public final class JmolConstants
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private static java.lang.String |
allCarbohydrates |
static java.lang.String |
allowedQuaternionFrames |
static int |
ALPHA_CARBON_VISIBILITY_FLAG |
static int[] |
altArgbsCpk |
static float |
ANGSTROMS_PER_BOHR |
static int |
ANIMATION_LOOP |
static int |
ANIMATION_ONCE |
static int |
ANIMATION_PALINDROME |
private static short[] |
anionLookupTable |
static int[] |
argbsAmino |
static int[] |
argbsChainAtom
some pastel colors
C0D0FF - pastel blue
B0FFB0 - pastel green
B0FFFF - pastel cyan
FFC0C8 - pink
FFC0FF - pastel magenta
FFFF80 - pastel yellow
FFDEAD - navajowhite
FFD070 - pastel gold
FF9898 - light coral
B4E444 - light yellow-green
C0C000 - light olive
FF8060 - light tomato
00FF7F - springgreen
cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
|
static int[] |
argbsChainHetero |
static int[] |
argbsCpk
Default table of CPK atom colors.
|
static int[] |
argbsCpkRasmol |
static int[] |
argbsFormalCharge |
static int |
argbShapelyBackbone |
static int |
argbShapelyDefault |
static int |
argbShapelySpecial |
static int[] |
argbsHbondType |
static int[] |
argbsIsosurfaceNegative |
static int[] |
argbsIsosurfacePositive |
static int[] |
argbsRoygbScale |
static int[] |
argbsRwbScale |
static int[] |
argbsShapely |
static int[] |
argbsStructure
In DRuMS, RasMol, and Chime, quoting from
http://www.umass.edu/microbio/rasmol/rascolor.htm
The RasMol structure color scheme colors the molecule by
protein secondary structure.
|
static int |
ATOM_IN_FRAME |
static int |
ATOM_SLABBED |
static byte |
ATOMID_ALPHA_CARBON |
static int |
ATOMID_ALPHA_ONLY_MASK |
static byte |
ATOMID_AMINO_NITROGEN |
private static int |
ATOMID_BACKBONE_MIN |
static byte |
ATOMID_C1_PRIME |
static byte |
ATOMID_C2 |
static byte |
ATOMID_C3_PRIME |
static byte |
ATOMID_C4 |
static byte |
ATOMID_C4_PRIME |
static byte |
ATOMID_C5 |
static byte |
ATOMID_C5M |
static byte |
ATOMID_C6 |
static byte |
ATOMID_C7 |
static byte |
ATOMID_C8 |
static byte |
ATOMID_CARBONYL_CARBON |
static byte |
ATOMID_CARBONYL_OD1 |
static byte |
ATOMID_CARBONYL_OD2 |
static byte |
ATOMID_CARBONYL_OE1 |
static byte |
ATOMID_CARBONYL_OE2 |
static byte |
ATOMID_CARBONYL_OXYGEN |
static int |
ATOMID_DISTINGUISHING_ATOM_MAX |
static byte |
ATOMID_H3T_TERMINUS |
static byte |
ATOMID_H5T_TERMINUS |
static byte |
ATOMID_HO3_PRIME |
static byte |
ATOMID_HO5_PRIME |
static int |
ATOMID_MAX |
static byte |
ATOMID_N1 |
static byte |
ATOMID_N2 |
static byte |
ATOMID_N3 |
static byte |
ATOMID_N4 |
static byte |
ATOMID_N6 |
static byte |
ATOMID_N7 |
static byte |
ATOMID_N9 |
static int |
ATOMID_NUCLEIC_MASK |
static byte |
ATOMID_NUCLEIC_PHOSPHORUS |
static byte |
ATOMID_O1 |
static byte |
ATOMID_O1P |
static byte |
ATOMID_O2 |
static byte |
ATOMID_O2_PRIME |
static byte |
ATOMID_O2P |
static byte |
ATOMID_O3_PRIME |
static byte |
ATOMID_O4 |
static byte |
ATOMID_O5_PRIME |
static byte |
ATOMID_O5T_TERMINUS |
static byte |
ATOMID_O6 |
static byte |
ATOMID_OP1 |
static byte |
ATOMID_OP2 |
static int |
ATOMID_PHOSPHORUS_ONLY_MASK |
static int |
ATOMID_PROTEIN_MASK |
static byte |
ATOMID_S4 |
static byte |
ATOMID_SG |
static byte |
ATOMID_TERMINATING_OXT |
static int |
AXES_DEFAULT_FONTSIZE |
static int |
AXES_MODE_BOUNDBOX
axes modes
|
static int |
AXES_MODE_MOLECULAR |
static int |
AXES_MODE_UNITCELL |
static 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 |
BACKBONE_VISIBILITY_FLAG |
static int |
BACKLIT |
private static java.lang.String[] |
bondOrderNames |
private static java.lang.String[] |
bondOrderNumbers |
private static int[] |
bondOrderValues |
(package private) static java.util.BitSet |
bsAnions |
(package private) static java.util.BitSet |
bsCations |
static int |
CALLBACK_ANIMFRAME |
static int |
CALLBACK_CLICK |
static int |
CALLBACK_COUNT |
static int |
CALLBACK_ECHO |
static int |
CALLBACK_ERROR |
static int |
CALLBACK_EVAL |
static int |
CALLBACK_HOVER |
static int |
CALLBACK_LOADSTRUCT |
static int |
CALLBACK_MEASURE |
static int |
CALLBACK_MESSAGE |
static int |
CALLBACK_MINIMIZATION |
static int |
CALLBACK_PICK |
static int |
CALLBACK_RESIZE |
static int |
CALLBACK_SCRIPT |
static int |
CALLBACK_SYNC |
private static 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 |
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 |
DEFAULT_STEREO_DEGREES |
static float |
DEFAULT_STRUT_RADIUS |
static int |
DRAW_ARC |
static int |
DRAW_ARROW |
static int |
DRAW_CIRCLE |
static int |
DRAW_CIRCULARPLANE |
static int |
DRAW_CURVE |
static int |
DRAW_CYLINDER |
static int |
DRAW_LINE |
static int |
DRAW_LINE_SEGMENT |
static int |
DRAW_MULTIPLE |
static int |
DRAW_NONE |
static int |
DRAW_PLANE |
static int |
DRAW_POINT |
static int |
DRAW_POLYGON |
static int |
DRAW_TRIANGLE |
static java.lang.String |
EMBEDDED_SCRIPT_TAG |
static java.lang.String |
EXPORT_DRIVER_LIST |
static int |
FILE_STATUS_MODELS_DELETED |
static int |
FILE_STATUS_MODELSET_CREATED |
static int |
FILE_STATUS_NOT_LOADED |
static int |
FILE_STATUS_ZAPPED |
static 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_CYSTEINE |
static int |
GROUPID_PROLINE |
private static int |
GROUPID_SOLVENTS |
private static int |
GROUPID_SULPHATE |
private static int |
GROUPID_WATER |
private static java.util.Hashtable |
htSpecialAtoms |
static int |
INFO_A |
static int |
INFO_ALPHA |
static int |
INFO_B |
static int |
INFO_BETA |
static int |
INFO_C |
static int |
INFO_DIMENSIONS |
static int |
INFO_GAMMA |
static int |
JMOL_DATA_OTHER |
static int |
JMOL_DATA_QUATERNION |
static int |
JMOL_DATA_RAMACHANDRAN |
static int |
LABEL_DEFAULT_FONTSIZE |
static int |
LABEL_DEFAULT_X_OFFSET |
static int |
LABEL_DEFAULT_Y_OFFSET |
static int |
LABEL_MAXIMUM_FONTSIZE |
static int |
LABEL_MINIMUM_FONTSIZE |
static java.lang.String |
LOAD_ATOM_DATA_TYPES |
static short |
madMultipleBondSmallMaximum |
static int |
MAXIMUM_AUTO_BOND_COUNT |
static int |
MEASURE_DEFAULT_FONTSIZE |
static int |
MINIMIZATION_ATOM_MAX |
static float |
MINIMIZE_FIXED_RANGE |
static java.lang.String |
MODELKIT_ZAP_STRING |
static java.lang.String |
MODELKIT_ZAP_TITLE |
static int |
MOUSE_DELETE |
static int |
MOUSE_MEASURE |
static int |
MOUSE_NONE |
static int |
MOUSE_PICK |
static int |
MOUSE_POPUP_MENU |
static int |
MOUSE_ROTATE |
static int |
MOUSE_ROTATE_Z |
static int |
MOUSE_SLAB_PLANE |
static int |
MOUSE_XLATE |
static int |
MOUSE_ZOOM |
static byte |
MULTIBOND_ALWAYS |
static byte |
MULTIBOND_NEVER |
static byte |
MULTIBOND_NOTSMALL |
static byte |
MULTIBOND_WIREFRAME |
static boolean |
officialRelease |
static byte |
PALETTE_ALTLOC |
static byte |
PALETTE_AMINO |
static byte |
PALETTE_CHAIN |
static byte |
PALETTE_CPK |
static byte |
PALETTE_ENERGY |
static byte |
PALETTE_FIXEDTEMP |
static byte |
PALETTE_FORMAL_CHARGE |
static byte |
PALETTE_GROUP |
static byte |
PALETTE_INSERTION |
static byte |
PALETTE_JMOL |
static byte |
PALETTE_MOLECULE |
static byte |
PALETTE_MONOMER |
static byte |
PALETTE_NONE |
static byte |
PALETTE_PARTIAL_CHARGE |
static byte |
PALETTE_POLYMER |
static byte |
PALETTE_PROPERTY |
static byte |
PALETTE_RASMOL |
static byte |
PALETTE_SHAPELY |
static byte |
PALETTE_STATIC |
static byte |
PALETTE_STRAIGHTNESS |
static byte |
PALETTE_STRUCTURE |
static byte |
PALETTE_SURFACE |
static byte |
PALETTE_TEMP |
static byte |
PALETTE_TYPE |
static byte |
PALETTE_UNKNOWN |
static byte |
PALETTE_VARIABLE |
static byte |
PALETTE_VOLATILE |
private static int |
paletteCount |
private static byte[] |
paletteIDs |
private static 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 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_CARBOHYDRATE |
static byte |
PROTEIN_STRUCTURE_DNA |
static byte |
PROTEIN_STRUCTURE_HELIX |
static byte |
PROTEIN_STRUCTURE_HELIX_310 |
static byte |
PROTEIN_STRUCTURE_HELIX_ALPHA |
static byte |
PROTEIN_STRUCTURE_HELIX_PI |
static byte |
PROTEIN_STRUCTURE_NONE |
static byte |
PROTEIN_STRUCTURE_NOT
Default table of PdbStructure colors
|
static byte |
PROTEIN_STRUCTURE_RNA |
static byte |
PROTEIN_STRUCTURE_SHEET |
static byte |
PROTEIN_STRUCTURE_TURN |
private static java.lang.String[] |
proteinStructureNames |
private static int[] |
quantumShellIDs |
private static java.lang.String[] |
quantumShellTags |
static float |
radiansPerDegree |
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_PLOT3D |
static int |
SHAPE_PMESH |
static int |
SHAPE_POLYHEDRA |
static int |
SHAPE_RIBBONS |
static int |
SHAPE_ROCKETS |
static int |
SHAPE_SSSTICKS |
static int |
SHAPE_STARS |
static int |
SHAPE_STICKS |
static int |
SHAPE_STRANDS |
static int |
SHAPE_STRUTS |
static int |
SHAPE_TRACE |
static int |
SHAPE_UCCAGE |
static int |
SHAPE_VECTORS |
static java.lang.String[] |
shapeClassBases |
static int |
SHELL_D_CARTESIAN |
static int |
SHELL_D_SPHERICAL |
static int |
SHELL_F_CARTESIAN |
static int |
SHELL_F_SPHERICAL |
static int |
SHELL_G_CARTESIAN |
static int |
SHELL_G_SPHERICAL |
static int |
SHELL_H_CARTESIAN |
static int |
SHELL_H_SPHERICAL |
static int |
SHELL_L |
static int |
SHELL_P |
static int |
SHELL_S |
static int |
SHELL_SP |
private static java.lang.String[][] |
shellOrder |
private static java.lang.String[] |
specialAtomNames |
static int |
STEREO_CUSTOM |
static int |
STEREO_DOUBLE |
static int |
STEREO_NONE |
static int |
STEREO_REDBLUE |
static int |
STEREO_REDCYAN |
static int |
STEREO_REDGREEN |
static int |
STEREO_UNKNOWN |
private static java.lang.String[] |
stereoModes |
static java.lang.String |
SUPPORTED_BASES |
static java.lang.String |
SUPPORTED_BASIS_FUNCTIONS |
static javax.vecmath.Vector3f[] |
unitAxisVectors |
static short[] |
vanderwaalsMars
Default table of van der Waals Radii.
|
static int |
VDW_AUTO |
static int |
VDW_AUTO_BABEL |
static int |
VDW_AUTO_JMOL |
static int |
VDW_AUTO_RASMOL |
static int |
VDW_BABEL |
static int |
VDW_BABEL21 |
static int |
VDW_JMOL |
static int |
VDW_NOJMOL |
static int |
VDW_RASMOL |
static int |
VDW_UNKNOWN |
static int |
VDW_USER |
(package private) static java.lang.String[] |
vdwLabels |
static java.lang.String |
version |
static int |
XY_ZTOP |
Constructor and Description |
---|
JmolConstants() |
Modifier and Type | Method and Description |
---|---|
static boolean |
checkCarbohydrate(java.lang.String group3) |
static java.lang.String |
embedScript(java.lang.String s) |
static int |
getArgbHbondType(int order) |
static float |
getBondingRadiusFloat(int atomicNumber,
int charge) |
private static float |
getBondingRadiusFloat(int atomicNumber,
int charge,
short[] table) |
static int |
getBondOrderFromFloat(float fOrder) |
static int |
getBondOrderFromString(java.lang.String bondOrderString) |
static java.lang.String |
getBondOrderNameFromOrder(int order) |
static java.lang.String |
getBondOrderNumberFromOrder(int 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 |
getCmlOrder(int order) |
static int |
getCovalentBondOrder(int order) |
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 int |
getPartialBondOrder(int order) |
static int |
getPartialBondOrderFromInteger(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m
and returns (n % 6) << 5 + (m % 0x1F)
|
static java.lang.String |
getProteinStructureName(int itype,
boolean isGeneric) |
static byte |
getProteinStructureType(java.lang.String type) |
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 |
getShapeClassName(int shapeID) |
static int |
getShapeVisibilityFlag(int shapeID) |
static java.lang.String[] |
getShellOrder(int i) |
static java.lang.String |
getSpecialAtomName(int atomID) |
static int |
getStereoMode(java.lang.String id) |
(package private) static java.lang.String |
getStereoModeName(int mode) |
static int |
getVanderwaalsMar(int i,
int iType) |
static java.lang.String |
getVdwLabel(int i) |
static int |
getVdwType(java.lang.String label) |
static boolean |
isHetero(java.lang.String group3) |
static boolean |
isPaletteVariable(byte pid) |
static boolean |
isShapeSecondary(int i) |
static byte |
lookupSpecialAtomID(java.lang.String atomName) |
static int |
modelValue(java.lang.String strDecimal) |
static byte |
pidOf(java.lang.Object value) |
static int |
shapeTokenIndex(int tok) |
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 java.lang.String SCRIPT_EDITOR_IGNORE
public static final int CALLBACK_ANIMFRAME
public static final int CALLBACK_ECHO
public static final int CALLBACK_ERROR
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_CLICK
public static final int CALLBACK_COUNT
public static final int FILE_STATUS_NOT_LOADED
public static final int FILE_STATUS_ZAPPED
public static final int FILE_STATUS_MODELSET_CREATED
public static final int FILE_STATUS_MODELS_DELETED
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 INFO_DIMENSIONS
public static final int JMOL_DATA_OTHER
public static final int JMOL_DATA_RAMACHANDRAN
public static final int JMOL_DATA_QUATERNION
public static final java.lang.String allowedQuaternionFrames
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 DRAW_LINE_SEGMENT
public static final int DRAW_POLYGON
public static final javax.vecmath.Vector3f center
public static final javax.vecmath.Vector3f axisX
public static final javax.vecmath.Vector3f axisY
public static final javax.vecmath.Vector3f axisZ
public static final javax.vecmath.Vector3f axisNX
public static final javax.vecmath.Vector3f axisNY
public static final javax.vecmath.Vector3f axisNZ
public static final javax.vecmath.Vector3f[] unitAxisVectors
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_STRUT_RADIUS
public static final float DEFAULT_BOND_TOLERANCE
public static final float DEFAULT_MIN_BOND_DISTANCE
public static final float DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE
public static final int MINIMIZATION_ATOM_MAX
public static final float MINIMIZE_FIXED_RANGE
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 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[] argbsHbondType
private static final java.lang.String[] bondOrderNames
private static final java.lang.String[] bondOrderNumbers
private static final int[] bondOrderValues
public static final float ANGSTROMS_PER_BOHR
public static final int FRONTLIT
public static final int BACKLIT
public static final int FULLYLIT
public static final int[] altArgbsCpk
public static final int firstIsotope
public static final int VDW_UNKNOWN
public static final int VDW_JMOL
public static final int VDW_BABEL
public static final int VDW_RASMOL
public static final int VDW_BABEL21
public static final int VDW_AUTO_JMOL
public static final int VDW_AUTO_BABEL
public static final int VDW_AUTO_RASMOL
public static final int VDW_NOJMOL
public static final int VDW_AUTO
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_ENERGY
public static final byte PALETTE_PROPERTY
public static final byte PALETTE_VARIABLE
public static final byte PALETTE_STRAIGHTNESS
public static final byte PALETTE_POLYMER
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_NOT
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 byte PROTEIN_STRUCTURE_CARBOHYDRATE
public static final byte PROTEIN_STRUCTURE_HELIX_310
public static final byte PROTEIN_STRUCTURE_HELIX_ALPHA
public static final byte PROTEIN_STRUCTURE_HELIX_PI
private 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
private 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_C4_PRIME
public static final byte ATOMID_C3_PRIME
public static final byte ATOMID_O3_PRIME
public static final byte ATOMID_C1_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_CARBONYL_OD1
public static final byte ATOMID_CARBONYL_OD2
public static final byte ATOMID_CARBONYL_OE1
public static final byte ATOMID_CARBONYL_OE2
public static final byte ATOMID_SG
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
private static java.util.Hashtable htSpecialAtoms
public static final int GROUPID_CYSTEINE
public static final int GROUPID_PROLINE
public static final int GROUPID_AMINO_MAX
private static final int GROUPID_WATER
private static final int GROUPID_SOLVENTS
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 MODELKIT_ZAP_STRING
public static final java.lang.String MODELKIT_ZAP_TITLE
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_STRUTS
public static final int SHAPE_LABELS
public static final int SHAPE_MEASURES
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_DOTS
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_PLOT3D
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 ATOM_IN_FRAME
public static final int ATOM_SLABBED
public static final java.lang.String PREVIOUS_MESH_ID
public static final int CARTOON_VISIBILITY_FLAG
public static final int BACKBONE_VISIBILITY_FLAG
public static final int ALPHA_CARBON_VISIBILITY_FLAG
public static final int DEFAULT_STEREO_DEGREES
public static final int STEREO_UNKNOWN
public static final int STEREO_NONE
public static final int STEREO_DOUBLE
public static final int STEREO_REDCYAN
public static final int STEREO_REDBLUE
public static final int STEREO_REDGREEN
public static final int STEREO_CUSTOM
private static final java.lang.String[] stereoModes
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_SPHERICAL
public static final int SHELL_D_CARTESIAN
public static final int SHELL_F_SPHERICAL
public static final int SHELL_F_CARTESIAN
public static final int SHELL_G_SPHERICAL
public static final int SHELL_G_CARTESIAN
public static final int SHELL_H_SPHERICAL
public static final int SHELL_H_CARTESIAN
public static final java.lang.String SUPPORTED_BASIS_FUNCTIONS
private static final java.lang.String[] quantumShellTags
private static final int[] quantumShellIDs
public static final java.lang.String SUPPORTED_BASES
private static final java.lang.String[][] shellOrder
public static final java.lang.String LOAD_ATOM_DATA_TYPES
public static final int ANIMATION_ONCE
public static final int ANIMATION_LOOP
public static final int ANIMATION_PALINDROME
public static final float radiansPerDegree
public static java.lang.String embedScript(java.lang.String s)
public static java.lang.String getCallbackName(int i)
public static int getCallbackId(java.lang.String callbackName)
public static java.lang.String getDrawTypeName(int drawType)
public static int getArgbHbondType(int order)
public static final int getBondOrderFromString(java.lang.String bondOrderString)
public static final int getPartialBondOrderFromInteger(int bondOrderInteger)
bondOrderInteger
- public static final int getCovalentBondOrder(int order)
public static final int getPartialBondOrder(int order)
public static final int getPartialBondDotted(int order)
public static final int getBondOrderFromFloat(float fOrder)
public static final java.lang.String getBondOrderNameFromOrder(int order)
public static java.lang.String getCmlOrder(int order)
public static final java.lang.String getBondOrderNumberFromOrder(int order)
order
- public static java.lang.String getVdwLabel(int i)
public static int getVdwType(java.lang.String label)
public static int getVanderwaalsMar(int i, int iType)
public static float getBondingRadiusFloat(int atomicNumber, int charge)
private static float getBondingRadiusFloat(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, boolean isGeneric)
public static final byte getProteinStructureType(java.lang.String type)
public static final java.lang.String getSpecialAtomName(int atomID)
public static byte lookupSpecialAtomID(java.lang.String atomName)
public static final boolean checkCarbohydrate(java.lang.String group3)
group3
- a potential group3 nameprivate static final java.lang.String getGroup3List()
public static final boolean isHetero(java.lang.String group3)
public static final boolean isShapeSecondary(int i)
public static final int shapeTokenIndex(int tok)
public static final java.lang.String getShapeClassName(int shapeID)
public static final int getShapeVisibilityFlag(int shapeID)
public 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 int modelValue(java.lang.String strDecimal)