org.jmol.viewer
Class JmolConstants
public final
class
JmolConstants
extends Object
Field Summary |
static int | ALPHA_CARBON_VISIBILITY_FLAG |
static float | ANGSTROMS_PER_BOHR |
static byte | ATOMID_ALPHA_CARBON |
static int | ATOMID_ALPHA_ONLY_MASK |
static byte | ATOMID_AMINO_NITROGEN |
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_O2P |
static byte | ATOMID_O2_PRIME |
static byte | ATOMID_O3_PRIME |
static byte | ATOMID_O4 |
static byte | ATOMID_O5T_TERMINUS |
static byte | ATOMID_O5_PRIME |
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 | ATOM_IN_MODEL |
static int | ATOM_SLABBED |
static int | AXES_DEFAULT_FONTSIZE |
static int | AXES_MODE_BOUNDBOX
axes modes |
static int | AXES_MODE_MOLECULAR |
static int | AXES_MODE_UNITCELL |
static String | allCarbohydrates |
static int[] | altArgbsCpk |
static int | altElementMax
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 int | argbShapelyBackbone |
static int | argbShapelyDefault |
static int | argbShapelySpecial |
static String[] | bondOrderNames |
static String[] | bondOrderNumbers |
static short[] | bondOrderValues |
static BitSet | bsAnions |
static BitSet | bsCations |
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_HBOND_SHIFT |
static short | BOND_HYDROGEN_MASK |
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_NEW |
static short | BOND_ORDER_ANY
Extended Bond Definition Types
|
static short | BOND_ORDER_NULL |
static short | BOND_ORDER_UNSPECIFIED |
static short | BOND_PARTIAL01 |
static short | BOND_PARTIAL12 |
static short | BOND_PARTIAL23 |
static short | BOND_PARTIAL32 |
static short | BOND_PARTIAL_MASK |
static short | BOND_STEREO_FAR |
static short | BOND_STEREO_MASK |
static short | BOND_STEREO_NEAR |
static short | BOND_SULFUR_MASK |
static String[] | callbackNames |
static short[] | cationLookupTable |
static String[] | connectOperationStrings |
static String | copyright |
static short[] | covalentMars
Default table of covalent Radii
stored as a short mar ... |
static String | cvsDate |
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 |
static int | CARTOON_VISIBILITY_FLAG |
static String | CLASSBASE_OPTIONS |
static int | CONNECT_AUTO_BOND |
static int | CONNECT_CREATE_ONLY |
static int | CONNECT_DELETE_BONDS |
static int | CONNECT_IDENTIFY_ONLY |
static int | CONNECT_MODIFY_ONLY |
static int | CONNECT_MODIFY_OR_CREATE |
static String | date |
static short | DEFAULT_BOND_MILLIANGSTROM_RADIUS |
static float | DEFAULT_BOND_RADIUS |
static float | DEFAULT_BOND_TOLERANCE |
static String | DEFAULT_FONTFACE |
static String | DEFAULT_FONTSTYLE |
static String | DEFAULT_HELP_PATH |
static float | DEFAULT_MAX_CONNECT_DISTANCE |
static float | DEFAULT_MIN_BOND_DISTANCE |
static float | DEFAULT_MIN_CONNECT_DISTANCE |
static int | DEFAULT_PERCENT_VDW_ATOM |
static int | 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 |
static String[] | elementNames |
static int | elementNumberMax
one larger than the last elementNumber, same as elementSymbols.length |
static String[] | elementSymbols
The default elementSymbols. |
static String | EMBEDDED_SCRIPT_TAG |
static 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 String | group3List |
static int | GROUPID_AMINO_MAX |
static int | GROUPID_PROLINE |
static int | GROUPID_SULPHATE |
static int | GROUPID_WATER |
static 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 |
static String | naturalIsotopes |
static boolean | officialRelease |
static int | paletteCount |
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 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 |
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 | 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 |
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 |
static 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 int[] | quantumShellIDs |
static String[] | quantumShellTags |
static String[] | shapeClassBases |
static int[] | shapeToks |
static String[][] | shellOrder |
static String[] | specialAtomNames |
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 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 |
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 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 String | version |
static int | VDW_BABEL |
static int | VDW_JMOL |
static int | VDW_RASMOL |
static int | VDW_USER |
static int | XY_ZTOP |
public static int ALPHA_CARBON_VISIBILITY_FLAG
public static final float ANGSTROMS_PER_BOHR
public static final byte ATOMID_ALPHA_CARBON
public static final int ATOMID_ALPHA_ONLY_MASK
public static final byte ATOMID_AMINO_NITROGEN
private static final int ATOMID_BACKBONE_MIN
public static final byte ATOMID_C2
public static final byte ATOMID_C3_PRIME
public static final byte ATOMID_C4
public static final byte ATOMID_C5
public static final byte ATOMID_C5M
public static final byte ATOMID_C6
public static final byte ATOMID_C7
public static final byte ATOMID_C8
public static final byte ATOMID_CARBONYL_CARBON
public static final byte ATOMID_CARBONYL_OXYGEN
public static final int ATOMID_DISTINGUISHING_ATOM_MAX
public static final byte ATOMID_H3T_TERMINUS
public static final byte ATOMID_H5T_TERMINUS
public static final byte ATOMID_HO3_PRIME
public static final byte ATOMID_HO5_PRIME
public static final int ATOMID_MAX
public static final byte ATOMID_N1
public static final byte ATOMID_N2
public static final byte ATOMID_N3
public static final byte ATOMID_N4
public static final byte ATOMID_N6
public static final byte ATOMID_N7
public static final byte ATOMID_N9
public static final int ATOMID_NUCLEIC_MASK
public static final byte ATOMID_NUCLEIC_PHOSPHORUS
public static final byte ATOMID_O1
public static final byte ATOMID_O1P
public static final byte ATOMID_O2
public static final byte ATOMID_O2P
public static final byte ATOMID_O2_PRIME
public static final byte ATOMID_O3_PRIME
public static final byte ATOMID_O4
public static final byte ATOMID_O5T_TERMINUS
public static final byte ATOMID_O5_PRIME
public static final byte ATOMID_O6
public static final byte ATOMID_OP1
public static final byte ATOMID_OP2
public static final int ATOMID_PHOSPHORUS_ONLY_MASK
public static final int ATOMID_PROTEIN_MASK
public static final byte ATOMID_S4
public static final byte ATOMID_TERMINATING_OXT
public static final int ATOM_IN_MODEL
public static final int ATOM_SLABBED
public static final int AXES_DEFAULT_FONTSIZE
public static final int AXES_MODE_BOUNDBOX
axes modes
public static final int AXES_MODE_MOLECULAR
public static final int AXES_MODE_UNITCELL
private static final String allCarbohydrates
public static final int[] altArgbsCpk
public static final int altElementMax
length of the altElementSymbols, altElementNames, altElementNumbers arrays
private static final String[] altElementNames
private static final short[] altElementNumbers
private static final String[] altElementSymbols
private static final short[] anionLookupTable
public static final int[] argbsAmino
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
public static final int[] argbsChainHetero
public static final int[] argbsCpk
Default table of CPK atom colors.
ghemical colors with a few proposed modifications
public static final int[] argbsCpkRasmol
public static final int[] argbsFormalCharge
public static final int[] argbsHbondType
public static final int[] argbsIsosurfaceNegative
public static final int[] argbsIsosurfacePositive
public static final int[] argbsRoygbScale
public static final int[] argbsRwbScale
public static final int[] argbsShapely
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.
public static final int argbShapelyBackbone
public static final int argbShapelyDefault
public static final int argbShapelySpecial
private static final String[] bondOrderNames
private static final String[] bondOrderNumbers
private static final short[] bondOrderValues
static BitSet bsAnions
static BitSet bsCations
public static final int BACKLIT
public static final short BOND_AROMATIC
public static final short BOND_AROMATIC_DOUBLE
public static final short BOND_AROMATIC_MASK
public static final short BOND_AROMATIC_SINGLE
public static final short BOND_COVALENT_DOUBLE
public static final short BOND_COVALENT_MASK
public static final short BOND_COVALENT_QUADRUPLE
public static final short BOND_COVALENT_SINGLE
public static final short BOND_COVALENT_TRIPLE
public static final short BOND_HBOND_SHIFT
public static final short BOND_HYDROGEN_MASK
public static final short BOND_H_CALC
public static final short BOND_H_CALC_MASK
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 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_REGULAR
public static final short BOND_NEW
public static final short BOND_ORDER_ANY
Extended Bond Definition Types
public static final short BOND_ORDER_NULL
public static final short BOND_ORDER_UNSPECIFIED
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_PARTIAL_MASK
public static final short BOND_STEREO_FAR
public static final short BOND_STEREO_MASK
public static final short BOND_STEREO_NEAR
public static final short BOND_SULFUR_MASK
private static final String[] callbackNames
private static final short[] cationLookupTable
private static final String[] connectOperationStrings
public static final String copyright
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
public static final String cvsDate
public static final int CALLBACK_ANIMFRAME
public static final int CALLBACK_COUNT
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 int CARTOON_VISIBILITY_FLAG
public static final String CLASSBASE_OPTIONS
public static final int CONNECT_AUTO_BOND
public static final int CONNECT_CREATE_ONLY
public static final int CONNECT_DELETE_BONDS
public static final int CONNECT_IDENTIFY_ONLY
public static final int CONNECT_MODIFY_ONLY
public static final int CONNECT_MODIFY_OR_CREATE
public static final String date
public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS
public static final float DEFAULT_BOND_RADIUS
public static final float DEFAULT_BOND_TOLERANCE
public static final String DEFAULT_FONTFACE
public static final String DEFAULT_FONTSTYLE
public static final String DEFAULT_HELP_PATH
public static final float DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MIN_BOND_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE
public static final int DEFAULT_PERCENT_VDW_ATOM
public static final int DRAW_ARC
public static final int DRAW_ARROW
public static final int DRAW_CIRCLE
public static final int DRAW_CIRCULARPLANE
public static final int DRAW_CURVE
public static final int DRAW_CYLINDER
public static final int DRAW_LINE
public static final int DRAW_MULTIPLE
public static final int DRAW_NONE
public static final int DRAW_PLANE
public static final int DRAW_POINT
public static final int DRAW_TRIANGLE
private static final String[] elementNames
public static final int elementNumberMax
one larger than the last elementNumber, same as elementSymbols.length
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".
public static final String EMBEDDED_SCRIPT_TAG
public static final String EXPORT_DRIVER_LIST
public static final int firstIsotope
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
public static final short FORMAL_CHARGE_COLIX_BLUE
public static final short FORMAL_CHARGE_COLIX_RED
public static final short FORMAL_CHARGE_COLIX_WHITE
public static final int FORMAL_CHARGE_INDEX_MAX
public static final int FORMAL_CHARGE_INDEX_WHITE
public static final int FORMAL_CHARGE_MAX
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
public static final int FORMAL_CHARGE_RANGE_SIZE
public static final int FRONTLIT
public static final int FULLYLIT
public static final int group3Count
public static final String group3List
public static final int GROUPID_AMINO_MAX
public static final int GROUPID_PROLINE
private static final int GROUPID_SULPHATE
private static final int GROUPID_WATER
private static Hashtable htElementMap
public static final int INFO_A
public static final int INFO_ALPHA
public static final int INFO_B
public static final int INFO_BETA
public static final int INFO_C
public static final int INFO_GAMMA
public static final int JMOL_DATA_OTHER
public static final int JMOL_DATA_QUATERNION
public static final int JMOL_DATA_RAMACHANDRAN
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 LABEL_MAXIMUM_FONTSIZE
public static final int LABEL_MINIMUM_FONTSIZE
public static final short madMultipleBondSmallMaximum
public static final int MAXIMUM_AUTO_BOND_COUNT
public static final int MEASURE_DEFAULT_FONTSIZE
public static final int MOUSE_DELETE
public static final int MOUSE_MEASURE
public static final int MOUSE_NONE
public static final int MOUSE_PICK
public static final int MOUSE_POPUP_MENU
public static final int MOUSE_ROTATE
public static final int MOUSE_ROTATE_Z
public static final int MOUSE_SLAB_PLANE
public static final int MOUSE_XLATE
public static final int MOUSE_ZOOM
public static final byte MULTIBOND_ALWAYS
public static final byte MULTIBOND_NEVER
public static final byte MULTIBOND_NOTSMALL
public static final byte MULTIBOND_WIREFRAME
private static final String naturalIsotopes
public static final boolean officialRelease
private static final int paletteCount
private static final byte[] paletteIDs
private static final String[] paletteNames
private static final String[] pickingModeNames
private static final String[] pickingStyleNames
public static final char[] predefinedGroup1Names
public static final String[] predefinedGroup3Names
public static String[] predefinedStatic
public static String[] predefinedVariable
public static final String[] proteinStructureNames
public static final byte PALETTE_ALTLOC
public static final byte PALETTE_AMINO
public static final byte PALETTE_CHAIN
public static final byte PALETTE_CPK
public static final byte PALETTE_FIXEDTEMP
public static final byte PALETTE_FORMAL_CHARGE
public static final byte PALETTE_GROUP
public static final byte PALETTE_INSERTION
public static final byte PALETTE_JMOL
public static final byte PALETTE_MOLECULE
public static final byte PALETTE_MONOMER
public static final byte PALETTE_NONE
public static final byte PALETTE_PARTIAL_CHARGE
public static final byte PALETTE_PROPERTY
public static final byte PALETTE_RASMOL
public static final byte PALETTE_SHAPELY
public static final byte PALETTE_STATIC
public static final byte PALETTE_STRAIGHTNESS
public static final byte PALETTE_STRUCTURE
public static final byte PALETTE_SURFACE
public static final byte PALETTE_TEMP
public static final byte PALETTE_TYPE
public static final byte PALETTE_UNKNOWN
public static final byte PALETTE_VARIABLE
public static final byte PALETTE_VOLATILE
public static final short PARTIAL_CHARGE_COLIX_BLUE
public static final short PARTIAL_CHARGE_COLIX_RED
public static final short PARTIAL_CHARGE_COLIX_WHITE
public static final int PARTIAL_CHARGE_RANGE_SIZE
public static final int PICKINGSTYLE_MEASURE_OFF
public static final int PICKINGSTYLE_MEASURE_ON
public static final int PICKINGSTYLE_SELECT_CHIME
public static final int PICKINGSTYLE_SELECT_DRAG
public static final int PICKINGSTYLE_SELECT_JMOL
picking styles
public static final int PICKINGSTYLE_SELECT_PFAAT
public static final int PICKINGSTYLE_SELECT_RASMOL
public static final int PICKING_CENTER
public static final int PICKING_DRAW
public static final int PICKING_IDENT
public static final int PICKING_LABEL
public static final int PICKING_MEASURE
public static final int PICKING_MEASURE_ANGLE
public static final int PICKING_MEASURE_DISTANCE
public static final int PICKING_MEASURE_TORSION
public static final int PICKING_NAVIGATE
public static final int PICKING_OFF
picking modes
public static final int PICKING_SELECT_ATOM
public static final int PICKING_SELECT_CHAIN
public static final int PICKING_SELECT_DRAG
public static final int PICKING_SELECT_ELEMENT
public static final int PICKING_SELECT_GROUP
public static final int PICKING_SELECT_MOLECULE
public static final int PICKING_SELECT_SITE
public static final int PICKING_SPIN
public static final String PREVIOUS_MESH_ID
public static final byte PROTEIN_STRUCTURE_DNA
public static final byte PROTEIN_STRUCTURE_HELIX
public static final byte PROTEIN_STRUCTURE_NONE
Default table of PdbStructure colors
public static final byte PROTEIN_STRUCTURE_RNA
public static final byte PROTEIN_STRUCTURE_SHEET
public static final byte PROTEIN_STRUCTURE_TURN
private static final int[] quantumShellIDs
private static final String[] quantumShellTags
public static final String[] shapeClassBases
public static final int[] shapeToks
private static final String[][] shellOrder
public static final String[] specialAtomNames
public static final int SHAPE_AXES
public static final int SHAPE_BACKBONE
public static final int SHAPE_BALLS
public static final int SHAPE_BBCAGE
public static final int SHAPE_CARTOON
public static final int SHAPE_DIPOLES
public static final int SHAPE_DOTS
public static final int SHAPE_DRAW
public static final int SHAPE_ECHO
public static final int SHAPE_ELLIPSOIDS
public static final int SHAPE_FRANK
public static final int SHAPE_GEOSURFACE
public static final int SHAPE_HALOS
public static final int SHAPE_HOVER
public static final int SHAPE_HSTICKS
public static final int SHAPE_ISOSURFACE
public static final int SHAPE_LABELS
public static final int SHAPE_LCAOCARTOON
public static final int SHAPE_MAX
public static final int SHAPE_MAX_HAS_ID
public static final int SHAPE_MAX_MESH_COLLECTION
public static final int SHAPE_MAX_SECONDARY
public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
public static final int SHAPE_MAX_SPECIAL
public static final int SHAPE_MAX_SURFACE
public static final int SHAPE_MEASURES
public static final int SHAPE_MESHRIBBON
public static final int SHAPE_MIN_HAS_ID
public static final int SHAPE_MIN_MESH_COLLECTION
public static final int SHAPE_MIN_SECONDARY
public static final int SHAPE_MIN_SPECIAL
public static final int SHAPE_MIN_SURFACE
public static final int SHAPE_MO
public static final int SHAPE_PMESH
public static final int SHAPE_POLYHEDRA
public static final int SHAPE_RIBBONS
public static final int SHAPE_ROCKETS
public static final int SHAPE_SSSTICKS
public static final int SHAPE_STARS
public static final int SHAPE_STICKS
public static final int SHAPE_STRANDS
public static final int SHAPE_TRACE
public static final int SHAPE_UCCAGE
public static final int SHAPE_VECTORS
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
public static final int SHELL_L
public static final int SHELL_P
public static final int SHELL_S
public static final int SHELL_SP
public static final int STEREO_CUSTOM
public static final int STEREO_DOUBLE
public static final int STEREO_NONE
public static final int STEREO_REDBLUE
public static final int STEREO_REDCYAN
public static final int STEREO_REDGREEN
public static final short[] vanderwaalsMars
static final String[] vdwLabels
public static final String version
public static final int VDW_BABEL
public static final int VDW_JMOL
public static final int VDW_RASMOL
public static final int VDW_USER
public static final int XY_ZTOP
public static final int altElementIndexFromNumber(int atomicAndIsotopeNumber)
Parameters: atomicAndIsotopeNumber (may be atomicNumber + isotopeNumber*128)
Returns: index into altElementNumbers
public static final String altElementNameFromIndex(int i)
Parameters: i index into altElementNames
Returns: elementName
public static final short altElementNumberFromIndex(int i)
Parameters: i index into altElementNumbers
Returns: elementNumber (may be atomicNumber + isotopeNumber*128)
public static final String altElementSymbolFromIndex(int i)
Parameters: i index into altElementSymbols
Returns: elementSymbol
public static final String altIsotopeSymbolFromIndex(int i)
Parameters: i index into altElementSymbols
Returns: 2H
public static final String canonicalizeQuantumSubshellTag(String tag)
public static final boolean checkCarbohydrate(String group3)
Parameters: group3 a potential group3 name
Returns: whether this is a carbohydrate from the list
public static int connectOperationFromString(String connectOperationString)
public static String connectOperationName(int i)
public static final String elementNameFromNumber(int elementNumber)
Parameters: elementNumber may be atomicNumber + isotopeNumber*128
Returns: elementName
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
public static final String elementSymbolFromNumber(int elementNumber)
Parameters: elementNumber may be atomicNumber + isotopeNumber*128
Returns: elementSymbol
public static int getArgbHbondType(short order)
public static short getBondingMar(int atomicNumber, int charge)
public static short getBondingMar(int atomicNumber, int charge, short[] table)
static final short getBondOrderFromFloat(float fOrder)
static final short getBondOrderFromString(String bondOrderString)
public static final String getBondOrderNameFromOrder(short order)
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
public static String getCallbackName(int i)
public static String getDrawTypeName(int drawType)
private static final String getGroup3List()
public static final byte getPaletteID(String paletteName)
public static final String getPaletteName(byte pid)
public static final int getPartialBondDotted(int order)
public static final short getPartialBondOrder(int order)
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
public static final int getPickingMode(String str)
public static final String getPickingModeName(int pickingMode)
public static final int getPickingStyle(String str)
public static final String getPickingStyleName(int pickingStyle)
public static final String getProteinStructureName(int itype)
public static final String getQuantumShellTag(int shell)
public static final int getQuantumShellTagID(String tag)
public static final int getQuantumShellTagIDSpherical(String tag)
public static final String getQuantumSubshellTag(int shell, int subshell)
public static final int getQuantumSubshellTagID(int shell, String tag)
public static final String getShapeClassName(int shapeID)
public static final int getShapeVisibilityFlag(int shapeID)
public static final String[] getShellOrder(int i)
public static int getVanderwaalsMar(int i, int scale)
public static int getVdwType(String label)
public static final boolean isHetero(String group3)
public static final boolean isNaturalIsotope(String isotopeSymbol)
public static boolean isPaletteVariable(byte pid)
public static final boolean isShapeSecondary(int i)
public static byte pidOf(Object value)
static final int shapeTokenIndex(int tok)