEREO_CUSTOM

STEREO_DOUBLE

public static final int STEREO_DOUBLE

STEREO_NONE

public static final int STEREO_NONE

STEREO_REDBLUE

public static final int STEREO_REDBLUE

STEREO_REDCYAN

public static final int STEREO_REDCYAN

STEREO_REDGREEN

public static final int STEREO_REDGREEN

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

vdwLabels

static final String[] vdwLabels

version

public static final String version

VDW_BABEL

public static final int VDW_BABEL

VDW_JMOL

public static final int VDW_JMOL

VDW_RASMOL

public static final int VDW_RASMOL

VDW_USER

public static final int VDW_USER

XY_ZTOP

public static final int XY_ZTOP

Method Detail

altElementIndexFromNumber

public static final int altElementIndexFromNumber(int atomicAndIsotopeNumber)

Parameters: atomicAndIsotopeNumber (may be atomicNumber + isotopeNumber*128)

Returns: index into altElementNumbers

altElementNameFromIndex

public static final 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 String altElementSymbolFromIndex(int i)

Parameters: i index into altElementSymbols

Returns: elementSymbol

altIsotopeSymbolFromIndex

public static final String altIsotopeSymbolFromIndex(int i)

Parameters: i index into altElementSymbols

Returns: 2H

canonicalizeQuantumSubshellTag

public static final String canonicalizeQuantumSubshellTag(String tag)

checkCarbohydrate

public static final boolean checkCarbohydrate(String group3)

Parameters: group3 a potential group3 name

Returns: whether this is a carbohydrate from the list

connectOperationFromString

public static int connectOperationFromString(String connectOperationString)

connectOperationName

public static String connectOperationName(int i)

elementNameFromNumber

public static final String elementNameFromNumber(int elementNumber)

Parameters: elementNumber may be atomicNumber + isotopeNumber*128

Returns: elementName

elementNumberFromSymbol

public static final short elementNumberFromSymbol(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 String elementSymbolFromNumber(int elementNumber)

Parameters: elementNumber may be atomicNumber + isotopeNumber*128

Returns: elementSymbol

getArgbHbondType

public static int getArgbHbondType(short order)

getBondingMar

public static short getBondingMar(int atomicNumber, int charge)

getBondingMar

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

getBondOrderFromFloat

static final short getBondOrderFromFloat(float fOrder)

getBondOrderFromString

static final short getBondOrderFromString(String bondOrderString)

getBondOrderNameFromOrder

public static final String getBondOrderNameFromOrder(short order)

getBondOrderNumberFromOrder

public static final 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

getCallbackName

public static String getCallbackName(int i)

getDrawTypeName

public static String getDrawTypeName(int drawType)

getGroup3List

private static final String getGroup3List()

getPaletteID

public static final byte getPaletteID(String paletteName)

getPaletteName

public static final String getPaletteName(byte pid)

getPartialBondDotted

public static final int getPartialBondDotted(int order)

getPartialBondOrder

public static final short getPartialBondOrder(int order)

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

getPickingMode

public static final int getPickingMode(String str)

getPickingModeName

public static final String getPickingModeName(int pickingMode)

getPickingStyle

public static final int getPickingStyle(String str)

getPickingStyleName

public static final String getPickingStyleName(int pickingStyle)

getProteinStructureName

public static final String getProteinStructureName(int itype)

getQuantumShellTag

public static final String getQuantumShellTag(int shell)

getQuantumShellTagID

public static final int getQuantumShellTagID(String tag)

getQuantumShellTagIDSpherical

public static final int getQuantumShellTagIDSpherical(String tag)

getQuantumSubshellTag

public static final String getQuantumSubshellTag(int shell, int subshell)

getQuantumSubshellTagID

public static final int getQuantumSubshellTagID(int shell, String tag)

getShapeClassName

public static final String getShapeClassName(int shapeID)

getShapeVisibilityFlag

public static final int getShapeVisibilityFlag(int shapeID)

getShellOrder

public static final String[] getShellOrder(int i)

getVanderwaalsMar

public static int getVanderwaalsMar(int i, int scale)

getVdwType

public static int getVdwType(String label)

isHetero

public static final boolean isHetero(String group3)

isNaturalIsotope

public static final boolean isNaturalIsotope(String isotopeSymbol)

isPaletteVariable

public static boolean isPaletteVariable(byte pid)

isShapeSecondary

public static final boolean isShapeSecondary(int i)

pidOf

public static byte pidOf(Object value)

shapeTokenIndex

static final int shapeTokenIndex(int tok)