|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.jmol.viewer.JmolConstants
public final class JmolConstants
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_MODEL
|
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 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_EVAL
|
static int |
CALLBACK_HOVER
|
static int |
CALLBACK_LOADSTRUCT
|
static int |
CALLBACK_MEASURE
|
static int |
CALLBACK_MESSAGE
|
static int |
CALLBACK_MINIMIZATION
|
static int |
CALLBACK_PICK
|
static int |
CALLBACK_RESIZE
|
static int |
CALLBACK_SCRIPT
|
static int |
CALLBACK_SYNC
|
private static java.lang.String[] |
callbackNames
|
static int |
CARTOON_VISIBILITY_FLAG
|
private static short[] |
cationLookupTable
|
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_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_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 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_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_DRAG
|
static int |
PICKING_SELECT_ELEMENT
|
static int |
PICKING_SELECT_GROUP
|
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 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 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 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)
|
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 |
---|
public static final java.lang.String copyright
public static final java.lang.String version
public static final java.lang.String cvsDate
public static final java.lang.String date
public static final boolean officialRelease
public static final java.lang.String CLASSBASE_OPTIONS
public static final java.lang.String DEFAULT_HELP_PATH
public static final java.lang.String EMBEDDED_SCRIPT_TAG
public static final int CALLBACK_ANIMFRAME
public static final int CALLBACK_ECHO
public static final int CALLBACK_EVAL
public static final int CALLBACK_HOVER
public static final int CALLBACK_LOADSTRUCT
public static final int CALLBACK_MEASURE
public static final int CALLBACK_MESSAGE
public static final int CALLBACK_MINIMIZATION
public static final int CALLBACK_PICK
public static final int CALLBACK_RESIZE
public static final int CALLBACK_SCRIPT
public static final int CALLBACK_SYNC
public static final int CALLBACK_COUNT
private static final java.lang.String[] callbackNames
public static final int INFO_A
public static final int INFO_B
public static final int INFO_C
public static final int INFO_ALPHA
public static final int INFO_BETA
public static final int INFO_GAMMA
public static final int JMOL_DATA_RAMACHANDRAN
public static final int JMOL_DATA_QUATERNION
public static final int JMOL_DATA_OTHER
public static final java.lang.String EXPORT_DRIVER_LIST
public static final int DRAW_MULTIPLE
public static final int DRAW_NONE
public static final int DRAW_POINT
public static final int DRAW_LINE
public static final int DRAW_TRIANGLE
public static final int DRAW_PLANE
public static final int DRAW_CYLINDER
public static final int DRAW_ARROW
public static final int DRAW_CIRCLE
public static final int DRAW_CURVE
public static final int DRAW_CIRCULARPLANE
public static final int DRAW_ARC
public static final int XY_ZTOP
public static final int DEFAULT_PERCENT_VDW_ATOM
public static final float DEFAULT_BOND_RADIUS
public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS
public static final float DEFAULT_BOND_TOLERANCE
public static final float DEFAULT_MIN_BOND_DISTANCE
public static final int CONNECT_DELETE_BONDS
public static final int CONNECT_MODIFY_ONLY
public static final int CONNECT_CREATE_ONLY
public static final int CONNECT_MODIFY_OR_CREATE
public static final int CONNECT_AUTO_BOND
public static final int CONNECT_IDENTIFY_ONLY
public static final float DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE
private static final java.lang.String[] connectOperationStrings
public static final int MOUSE_NONE
public static final int MOUSE_ROTATE
public static final int MOUSE_ZOOM
public static final int MOUSE_XLATE
public static final int MOUSE_PICK
public static final int MOUSE_DELETE
public static final int MOUSE_MEASURE
public static final int MOUSE_ROTATE_Z
public static final int MOUSE_SLAB_PLANE
public static final int MOUSE_POPUP_MENU
public static final byte MULTIBOND_NEVER
public static final byte MULTIBOND_WIREFRAME
public static final byte MULTIBOND_NOTSMALL
public static final byte MULTIBOND_ALWAYS
public static final short madMultipleBondSmallMaximum
public static final int AXES_MODE_BOUNDBOX
public static final int AXES_MODE_MOLECULAR
public static final int AXES_MODE_UNITCELL
public static final int PICKING_OFF
public static final int PICKING_IDENT
public static final int PICKING_LABEL
public static final int PICKING_CENTER
public static final int PICKING_DRAW
public static final int PICKING_SPIN
public static final int PICKING_SELECT_ATOM
public static final int PICKING_SELECT_GROUP
public static final int PICKING_SELECT_CHAIN
public static final int PICKING_SELECT_MOLECULE
public static final int PICKING_SELECT_SITE
public static final int PICKING_SELECT_ELEMENT
public static final int PICKING_SELECT_DRAG
public static final int PICKING_MEASURE
public static final int PICKING_MEASURE_DISTANCE
public static final int PICKING_MEASURE_ANGLE
public static final int PICKING_MEASURE_TORSION
public static final int PICKING_NAVIGATE
private static final java.lang.String[] pickingModeNames
public static final int PICKINGSTYLE_SELECT_JMOL
public static final int PICKINGSTYLE_SELECT_CHIME
public static final int PICKINGSTYLE_SELECT_RASMOL
public static final int PICKINGSTYLE_SELECT_PFAAT
public static final int PICKINGSTYLE_SELECT_DRAG
public static final int PICKINGSTYLE_MEASURE_ON
public static final int PICKINGSTYLE_MEASURE_OFF
private static final java.lang.String[] pickingStyleNames
public static final short BOND_ORDER_ANY
public static final short BOND_ORDER_NULL
public static final short BOND_HBOND_SHIFT
public static final short BOND_NEW
public static final short BOND_HYDROGEN_MASK
public static final short BOND_H_REGULAR
public static final short BOND_H_CALC_MASK
public static final short BOND_H_CALC
public static final short BOND_H_PLUS_2
public static final short BOND_H_PLUS_3
public static final short BOND_H_PLUS_4
public static final short BOND_H_PLUS_5
public static final short BOND_H_MINUS_3
public static final short BOND_H_MINUS_4
public static final short BOND_H_NUCLEOTIDE
public static final int[] argbsHbondType
public static final short BOND_STEREO_MASK
public static final short BOND_STEREO_NEAR
public static final short BOND_STEREO_FAR
public static final short BOND_AROMATIC_MASK
public static final short BOND_AROMATIC_SINGLE
public static final short BOND_AROMATIC_DOUBLE
public static final short BOND_AROMATIC
public static final short BOND_SULFUR_MASK
public static final short BOND_PARTIAL_MASK
public static final short BOND_PARTIAL01
public static final short BOND_PARTIAL12
public static final short BOND_PARTIAL23
public static final short BOND_PARTIAL32
public static final short BOND_COVALENT_MASK
public static final short BOND_COVALENT_SINGLE
public static final short BOND_COVALENT_DOUBLE
public static final short BOND_COVALENT_TRIPLE
public static final short BOND_COVALENT_QUADRUPLE
public static final short BOND_ORDER_UNSPECIFIED
private static final java.lang.String[] bondOrderNames
private static final java.lang.String[] bondOrderNumbers
private static final short[] bondOrderValues
public static final float ANGSTROMS_PER_BOHR
public static final int FRONTLIT
public static final int BACKLIT
public static final int FULLYLIT
private static final java.lang.String[] elementSymbols
public static final int elementNumberMax
private static java.util.Hashtable htElementMap
private static final java.lang.String[] elementNames
private static final java.lang.String naturalIsotopes
private static final short[] altElementNumbers
private static final java.lang.String[] altElementSymbols
private static final java.lang.String[] altElementNames
public static final int[] altArgbsCpk
public static final int firstIsotope
public static final int altElementMax
public static final int VDW_JMOL
public static final int VDW_BABEL
public static final int VDW_RASMOL
public static final int VDW_USER
static final java.lang.String[] vdwLabels
public static final short[] vanderwaalsMars
private static final short[] covalentMars
public static final int FORMAL_CHARGE_MIN
public static final int FORMAL_CHARGE_MAX
private static final short[] cationLookupTable
private static final short[] anionLookupTable
static java.util.BitSet bsCations
static java.util.BitSet bsAnions
public static final int MAXIMUM_AUTO_BOND_COUNT
public static final byte PALETTE_VOLATILE
public static final byte PALETTE_STATIC
public static final byte PALETTE_UNKNOWN
public static final byte PALETTE_NONE
public static final byte PALETTE_CPK
public static final byte PALETTE_PARTIAL_CHARGE
public static final byte PALETTE_FORMAL_CHARGE
public static final byte PALETTE_TEMP
public static final byte PALETTE_FIXEDTEMP
public static final byte PALETTE_SURFACE
public static final byte PALETTE_STRUCTURE
public static final byte PALETTE_AMINO
public static final byte PALETTE_SHAPELY
public static final byte PALETTE_CHAIN
public static final byte PALETTE_GROUP
public static final byte PALETTE_MONOMER
public static final byte PALETTE_MOLECULE
public static final byte PALETTE_ALTLOC
public static final byte PALETTE_INSERTION
public static final byte PALETTE_JMOL
public static final byte PALETTE_RASMOL
public static final byte PALETTE_TYPE
public static final byte PALETTE_PROPERTY
public static final byte PALETTE_VARIABLE
public static final byte PALETTE_STRAIGHTNESS
private static final java.lang.String[] paletteNames
private static final byte[] paletteIDs
private static final int paletteCount
public static final int[] argbsCpk
public static final int[] argbsCpkRasmol
public static final byte PROTEIN_STRUCTURE_NONE
public static final byte PROTEIN_STRUCTURE_TURN
public static final byte PROTEIN_STRUCTURE_SHEET
public static final byte PROTEIN_STRUCTURE_HELIX
public static final byte PROTEIN_STRUCTURE_DNA
public static final byte PROTEIN_STRUCTURE_RNA
public static final java.lang.String[] proteinStructureNames
public static final int[] argbsStructure
public static final int[] argbsAmino
public static final int argbShapelyBackbone
public static final int argbShapelySpecial
public static final int argbShapelyDefault
public static final int[] argbsChainAtom
public static final int[] argbsChainHetero
public static final short FORMAL_CHARGE_COLIX_RED
public static final short FORMAL_CHARGE_COLIX_WHITE
public static final short FORMAL_CHARGE_COLIX_BLUE
public static final int FORMAL_CHARGE_RANGE_SIZE
public static final int[] argbsFormalCharge
public static final int FORMAL_CHARGE_INDEX_WHITE
public static final int FORMAL_CHARGE_INDEX_MAX
public static final short PARTIAL_CHARGE_COLIX_RED
public static final short PARTIAL_CHARGE_COLIX_WHITE
public static final short PARTIAL_CHARGE_COLIX_BLUE
public static final int PARTIAL_CHARGE_RANGE_SIZE
public static final int[] argbsRwbScale
public static final int[] argbsRoygbScale
public static final int[] argbsIsosurfacePositive
public static final int[] argbsIsosurfaceNegative
public static final java.lang.String[] specialAtomNames
public static final int ATOMID_MAX
public static final byte ATOMID_AMINO_NITROGEN
public static final byte ATOMID_ALPHA_CARBON
public static final byte ATOMID_CARBONYL_CARBON
public static final byte ATOMID_CARBONYL_OXYGEN
public static final byte ATOMID_O1
public static final int ATOMID_ALPHA_ONLY_MASK
public static final int ATOMID_PROTEIN_MASK
public static final byte ATOMID_O5_PRIME
public static final byte ATOMID_C3_PRIME
public static final byte ATOMID_O3_PRIME
public static final int ATOMID_NUCLEIC_MASK
public static final byte ATOMID_NUCLEIC_PHOSPHORUS
public static final int ATOMID_PHOSPHORUS_ONLY_MASK
public static final int ATOMID_DISTINGUISHING_ATOM_MAX
public static final byte ATOMID_N1
public static final byte ATOMID_C2
public static final byte ATOMID_N3
public static final byte ATOMID_C4
public static final byte ATOMID_C5
public static final byte ATOMID_C6
public static final byte ATOMID_O2
public static final byte ATOMID_N7
public static final byte ATOMID_C8
public static final byte ATOMID_N9
public static final byte ATOMID_N4
public static final byte ATOMID_N2
public static final byte ATOMID_N6
public static final byte ATOMID_C5M
public static final byte ATOMID_O6
public static final byte ATOMID_O4
public static final byte ATOMID_S4
public static final byte ATOMID_C7
private static final int ATOMID_BACKBONE_MIN
public static final byte ATOMID_TERMINATING_OXT
public static final byte ATOMID_H5T_TERMINUS
public static final byte ATOMID_O5T_TERMINUS
public static final byte ATOMID_O1P
public static final byte ATOMID_OP1
public static final byte ATOMID_O2P
public static final byte ATOMID_OP2
public static final byte ATOMID_O2_PRIME
public static final byte ATOMID_H3T_TERMINUS
public static final byte ATOMID_HO3_PRIME
public static final byte ATOMID_HO5_PRIME
public static final int GROUPID_PROLINE
public static final int GROUPID_AMINO_MAX
private static final int GROUPID_WATER
private static final int GROUPID_SULPHATE
public static final java.lang.String[] predefinedGroup3Names
public static final int[] argbsShapely
private static final java.lang.String allCarbohydrates
public static final java.lang.String group3List
public static final int group3Count
public static final char[] predefinedGroup1Names
public static java.lang.String[] predefinedVariable
public static java.lang.String[] predefinedStatic
public static final java.lang.String DEFAULT_FONTFACE
public static final java.lang.String DEFAULT_FONTSTYLE
public static final int LABEL_MINIMUM_FONTSIZE
public static final int LABEL_MAXIMUM_FONTSIZE
public static final int LABEL_DEFAULT_FONTSIZE
public static final int LABEL_DEFAULT_X_OFFSET
public static final int LABEL_DEFAULT_Y_OFFSET
public static final int MEASURE_DEFAULT_FONTSIZE
public static final int AXES_DEFAULT_FONTSIZE
public static final int SHAPE_BALLS
public static final int SHAPE_STICKS
public static final int SHAPE_HSTICKS
public static final int SHAPE_SSSTICKS
public static final int SHAPE_LABELS
public static final int SHAPE_MEASURES
public static final int SHAPE_DOTS
public static final int SHAPE_STARS
public static final int SHAPE_HALOS
public static final int SHAPE_MIN_SECONDARY
public static final int SHAPE_BACKBONE
public static final int SHAPE_TRACE
public static final int SHAPE_CARTOON
public static final int SHAPE_STRANDS
public static final int SHAPE_MESHRIBBON
public static final int SHAPE_RIBBONS
public static final int SHAPE_ROCKETS
public static final int SHAPE_MAX_SECONDARY
public static final int SHAPE_MIN_SPECIAL
public static final int SHAPE_DIPOLES
public static final int SHAPE_VECTORS
public static final int SHAPE_GEOSURFACE
public static final int SHAPE_ELLIPSOIDS
public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
public static final int SHAPE_POLYHEDRA
public static final int SHAPE_MIN_HAS_ID
public static final int SHAPE_MIN_MESH_COLLECTION
public static final int SHAPE_DRAW
public static final int SHAPE_MAX_SPECIAL
public static final int SHAPE_MIN_SURFACE
public static final int SHAPE_ISOSURFACE
public static final int SHAPE_LCAOCARTOON
public static final int SHAPE_MO
public static final int SHAPE_PMESH
public static final int SHAPE_MAX_SURFACE
public static final int SHAPE_MAX_MESH_COLLECTION
public static final int SHAPE_ECHO
public static final int SHAPE_MAX_HAS_ID
public static final int SHAPE_AXES
public static final int SHAPE_BBCAGE
public static final int SHAPE_UCCAGE
public static final int SHAPE_HOVER
public static final int SHAPE_FRANK
public static final int SHAPE_MAX
public static final java.lang.String[] shapeClassBases
public static final int[] shapeToks
public static final int ATOM_IN_MODEL
public static final int ATOM_SLABBED
public static final java.lang.String PREVIOUS_MESH_ID
public static int CARTOON_VISIBILITY_FLAG
public static int ALPHA_CARBON_VISIBILITY_FLAG
static final int STEREO_UNKNOWN
static final int STEREO_NONE
static final int STEREO_DOUBLE
static final int STEREO_REDCYAN
static final int STEREO_REDBLUE
static final int STEREO_REDGREEN
static final int STEREO_CUSTOM
private static final java.lang.String[] stereoModes
private static final java.lang.String[][] shellOrder
public static final int SHELL_S
public static final int SHELL_P
public static final int SHELL_SP
public static final int SHELL_L
public static final int SHELL_D_CARTESIAN
public static final int SHELL_D_SPHERICAL
public static final int SHELL_F_CARTESIAN
public static final int SHELL_F_SPHERICAL
private static final java.lang.String[] quantumShellTags
private static final int[] quantumShellIDs
Constructor Detail |
---|
public JmolConstants()
Method Detail |
---|
public static java.lang.String getCallbackName(int i)
public static java.lang.String getDrawTypeName(int drawType)
public static int connectOperationFromString(java.lang.String connectOperationString)
public static java.lang.String connectOperationName(int i)
public static final java.lang.String getPickingModeName(int pickingMode)
public static final int getPickingMode(java.lang.String str)
public static final java.lang.String getPickingStyleName(int pickingStyle)
public static final int getPickingStyle(java.lang.String str)
public static int getArgbHbondType(short order)
static final short getBondOrderFromString(java.lang.String bondOrderString)
static final short getPartialBondOrderFromInteger(int bondOrderInteger)
bondOrderInteger
-
public static final short getPartialBondOrder(int order)
public static final int getPartialBondDotted(int order)
static final short getBondOrderFromFloat(float fOrder)
public static final java.lang.String getBondOrderNameFromOrder(short order)
public static final java.lang.String getBondOrderNumberFromOrder(short order)
order
-
public static final short elementNumberFromSymbol(java.lang.String elementSymbol)
elementSymbol
- First char must be upper case, second char accepts upper or lower case
public static final java.lang.String elementSymbolFromNumber(int elementNumber)
elementNumber
- may be atomicNumber + isotopeNumber*128
public static final java.lang.String elementNameFromNumber(int elementNumber)
elementNumber
- may be atomicNumber + isotopeNumber*128
public static final java.lang.String altElementNameFromIndex(int i)
i
- index into altElementNames
public static final short altElementNumberFromIndex(int i)
i
- index into altElementNumbers
public static final java.lang.String altElementSymbolFromIndex(int i)
i
- index into altElementSymbols
public static final java.lang.String altIsotopeSymbolFromIndex(int i)
i
- index into altElementSymbols
public static final int altElementIndexFromNumber(int atomicAndIsotopeNumber)
atomicAndIsotopeNumber
- (may be atomicNumber + isotopeNumber*128)
public static final boolean isNaturalIsotope(java.lang.String isotopeSymbol)
public static int getVdwType(java.lang.String label)
public static int getVanderwaalsMar(int i, int scale)
public static short getBondingMar(int atomicNumber, int charge)
public static short getBondingMar(int atomicNumber, int charge, short[] table)
public static byte pidOf(java.lang.Object value)
public static boolean isPaletteVariable(byte pid)
public static final byte getPaletteID(java.lang.String paletteName)
public static final java.lang.String getPaletteName(byte pid)
public static final java.lang.String getProteinStructureName(int itype)
public static final boolean checkCarbohydrate(java.lang.String group3)
group3
- a potential group3 name
private static final java.lang.String getGroup3List()
public static final boolean isHetero(java.lang.String group3)
public static final boolean isShapeSecondary(int i)
static final int shapeTokenIndex(int tok)
public static final java.lang.String getShapeClassName(int shapeID)
public static final int getShapeVisibilityFlag(int shapeID)
static int getStereoMode(java.lang.String id)
static java.lang.String getStereoModeName(int mode)
public static final java.lang.String[] getShellOrder(int i)
public static final int getQuantumShellTagID(java.lang.String tag)
public static final int getQuantumShellTagIDSpherical(java.lang.String tag)
public static final java.lang.String getQuantumShellTag(int shell)
public static final java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)
public static final int getQuantumSubshellTagID(int shell, java.lang.String tag)
public static final java.lang.String getQuantumSubshellTag(int shell, int subshell)
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |