org.jmol.viewer
Class JmolConstants
java.lang.Object
org.jmol.viewer.JmolConstants
public final class JmolConstants
- extends Object
Field Summary |
private static String |
allCarbohydrates
|
static 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 Vector3f |
axisNX
|
static Vector3f |
axisNY
|
static Vector3f |
axisNZ
|
static Vector3f |
axisX
|
static Vector3f |
axisY
|
static Vector3f |
axisZ
|
static int |
BACKBONE_VISIBILITY_FLAG
|
static int |
BACKLIT
|
private static String[] |
bondOrderNames
|
private static String[] |
bondOrderNumbers
|
private static int[] |
bondOrderValues
|
(package private) static BitSet |
bsAnions
|
(package private) static 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 String[] |
callbackNames
|
static int |
CARTOON_VISIBILITY_FLAG
|
private static short[] |
cationLookupTable
|
static Vector3f |
center
|
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 |
copyright
|
private static short[] |
covalentMars
Default table of covalent Radii
stored as a short mar ... |
static String |
cvsDate
|
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 |
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 String |
EMBEDDED_SCRIPT_TAG
|
static 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 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_CYSTEINE
|
static int |
GROUPID_PROLINE
|
private static int |
GROUPID_SOLVENTS
|
private static int |
GROUPID_SULPHATE
|
private static int |
GROUPID_WATER
|
private static 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 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 String |
MODELKIT_ZAP_STRING
|
static 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 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 String[] |
predefinedGroup3Names
|
static String[] |
predefinedStatic
|
static String[] |
predefinedVariable
|
static 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 String[] |
proteinStructureNames
|
private static int[] |
quantumShellIDs
|
private static String[] |
quantumShellTags
|
static float |
radiansPerDegree
|
static 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 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 String[][] |
shellOrder
|
private static 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 String[] |
stereoModes
|
static String |
SUPPORTED_BASES
|
static String |
SUPPORTED_BASIS_FUNCTIONS
|
static 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 String[] |
vdwLabels
|
static String |
version
|
static int |
XY_ZTOP
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
copyright
public static final String copyright
- See Also:
- Constant Field Values
version
public static final String version
cvsDate
public static final String cvsDate
- See Also:
- Constant Field Values
date
public static final String date
officialRelease
public static final boolean officialRelease
- See Also:
- Constant Field Values
CLASSBASE_OPTIONS
public static final String CLASSBASE_OPTIONS
- See Also:
- Constant Field Values
DEFAULT_HELP_PATH
public static final String DEFAULT_HELP_PATH
- See Also:
- Constant Field Values
EMBEDDED_SCRIPT_TAG
public static final String EMBEDDED_SCRIPT_TAG
- See Also:
- Constant Field Values
SCRIPT_EDITOR_IGNORE
public static final String SCRIPT_EDITOR_IGNORE
- See Also:
- Constant Field Values
CALLBACK_ANIMFRAME
public static final int CALLBACK_ANIMFRAME
- See Also:
- Constant Field Values
CALLBACK_ECHO
public static final int CALLBACK_ECHO
- See Also:
- Constant Field Values
CALLBACK_ERROR
public static final int CALLBACK_ERROR
- See Also:
- Constant Field Values
CALLBACK_EVAL
public static final int CALLBACK_EVAL
- See Also:
- Constant Field Values
CALLBACK_HOVER
public static final int CALLBACK_HOVER
- See Also:
- Constant Field Values
CALLBACK_LOADSTRUCT
public static final int CALLBACK_LOADSTRUCT
- See Also:
- Constant Field Values
CALLBACK_MEASURE
public static final int CALLBACK_MEASURE
- See Also:
- Constant Field Values
CALLBACK_MESSAGE
public static final int CALLBACK_MESSAGE
- See Also:
- Constant Field Values
CALLBACK_MINIMIZATION
public static final int CALLBACK_MINIMIZATION
- See Also:
- Constant Field Values
CALLBACK_PICK
public static final int CALLBACK_PICK
- See Also:
- Constant Field Values
CALLBACK_RESIZE
public static final int CALLBACK_RESIZE
- See Also:
- Constant Field Values
CALLBACK_SCRIPT
public static final int CALLBACK_SCRIPT
- See Also:
- Constant Field Values
CALLBACK_SYNC
public static final int CALLBACK_SYNC
- See Also:
- Constant Field Values
CALLBACK_CLICK
public static final int CALLBACK_CLICK
- See Also:
- Constant Field Values
CALLBACK_COUNT
public static final int CALLBACK_COUNT
- See Also:
- Constant Field Values
FILE_STATUS_NOT_LOADED
public static final int FILE_STATUS_NOT_LOADED
- See Also:
- Constant Field Values
FILE_STATUS_ZAPPED
public static final int FILE_STATUS_ZAPPED
- See Also:
- Constant Field Values
FILE_STATUS_MODELSET_CREATED
public static final int FILE_STATUS_MODELSET_CREATED
- See Also:
- Constant Field Values
FILE_STATUS_MODELS_DELETED
public static final int FILE_STATUS_MODELS_DELETED
- See Also:
- Constant Field Values
callbackNames
private static final String[] callbackNames
INFO_A
public static final int INFO_A
- See Also:
- Constant Field Values
INFO_B
public static final int INFO_B
- See Also:
- Constant Field Values
INFO_C
public static final int INFO_C
- See Also:
- Constant Field Values
INFO_ALPHA
public static final int INFO_ALPHA
- See Also:
- Constant Field Values
INFO_BETA
public static final int INFO_BETA
- See Also:
- Constant Field Values
INFO_GAMMA
public static final int INFO_GAMMA
- See Also:
- Constant Field Values
INFO_DIMENSIONS
public static final int INFO_DIMENSIONS
- See Also:
- Constant Field Values
JMOL_DATA_OTHER
public static final int JMOL_DATA_OTHER
- See Also:
- Constant Field Values
JMOL_DATA_RAMACHANDRAN
public static final int JMOL_DATA_RAMACHANDRAN
- See Also:
- Constant Field Values
JMOL_DATA_QUATERNION
public static final int JMOL_DATA_QUATERNION
- See Also:
- Constant Field Values
allowedQuaternionFrames
public static final String allowedQuaternionFrames
- See Also:
- Constant Field Values
EXPORT_DRIVER_LIST
public static final String EXPORT_DRIVER_LIST
- See Also:
- Constant Field Values
DRAW_MULTIPLE
public static final int DRAW_MULTIPLE
- See Also:
- Constant Field Values
DRAW_NONE
public static final int DRAW_NONE
- See Also:
- Constant Field Values
DRAW_POINT
public static final int DRAW_POINT
- See Also:
- Constant Field Values
DRAW_LINE
public static final int DRAW_LINE
- See Also:
- Constant Field Values
DRAW_TRIANGLE
public static final int DRAW_TRIANGLE
- See Also:
- Constant Field Values
DRAW_PLANE
public static final int DRAW_PLANE
- See Also:
- Constant Field Values
DRAW_CYLINDER
public static final int DRAW_CYLINDER
- See Also:
- Constant Field Values
DRAW_ARROW
public static final int DRAW_ARROW
- See Also:
- Constant Field Values
DRAW_CIRCLE
public static final int DRAW_CIRCLE
- See Also:
- Constant Field Values
DRAW_CURVE
public static final int DRAW_CURVE
- See Also:
- Constant Field Values
DRAW_CIRCULARPLANE
public static final int DRAW_CIRCULARPLANE
- See Also:
- Constant Field Values
DRAW_ARC
public static final int DRAW_ARC
- See Also:
- Constant Field Values
DRAW_LINE_SEGMENT
public static final int DRAW_LINE_SEGMENT
- See Also:
- Constant Field Values
DRAW_POLYGON
public static final int DRAW_POLYGON
- See Also:
- Constant Field Values
center
public static final Vector3f center
axisX
public static final Vector3f axisX
axisY
public static final Vector3f axisY
axisZ
public static final Vector3f axisZ
axisNX
public static final Vector3f axisNX
axisNY
public static final Vector3f axisNY
axisNZ
public static final Vector3f axisNZ
unitAxisVectors
public static final Vector3f[] unitAxisVectors
XY_ZTOP
public static final int XY_ZTOP
- See Also:
- Constant Field Values
DEFAULT_PERCENT_VDW_ATOM
public static final int DEFAULT_PERCENT_VDW_ATOM
- See Also:
- Constant Field Values
DEFAULT_BOND_RADIUS
public static final float DEFAULT_BOND_RADIUS
- See Also:
- Constant Field Values
DEFAULT_BOND_MILLIANGSTROM_RADIUS
public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS
- See Also:
- Constant Field Values
DEFAULT_STRUT_RADIUS
public static final float DEFAULT_STRUT_RADIUS
- See Also:
- Constant Field Values
DEFAULT_BOND_TOLERANCE
public static final float DEFAULT_BOND_TOLERANCE
- See Also:
- Constant Field Values
DEFAULT_MIN_BOND_DISTANCE
public static final float DEFAULT_MIN_BOND_DISTANCE
- See Also:
- Constant Field Values
DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MAX_CONNECT_DISTANCE
- See Also:
- Constant Field Values
DEFAULT_MIN_CONNECT_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE
- See Also:
- Constant Field Values
MINIMIZATION_ATOM_MAX
public static final int MINIMIZATION_ATOM_MAX
- See Also:
- Constant Field Values
MINIMIZE_FIXED_RANGE
public static final float MINIMIZE_FIXED_RANGE
- See Also:
- Constant Field Values
CONNECT_DELETE_BONDS
public static final int CONNECT_DELETE_BONDS
- See Also:
- Constant Field Values
CONNECT_MODIFY_ONLY
public static final int CONNECT_MODIFY_ONLY
- See Also:
- Constant Field Values
CONNECT_CREATE_ONLY
public static final int CONNECT_CREATE_ONLY
- See Also:
- Constant Field Values
CONNECT_MODIFY_OR_CREATE
public static final int CONNECT_MODIFY_OR_CREATE
- See Also:
- Constant Field Values
CONNECT_AUTO_BOND
public static final int CONNECT_AUTO_BOND
- See Also:
- Constant Field Values
CONNECT_IDENTIFY_ONLY
public static final int CONNECT_IDENTIFY_ONLY
- See Also:
- Constant Field Values
MOUSE_NONE
public static final int MOUSE_NONE
- See Also:
- Constant Field Values
MOUSE_ROTATE
public static final int MOUSE_ROTATE
- See Also:
- Constant Field Values
MOUSE_ZOOM
public static final int MOUSE_ZOOM
- See Also:
- Constant Field Values
MOUSE_XLATE
public static final int MOUSE_XLATE
- See Also:
- Constant Field Values
MOUSE_PICK
public static final int MOUSE_PICK
- See Also:
- Constant Field Values
MOUSE_DELETE
public static final int MOUSE_DELETE
- See Also:
- Constant Field Values
MOUSE_MEASURE
public static final int MOUSE_MEASURE
- See Also:
- Constant Field Values
MOUSE_ROTATE_Z
public static final int MOUSE_ROTATE_Z
- See Also:
- Constant Field Values
MOUSE_SLAB_PLANE
public static final int MOUSE_SLAB_PLANE
- See Also:
- Constant Field Values
MOUSE_POPUP_MENU
public static final int MOUSE_POPUP_MENU
- See Also:
- Constant Field Values
MULTIBOND_NEVER
public static final byte MULTIBOND_NEVER
- See Also:
- Constant Field Values
MULTIBOND_WIREFRAME
public static final byte MULTIBOND_WIREFRAME
- See Also:
- Constant Field Values
MULTIBOND_NOTSMALL
public static final byte MULTIBOND_NOTSMALL
- See Also:
- Constant Field Values
MULTIBOND_ALWAYS
public static final byte MULTIBOND_ALWAYS
- See Also:
- Constant Field Values
madMultipleBondSmallMaximum
public static final short madMultipleBondSmallMaximum
- See Also:
- Constant Field Values
AXES_MODE_BOUNDBOX
public static final int AXES_MODE_BOUNDBOX
- axes modes
- See Also:
- Constant Field Values
AXES_MODE_MOLECULAR
public static final int AXES_MODE_MOLECULAR
- See Also:
- Constant Field Values
AXES_MODE_UNITCELL
public static final int AXES_MODE_UNITCELL
- See Also:
- Constant Field Values
argbsHbondType
public static final int[] argbsHbondType
bondOrderNames
private static final String[] bondOrderNames
bondOrderNumbers
private static final String[] bondOrderNumbers
bondOrderValues
private static final int[] bondOrderValues
ANGSTROMS_PER_BOHR
public static final float ANGSTROMS_PER_BOHR
- See Also:
- Constant Field Values
FRONTLIT
public static final int FRONTLIT
- See Also:
- Constant Field Values
BACKLIT
public static final int BACKLIT
- See Also:
- Constant Field Values
FULLYLIT
public static final int FULLYLIT
- See Also:
- Constant Field Values
altArgbsCpk
public static final int[] altArgbsCpk
VDW_UNKNOWN
public static final int VDW_UNKNOWN
- See Also:
- Constant Field Values
VDW_JMOL
public static final int VDW_JMOL
- See Also:
- Constant Field Values
VDW_BABEL
public static final int VDW_BABEL
- See Also:
- Constant Field Values
VDW_RASMOL
public static final int VDW_RASMOL
- See Also:
- Constant Field Values
VDW_BABEL21
public static final int VDW_BABEL21
- See Also:
- Constant Field Values
VDW_AUTO_JMOL
public static final int VDW_AUTO_JMOL
- See Also:
- Constant Field Values
VDW_AUTO_BABEL
public static final int VDW_AUTO_BABEL
- See Also:
- Constant Field Values
VDW_AUTO_RASMOL
public static final int VDW_AUTO_RASMOL
- See Also:
- Constant Field Values
VDW_NOJMOL
public static final int VDW_NOJMOL
- See Also:
- Constant Field Values
VDW_AUTO
public static final int VDW_AUTO
- See Also:
- Constant Field Values
VDW_USER
public static final int VDW_USER
- See Also:
- Constant Field Values
vdwLabels
static final String[] vdwLabels
vanderwaalsMars
public static final short[] vanderwaalsMars
- Default table of van der Waals Radii.
values are stored as MAR -- Milli Angstrom Radius
Used for spacefill rendering of atoms.
Values taken from OpenBabel.
Note that AUTO_JMOL, AUTO_BABEL, and AUTO_RASMOL are 4, 5, and 6, respectively,
so their mod will be JMOL, BABEL, and RASMOL. AUTO is 8, so will default to Jmol
- See Also:
- openbabel.sourceforge.net,
vdw_comparison.xls
covalentMars
private static final short[] covalentMars
- Default table of covalent Radii
stored as a short mar ... Milli Angstrom Radius
Values taken from OpenBabel.
- See Also:
- openbabel.sourceforge.net
FORMAL_CHARGE_MIN
public static final int FORMAL_CHARGE_MIN
- ionic radii are looked up using an array of shorts (16 bits each)
that contains the atomic number, the charge, and the radius in two
consecutive values, encoded as follows:
(atomicNumber << 4) + (charge + 4), radiusAngstroms*1000
That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius
This allows for charges from -4 to 11, but we only really have -4 to 7.
This data is from
Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143
(scanned for Jmol by Phillip Barak, Jan 2004)
Reorganized from two separate arrays 9/2006 by Bob Hanson, who thought
it was just too hard to look these up and, if necessary, add or modify.
At the same time, the table was split into cations and anions for easier
retrieval.
O- and N+ removed 9/2008 - BH. The problem is that
the formal charge is used to determine bonding radius.
But these formal charges are different than the charges used in
compilation of HCP data (which is crystal ionic radii).
Specifically, because O- and N+ are very common in organic
compounds, I have removed their radii from the table FOR OUR PURPOSES HERE.
I suppose there are some ionic compounds that have O- and N+ as
isolated ions, but what they would be I have no clue. Better to
be safe and go with somewhat more reasonable values.
Argh. Changed for Jmol 11.6.RC15
- See Also:
- Constant Field Values
FORMAL_CHARGE_MAX
public static final int FORMAL_CHARGE_MAX
- See Also:
- Constant Field Values
cationLookupTable
private static final short[] cationLookupTable
anionLookupTable
private static final short[] anionLookupTable
bsCations
static BitSet bsCations
bsAnions
static BitSet bsAnions
MAXIMUM_AUTO_BOND_COUNT
public static final int MAXIMUM_AUTO_BOND_COUNT
- See Also:
- Constant Field Values
PALETTE_VOLATILE
public static final byte PALETTE_VOLATILE
- See Also:
- Constant Field Values
PALETTE_STATIC
public static final byte PALETTE_STATIC
- See Also:
- Constant Field Values
PALETTE_UNKNOWN
public static final byte PALETTE_UNKNOWN
- See Also:
- Constant Field Values
PALETTE_NONE
public static final byte PALETTE_NONE
- See Also:
- Constant Field Values
PALETTE_CPK
public static final byte PALETTE_CPK
- See Also:
- Constant Field Values
PALETTE_PARTIAL_CHARGE
public static final byte PALETTE_PARTIAL_CHARGE
- See Also:
- Constant Field Values
PALETTE_FORMAL_CHARGE
public static final byte PALETTE_FORMAL_CHARGE
- See Also:
- Constant Field Values
PALETTE_TEMP
public static final byte PALETTE_TEMP
- See Also:
- Constant Field Values
PALETTE_FIXEDTEMP
public static final byte PALETTE_FIXEDTEMP
- See Also:
- Constant Field Values
PALETTE_SURFACE
public static final byte PALETTE_SURFACE
- See Also:
- Constant Field Values
PALETTE_STRUCTURE
public static final byte PALETTE_STRUCTURE
- See Also:
- Constant Field Values
PALETTE_AMINO
public static final byte PALETTE_AMINO
- See Also:
- Constant Field Values
PALETTE_SHAPELY
public static final byte PALETTE_SHAPELY
- See Also:
- Constant Field Values
PALETTE_CHAIN
public static final byte PALETTE_CHAIN
- See Also:
- Constant Field Values
PALETTE_GROUP
public static final byte PALETTE_GROUP
- See Also:
- Constant Field Values
PALETTE_MONOMER
public static final byte PALETTE_MONOMER
- See Also:
- Constant Field Values
PALETTE_MOLECULE
public static final byte PALETTE_MOLECULE
- See Also:
- Constant Field Values
PALETTE_ALTLOC
public static final byte PALETTE_ALTLOC
- See Also:
- Constant Field Values
PALETTE_INSERTION
public static final byte PALETTE_INSERTION
- See Also:
- Constant Field Values
PALETTE_JMOL
public static final byte PALETTE_JMOL
- See Also:
- Constant Field Values
PALETTE_RASMOL
public static final byte PALETTE_RASMOL
- See Also:
- Constant Field Values
PALETTE_TYPE
public static final byte PALETTE_TYPE
- See Also:
- Constant Field Values
PALETTE_ENERGY
public static final byte PALETTE_ENERGY
- See Also:
- Constant Field Values
PALETTE_PROPERTY
public static final byte PALETTE_PROPERTY
- See Also:
- Constant Field Values
PALETTE_VARIABLE
public static final byte PALETTE_VARIABLE
- See Also:
- Constant Field Values
PALETTE_STRAIGHTNESS
public static final byte PALETTE_STRAIGHTNESS
- See Also:
- Constant Field Values
PALETTE_POLYMER
public static final byte PALETTE_POLYMER
- See Also:
- Constant Field Values
paletteNames
private static final String[] paletteNames
paletteIDs
private static final byte[] paletteIDs
paletteCount
private static final int paletteCount
argbsCpk
public static final int[] argbsCpk
- Default table of CPK atom colors.
ghemical colors with a few proposed modifications
argbsCpkRasmol
public static final int[] argbsCpkRasmol
PROTEIN_STRUCTURE_NOT
public static final byte PROTEIN_STRUCTURE_NOT
- Default table of PdbStructure colors
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_NONE
public static final byte PROTEIN_STRUCTURE_NONE
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_TURN
public static final byte PROTEIN_STRUCTURE_TURN
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_SHEET
public static final byte PROTEIN_STRUCTURE_SHEET
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_HELIX
public static final byte PROTEIN_STRUCTURE_HELIX
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_DNA
public static final byte PROTEIN_STRUCTURE_DNA
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_RNA
public static final byte PROTEIN_STRUCTURE_RNA
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_CARBOHYDRATE
public static final byte PROTEIN_STRUCTURE_CARBOHYDRATE
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_HELIX_310
public static final byte PROTEIN_STRUCTURE_HELIX_310
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_HELIX_ALPHA
public static final byte PROTEIN_STRUCTURE_HELIX_ALPHA
- See Also:
- Constant Field Values
PROTEIN_STRUCTURE_HELIX_PI
public static final byte PROTEIN_STRUCTURE_HELIX_PI
- See Also:
- Constant Field Values
proteinStructureNames
private static final String[] proteinStructureNames
argbsStructure
public static final int[] argbsStructure
- In DRuMS, RasMol, and Chime, quoting from
http://www.umass.edu/microbio/rasmol/rascolor.htm
The RasMol structure color scheme colors the molecule by
protein secondary structure.
Structure Decimal RGB Hex RGB
Alpha helices red-magenta [255,0,128] FF 00 80 *
Beta strands yellow [255,200,0] FF C8 00 *
Turns pale blue [96,128,255] 60 80 FF
Other white [255,255,255] FF FF FF
Values given in the 1994 RasMol 2.5 Quick Reference Card ([240,0,128]
and [255,255,0]) are not correct for RasMol 2.6-beta-2a.
This correction was made above on Dec 5, 1998.
argbsAmino
public static final int[] argbsAmino
argbShapelyBackbone
public static final int argbShapelyBackbone
- See Also:
- Constant Field Values
argbShapelySpecial
public static final int argbShapelySpecial
- See Also:
- Constant Field Values
argbShapelyDefault
public static final int argbShapelyDefault
- See Also:
- Constant Field Values
argbsChainAtom
public static final int[] argbsChainAtom
- some pastel colors
C0D0FF - pastel blue
B0FFB0 - pastel green
B0FFFF - pastel cyan
FFC0C8 - pink
FFC0FF - pastel magenta
FFFF80 - pastel yellow
FFDEAD - navajowhite
FFD070 - pastel gold
FF9898 - light coral
B4E444 - light yellow-green
C0C000 - light olive
FF8060 - light tomato
00FF7F - springgreen
cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
argbsChainHetero
public static final int[] argbsChainHetero
FORMAL_CHARGE_COLIX_RED
public static final short FORMAL_CHARGE_COLIX_RED
FORMAL_CHARGE_COLIX_WHITE
public static final short FORMAL_CHARGE_COLIX_WHITE
FORMAL_CHARGE_COLIX_BLUE
public static final short FORMAL_CHARGE_COLIX_BLUE
FORMAL_CHARGE_RANGE_SIZE
public static final int FORMAL_CHARGE_RANGE_SIZE
- See Also:
- Constant Field Values
argbsFormalCharge
public static final int[] argbsFormalCharge
FORMAL_CHARGE_INDEX_WHITE
public static final int FORMAL_CHARGE_INDEX_WHITE
- See Also:
- Constant Field Values
FORMAL_CHARGE_INDEX_MAX
public static final int FORMAL_CHARGE_INDEX_MAX
PARTIAL_CHARGE_COLIX_RED
public static final short PARTIAL_CHARGE_COLIX_RED
PARTIAL_CHARGE_COLIX_WHITE
public static final short PARTIAL_CHARGE_COLIX_WHITE
PARTIAL_CHARGE_COLIX_BLUE
public static final short PARTIAL_CHARGE_COLIX_BLUE
PARTIAL_CHARGE_RANGE_SIZE
public static final int PARTIAL_CHARGE_RANGE_SIZE
- See Also:
- Constant Field Values
argbsRwbScale
public static final int[] argbsRwbScale
argbsRoygbScale
public static final int[] argbsRoygbScale
argbsIsosurfacePositive
public static final int[] argbsIsosurfacePositive
argbsIsosurfaceNegative
public static final int[] argbsIsosurfaceNegative
specialAtomNames
private static final String[] specialAtomNames
ATOMID_MAX
public static final int ATOMID_MAX
ATOMID_AMINO_NITROGEN
public static final byte ATOMID_AMINO_NITROGEN
- See Also:
- Constant Field Values
ATOMID_ALPHA_CARBON
public static final byte ATOMID_ALPHA_CARBON
- See Also:
- Constant Field Values
ATOMID_CARBONYL_CARBON
public static final byte ATOMID_CARBONYL_CARBON
- See Also:
- Constant Field Values
ATOMID_CARBONYL_OXYGEN
public static final byte ATOMID_CARBONYL_OXYGEN
- See Also:
- Constant Field Values
ATOMID_O1
public static final byte ATOMID_O1
- See Also:
- Constant Field Values
ATOMID_ALPHA_ONLY_MASK
public static final int ATOMID_ALPHA_ONLY_MASK
- See Also:
- Constant Field Values
ATOMID_PROTEIN_MASK
public static final int ATOMID_PROTEIN_MASK
- See Also:
- Constant Field Values
ATOMID_O5_PRIME
public static final byte ATOMID_O5_PRIME
- See Also:
- Constant Field Values
ATOMID_C4_PRIME
public static final byte ATOMID_C4_PRIME
- See Also:
- Constant Field Values
ATOMID_C3_PRIME
public static final byte ATOMID_C3_PRIME
- See Also:
- Constant Field Values
ATOMID_O3_PRIME
public static final byte ATOMID_O3_PRIME
- See Also:
- Constant Field Values
ATOMID_C1_PRIME
public static final byte ATOMID_C1_PRIME
- See Also:
- Constant Field Values
ATOMID_NUCLEIC_MASK
public static final int ATOMID_NUCLEIC_MASK
- See Also:
- Constant Field Values
ATOMID_NUCLEIC_PHOSPHORUS
public static final byte ATOMID_NUCLEIC_PHOSPHORUS
- See Also:
- Constant Field Values
ATOMID_PHOSPHORUS_ONLY_MASK
public static final int ATOMID_PHOSPHORUS_ONLY_MASK
- See Also:
- Constant Field Values
ATOMID_DISTINGUISHING_ATOM_MAX
public static final int ATOMID_DISTINGUISHING_ATOM_MAX
- See Also:
- Constant Field Values
ATOMID_CARBONYL_OD1
public static final byte ATOMID_CARBONYL_OD1
- See Also:
- Constant Field Values
ATOMID_CARBONYL_OD2
public static final byte ATOMID_CARBONYL_OD2
- See Also:
- Constant Field Values
ATOMID_CARBONYL_OE1
public static final byte ATOMID_CARBONYL_OE1
- See Also:
- Constant Field Values
ATOMID_CARBONYL_OE2
public static final byte ATOMID_CARBONYL_OE2
- See Also:
- Constant Field Values
ATOMID_SG
public static final byte ATOMID_SG
- See Also:
- Constant Field Values
ATOMID_N1
public static final byte ATOMID_N1
- See Also:
- Constant Field Values
ATOMID_C2
public static final byte ATOMID_C2
- See Also:
- Constant Field Values
ATOMID_N3
public static final byte ATOMID_N3
- See Also:
- Constant Field Values
ATOMID_C4
public static final byte ATOMID_C4
- See Also:
- Constant Field Values
ATOMID_C5
public static final byte ATOMID_C5
- See Also:
- Constant Field Values
ATOMID_C6
public static final byte ATOMID_C6
- See Also:
- Constant Field Values
ATOMID_O2
public static final byte ATOMID_O2
- See Also:
- Constant Field Values
ATOMID_N7
public static final byte ATOMID_N7
- See Also:
- Constant Field Values
ATOMID_C8
public static final byte ATOMID_C8
- See Also:
- Constant Field Values
ATOMID_N9
public static final byte ATOMID_N9
- See Also:
- Constant Field Values
ATOMID_N4
public static final byte ATOMID_N4
- See Also:
- Constant Field Values
ATOMID_N2
public static final byte ATOMID_N2
- See Also:
- Constant Field Values
ATOMID_N6
public static final byte ATOMID_N6
- See Also:
- Constant Field Values
ATOMID_C5M
public static final byte ATOMID_C5M
- See Also:
- Constant Field Values
ATOMID_O6
public static final byte ATOMID_O6
- See Also:
- Constant Field Values
ATOMID_O4
public static final byte ATOMID_O4
- See Also:
- Constant Field Values
ATOMID_S4
public static final byte ATOMID_S4
- See Also:
- Constant Field Values
ATOMID_C7
public static final byte ATOMID_C7
- See Also:
- Constant Field Values
ATOMID_BACKBONE_MIN
private static final int ATOMID_BACKBONE_MIN
- See Also:
- Constant Field Values
ATOMID_TERMINATING_OXT
public static final byte ATOMID_TERMINATING_OXT
- See Also:
- Constant Field Values
ATOMID_H5T_TERMINUS
public static final byte ATOMID_H5T_TERMINUS
- See Also:
- Constant Field Values
ATOMID_O5T_TERMINUS
public static final byte ATOMID_O5T_TERMINUS
- See Also:
- Constant Field Values
ATOMID_O1P
public static final byte ATOMID_O1P
- See Also:
- Constant Field Values
ATOMID_OP1
public static final byte ATOMID_OP1
- See Also:
- Constant Field Values
ATOMID_O2P
public static final byte ATOMID_O2P
- See Also:
- Constant Field Values
ATOMID_OP2
public static final byte ATOMID_OP2
- See Also:
- Constant Field Values
ATOMID_O2_PRIME
public static final byte ATOMID_O2_PRIME
- See Also:
- Constant Field Values
ATOMID_H3T_TERMINUS
public static final byte ATOMID_H3T_TERMINUS
- See Also:
- Constant Field Values
ATOMID_HO3_PRIME
public static final byte ATOMID_HO3_PRIME
- See Also:
- Constant Field Values
ATOMID_HO5_PRIME
public static final byte ATOMID_HO5_PRIME
- See Also:
- Constant Field Values
htSpecialAtoms
private static Hashtable htSpecialAtoms
GROUPID_CYSTEINE
public static final int GROUPID_CYSTEINE
- See Also:
- Constant Field Values
GROUPID_PROLINE
public static final int GROUPID_PROLINE
- See Also:
- Constant Field Values
GROUPID_AMINO_MAX
public static final int GROUPID_AMINO_MAX
- See Also:
- Constant Field Values
GROUPID_WATER
private static final int GROUPID_WATER
- See Also:
- Constant Field Values
GROUPID_SOLVENTS
private static final int GROUPID_SOLVENTS
- See Also:
- Constant Field Values
GROUPID_SULPHATE
private static final int GROUPID_SULPHATE
- See Also:
- Constant Field Values
predefinedGroup3Names
public static final String[] predefinedGroup3Names
argbsShapely
public static final int[] argbsShapely
allCarbohydrates
private static final String allCarbohydrates
- See Also:
- Constant Field Values
group3List
public static final String group3List
group3Count
public static final int group3Count
predefinedGroup1Names
public static final char[] predefinedGroup1Names
predefinedVariable
public static String[] predefinedVariable
predefinedStatic
public static String[] predefinedStatic
MODELKIT_ZAP_STRING
public static final String MODELKIT_ZAP_STRING
- See Also:
- Constant Field Values
MODELKIT_ZAP_TITLE
public static final String MODELKIT_ZAP_TITLE
- See Also:
- Constant Field Values
DEFAULT_FONTFACE
public static final String DEFAULT_FONTFACE
- See Also:
- Constant Field Values
DEFAULT_FONTSTYLE
public static final String DEFAULT_FONTSTYLE
- See Also:
- Constant Field Values
LABEL_MINIMUM_FONTSIZE
public static final int LABEL_MINIMUM_FONTSIZE
- See Also:
- Constant Field Values
LABEL_MAXIMUM_FONTSIZE
public static final int LABEL_MAXIMUM_FONTSIZE
- See Also:
- Constant Field Values
LABEL_DEFAULT_FONTSIZE
public static final int LABEL_DEFAULT_FONTSIZE
- See Also:
- Constant Field Values
LABEL_DEFAULT_X_OFFSET
public static final int LABEL_DEFAULT_X_OFFSET
- See Also:
- Constant Field Values
LABEL_DEFAULT_Y_OFFSET
public static final int LABEL_DEFAULT_Y_OFFSET
- See Also:
- Constant Field Values
MEASURE_DEFAULT_FONTSIZE
public static final int MEASURE_DEFAULT_FONTSIZE
- See Also:
- Constant Field Values
AXES_DEFAULT_FONTSIZE
public static final int AXES_DEFAULT_FONTSIZE
- See Also:
- Constant Field Values
SHAPE_BALLS
public static final int SHAPE_BALLS
- See Also:
- Constant Field Values
SHAPE_STICKS
public static final int SHAPE_STICKS
- See Also:
- Constant Field Values
SHAPE_HSTICKS
public static final int SHAPE_HSTICKS
- See Also:
- Constant Field Values
SHAPE_SSSTICKS
public static final int SHAPE_SSSTICKS
- See Also:
- Constant Field Values
SHAPE_STRUTS
public static final int SHAPE_STRUTS
- See Also:
- Constant Field Values
SHAPE_LABELS
public static final int SHAPE_LABELS
- See Also:
- Constant Field Values
SHAPE_MEASURES
public static final int SHAPE_MEASURES
- See Also:
- Constant Field Values
SHAPE_STARS
public static final int SHAPE_STARS
- See Also:
- Constant Field Values
SHAPE_HALOS
public static final int SHAPE_HALOS
- See Also:
- Constant Field Values
SHAPE_MIN_SECONDARY
public static final int SHAPE_MIN_SECONDARY
- See Also:
- Constant Field Values
SHAPE_BACKBONE
public static final int SHAPE_BACKBONE
- See Also:
- Constant Field Values
SHAPE_TRACE
public static final int SHAPE_TRACE
- See Also:
- Constant Field Values
SHAPE_CARTOON
public static final int SHAPE_CARTOON
- See Also:
- Constant Field Values
SHAPE_STRANDS
public static final int SHAPE_STRANDS
- See Also:
- Constant Field Values
SHAPE_MESHRIBBON
public static final int SHAPE_MESHRIBBON
- See Also:
- Constant Field Values
SHAPE_RIBBONS
public static final int SHAPE_RIBBONS
- See Also:
- Constant Field Values
SHAPE_ROCKETS
public static final int SHAPE_ROCKETS
- See Also:
- Constant Field Values
SHAPE_MAX_SECONDARY
public static final int SHAPE_MAX_SECONDARY
- See Also:
- Constant Field Values
SHAPE_MIN_SPECIAL
public static final int SHAPE_MIN_SPECIAL
- See Also:
- Constant Field Values
SHAPE_DOTS
public static final int SHAPE_DOTS
- See Also:
- Constant Field Values
SHAPE_DIPOLES
public static final int SHAPE_DIPOLES
- See Also:
- Constant Field Values
SHAPE_VECTORS
public static final int SHAPE_VECTORS
- See Also:
- Constant Field Values
SHAPE_GEOSURFACE
public static final int SHAPE_GEOSURFACE
- See Also:
- Constant Field Values
SHAPE_ELLIPSOIDS
public static final int SHAPE_ELLIPSOIDS
- See Also:
- Constant Field Values
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
- See Also:
- Constant Field Values
SHAPE_POLYHEDRA
public static final int SHAPE_POLYHEDRA
- See Also:
- Constant Field Values
SHAPE_MIN_HAS_ID
public static final int SHAPE_MIN_HAS_ID
- See Also:
- Constant Field Values
SHAPE_MIN_MESH_COLLECTION
public static final int SHAPE_MIN_MESH_COLLECTION
- See Also:
- Constant Field Values
SHAPE_DRAW
public static final int SHAPE_DRAW
- See Also:
- Constant Field Values
SHAPE_MAX_SPECIAL
public static final int SHAPE_MAX_SPECIAL
- See Also:
- Constant Field Values
SHAPE_MIN_SURFACE
public static final int SHAPE_MIN_SURFACE
- See Also:
- Constant Field Values
SHAPE_ISOSURFACE
public static final int SHAPE_ISOSURFACE
- See Also:
- Constant Field Values
SHAPE_LCAOCARTOON
public static final int SHAPE_LCAOCARTOON
- See Also:
- Constant Field Values
SHAPE_MO
public static final int SHAPE_MO
- See Also:
- Constant Field Values
SHAPE_PMESH
public static final int SHAPE_PMESH
- See Also:
- Constant Field Values
SHAPE_PLOT3D
public static final int SHAPE_PLOT3D
- See Also:
- Constant Field Values
SHAPE_MAX_SURFACE
public static final int SHAPE_MAX_SURFACE
- See Also:
- Constant Field Values
SHAPE_MAX_MESH_COLLECTION
public static final int SHAPE_MAX_MESH_COLLECTION
- See Also:
- Constant Field Values
SHAPE_ECHO
public static final int SHAPE_ECHO
- See Also:
- Constant Field Values
SHAPE_MAX_HAS_ID
public static final int SHAPE_MAX_HAS_ID
- See Also:
- Constant Field Values
SHAPE_AXES
public static final int SHAPE_AXES
- See Also:
- Constant Field Values
SHAPE_BBCAGE
public static final int SHAPE_BBCAGE
- See Also:
- Constant Field Values
SHAPE_UCCAGE
public static final int SHAPE_UCCAGE
- See Also:
- Constant Field Values
SHAPE_HOVER
public static final int SHAPE_HOVER
- See Also:
- Constant Field Values
SHAPE_FRANK
public static final int SHAPE_FRANK
- See Also:
- Constant Field Values
SHAPE_MAX
public static final int SHAPE_MAX
- See Also:
- Constant Field Values
shapeClassBases
public static final String[] shapeClassBases
ATOM_IN_FRAME
public static final int ATOM_IN_FRAME
- See Also:
- Constant Field Values
ATOM_SLABBED
public static final int ATOM_SLABBED
- See Also:
- Constant Field Values
PREVIOUS_MESH_ID
public static final String PREVIOUS_MESH_ID
- See Also:
- Constant Field Values
CARTOON_VISIBILITY_FLAG
public static final int CARTOON_VISIBILITY_FLAG
BACKBONE_VISIBILITY_FLAG
public static final int BACKBONE_VISIBILITY_FLAG
ALPHA_CARBON_VISIBILITY_FLAG
public static final int ALPHA_CARBON_VISIBILITY_FLAG
DEFAULT_STEREO_DEGREES
public static final int DEFAULT_STEREO_DEGREES
- See Also:
- Constant Field Values
STEREO_UNKNOWN
public static final int STEREO_UNKNOWN
- See Also:
- Constant Field Values
STEREO_NONE
public static final int STEREO_NONE
- See Also:
- Constant Field Values
STEREO_DOUBLE
public static final int STEREO_DOUBLE
- See Also:
- Constant Field Values
STEREO_REDCYAN
public static final int STEREO_REDCYAN
- See Also:
- Constant Field Values
STEREO_REDBLUE
public static final int STEREO_REDBLUE
- See Also:
- Constant Field Values
STEREO_REDGREEN
public static final int STEREO_REDGREEN
- See Also:
- Constant Field Values
STEREO_CUSTOM
public static final int STEREO_CUSTOM
- See Also:
- Constant Field Values
stereoModes
private static final String[] stereoModes
SHELL_S
public static final int SHELL_S
- See Also:
- Constant Field Values
SHELL_P
public static final int SHELL_P
- See Also:
- Constant Field Values
SHELL_SP
public static final int SHELL_SP
- See Also:
- Constant Field Values
SHELL_L
public static final int SHELL_L
- See Also:
- Constant Field Values
SHELL_D_SPHERICAL
public static final int SHELL_D_SPHERICAL
- See Also:
- Constant Field Values
SHELL_D_CARTESIAN
public static final int SHELL_D_CARTESIAN
- See Also:
- Constant Field Values
SHELL_F_SPHERICAL
public static final int SHELL_F_SPHERICAL
- See Also:
- Constant Field Values
SHELL_F_CARTESIAN
public static final int SHELL_F_CARTESIAN
- See Also:
- Constant Field Values
SHELL_G_SPHERICAL
public static final int SHELL_G_SPHERICAL
- See Also:
- Constant Field Values
SHELL_G_CARTESIAN
public static final int SHELL_G_CARTESIAN
- See Also:
- Constant Field Values
SHELL_H_SPHERICAL
public static final int SHELL_H_SPHERICAL
- See Also:
- Constant Field Values
SHELL_H_CARTESIAN
public static final int SHELL_H_CARTESIAN
- See Also:
- Constant Field Values
SUPPORTED_BASIS_FUNCTIONS
public static final String SUPPORTED_BASIS_FUNCTIONS
- See Also:
- Constant Field Values
quantumShellTags
private static final String[] quantumShellTags
quantumShellIDs
private static final int[] quantumShellIDs
SUPPORTED_BASES
public static final String SUPPORTED_BASES
- See Also:
- Constant Field Values
shellOrder
private static final String[][] shellOrder
LOAD_ATOM_DATA_TYPES
public static final String LOAD_ATOM_DATA_TYPES
- See Also:
- Constant Field Values
ANIMATION_ONCE
public static final int ANIMATION_ONCE
- See Also:
- Constant Field Values
ANIMATION_LOOP
public static final int ANIMATION_LOOP
- See Also:
- Constant Field Values
ANIMATION_PALINDROME
public static final int ANIMATION_PALINDROME
- See Also:
- Constant Field Values
radiansPerDegree
public static final float radiansPerDegree
- See Also:
- Constant Field Values
JmolConstants
public JmolConstants()
embedScript
public static String embedScript(String s)
getCallbackName
public static String getCallbackName(int i)
getCallbackId
public static int getCallbackId(String callbackName)
getDrawTypeName
public static String getDrawTypeName(int drawType)
getArgbHbondType
public static int getArgbHbondType(int order)
getBondOrderFromString
public static final int getBondOrderFromString(String bondOrderString)
getPartialBondOrderFromInteger
public static final int 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
getCovalentBondOrder
public static final int getCovalentBondOrder(int order)
getPartialBondOrder
public static final int getPartialBondOrder(int order)
getPartialBondDotted
public static final int getPartialBondDotted(int order)
getBondOrderFromFloat
public static final int getBondOrderFromFloat(float fOrder)
getBondOrderNameFromOrder
public static final String getBondOrderNameFromOrder(int order)
getCmlOrder
public static String getCmlOrder(int order)
getBondOrderNumberFromOrder
public static final String getBondOrderNumberFromOrder(int order)
- used for formatting labels and in the connect PARTIAL command
- Parameters:
order
-
- Returns:
- a string representation to preserve float n.m
getVdwLabel
public static String getVdwLabel(int i)
getVdwType
public static int getVdwType(String label)
getVanderwaalsMar
public static int getVanderwaalsMar(int i,
int iType)
getBondingRadiusFloat
public static float getBondingRadiusFloat(int atomicNumber,
int charge)
getBondingRadiusFloat
private static float getBondingRadiusFloat(int atomicNumber,
int charge,
short[] table)
pidOf
public static byte pidOf(Object value)
isPaletteVariable
public static boolean isPaletteVariable(byte pid)
getPaletteID
public static final byte getPaletteID(String paletteName)
getPaletteName
public static final String getPaletteName(byte pid)
getProteinStructureName
public static final String getProteinStructureName(int itype,
boolean isGeneric)
getProteinStructureType
public static final byte getProteinStructureType(String type)
getSpecialAtomName
public static final String getSpecialAtomName(int atomID)
lookupSpecialAtomID
public static byte lookupSpecialAtomID(String atomName)
checkCarbohydrate
public static final boolean checkCarbohydrate(String group3)
- Parameters:
group3
- a potential group3 name
- Returns:
- whether this is a carbohydrate from the list
getGroup3List
private static final String getGroup3List()
isHetero
public static final boolean isHetero(String group3)
isShapeSecondary
public static final boolean isShapeSecondary(int i)
shapeTokenIndex
public static final int shapeTokenIndex(int tok)
getShapeClassName
public static final String getShapeClassName(int shapeID)
getShapeVisibilityFlag
public static final int getShapeVisibilityFlag(int shapeID)
getStereoMode
public static int getStereoMode(String id)
getStereoModeName
static String getStereoModeName(int mode)
getShellOrder
public static final String[] getShellOrder(int i)
getQuantumShellTagID
public static final int getQuantumShellTagID(String tag)
getQuantumShellTagIDSpherical
public static final int getQuantumShellTagIDSpherical(String tag)
getQuantumShellTag
public static final String getQuantumShellTag(int shell)
modelValue
public static int modelValue(String strDecimal)