org.jmol.viewer
Class JmolConstants

java.lang.Object
  extended by org.jmol.viewer.JmolConstants

public final class JmolConstants
extends java.lang.Object


Field Summary
private static java.lang.String aaPlus
           
private static java.lang.String aaSp2
           
static java.lang.String ADD_HYDROGEN_TITLE
           
private static java.lang.String allCarbohydrates
           
static java.lang.String allowedQuaternionFrames
           
static int[] altArgbsCpk
           
static float ANGSTROMS_PER_BOHR
           
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[] argbsFormalCharge
           
static int argbShapelyBackbone
           
static int argbShapelyDefault
           
static int argbShapelySpecial
           
static int argbsIsosurfaceNegative
           
static int argbsIsosurfacePositive
           
static int[] argbsRoygbScale
           
static int[] argbsRwbScale
           
static int[] argbsShapely
           
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 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 javax.vecmath.Vector3f center
           
static java.lang.String CLASSBASE_OPTIONS
           
static java.lang.String copyright
           
static int CURSOR_CROSSHAIR
           
static int CURSOR_DEFAULT
           
static int CURSOR_HAND
           
static int CURSOR_MOVE
           
static int CURSOR_WAIT
           
static int CURSOR_ZOOM
           
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 float DEFAULT_STRUT_RADIUS
           
static java.lang.String EMBEDDED_SCRIPT_TAG
           
static java.lang.String EXPORT_DRIVER_LIST
           
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_RANGE_SIZE
           
static int group3Count
           
static java.lang.String group3List
           
static int GROUPID_AMINO_MAX
           
static int GROUPID_ARGININE
           
static int GROUPID_ASPARAGINE
           
static int GROUPID_ASPARTATE
           
static int GROUPID_CYSTEINE
           
static int GROUPID_GLUTAMATE
           
static int GROUPID_GLUTAMINE
           
static int GROUPID_HISTIDINE
           
private static int GROUPID_ION_MAX
           
private static int GROUPID_ION_MIN
           
static int GROUPID_LYSINE
           
static int GROUPID_NUCLEIC_MAX
           
static int GROUPID_PROLINE
           
private static int GROUPID_SOLVENT_MIN
           
static int GROUPID_TRYPTOPHAN
           
private static int GROUPID_WATER
           
private static java.util.Map<java.lang.String,java.lang.Integer> htSpecialAtoms
           
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_NONE
           
static byte MULTIBOND_ALWAYS
           
static byte MULTIBOND_NEVER
           
static byte MULTIBOND_NOTSMALL
           
static byte MULTIBOND_WIREFRAME
           
private static java.lang.String naNoH
           
static boolean officialRelease
           
static short PARTIAL_CHARGE_COLIX_BLUE
           
static short PARTIAL_CHARGE_COLIX_RED
           
static short PARTIAL_CHARGE_COLIX_WHITE
           
static int PARTIAL_CHARGE_RANGE_SIZE
           
private static java.lang.String[] pdbBondInfo
           
private static int[] pdbHydrogenCount
           
static char[] predefinedGroup1Names
           
static java.lang.String[] predefinedGroup3Names
           
static java.lang.String[] predefinedStatic
           
static java.lang.String[] predefinedVariable
           
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_CONTACT
           
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
           
private static java.lang.String[] specialAtomNames
           
static javax.vecmath.Vector3f[] unitAxisVectors
           
static java.lang.String VdwPROBE
           
static java.lang.String version
           
static int XY_ZTOP
           
 
Constructor Summary
JmolConstants()
           
 
Method Summary
static boolean checkCarbohydrate(java.lang.String group3)
           
static java.lang.String embedScript(java.lang.String s)
           
static boolean getAminoAcidValenceAndCharge(java.lang.String res, java.lang.String name, int[] ret)
          returns an array if we have special hybridization or charge
private static java.lang.String getGroup3List()
           
private static int getGroup3Pt(java.lang.String group3)
           
static java.lang.String[][] getPdbBondInfo(int pt)
           
static java.lang.String getShapeClassName(int shapeID)
           
static int getShapeVisibilityFlag(int shapeID)
           
static java.lang.String getSpecialAtomName(int atomID)
           
static int getStandardPdbHydrogenCount(int pt)
           
static boolean isHetero(java.lang.String group3)
           
static boolean isShapeSecondary(int i)
           
static byte lookupSpecialAtomID(java.lang.String atomName)
           
static int shapeTokenIndex(int tok)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

copyright

public static final java.lang.String copyright
See Also:
Constant Field Values

version

public static final java.lang.String version

cvsDate

public static final java.lang.String cvsDate
See Also:
Constant Field Values

date

public static final java.lang.String date

officialRelease

public static final boolean officialRelease
See Also:
Constant Field Values

CLASSBASE_OPTIONS

public static final java.lang.String CLASSBASE_OPTIONS
See Also:
Constant Field Values

DEFAULT_HELP_PATH

public static final java.lang.String DEFAULT_HELP_PATH
See Also:
Constant Field Values

EMBEDDED_SCRIPT_TAG

public static final java.lang.String EMBEDDED_SCRIPT_TAG
See Also:
Constant Field Values

SCRIPT_EDITOR_IGNORE

public static final java.lang.String SCRIPT_EDITOR_IGNORE
See Also:
Constant Field Values

LOAD_ATOM_DATA_TYPES

public static final java.lang.String LOAD_ATOM_DATA_TYPES
See Also:
Constant Field Values

radiansPerDegree

public static final float radiansPerDegree
See Also:
Constant Field Values

allowedQuaternionFrames

public static final java.lang.String allowedQuaternionFrames
See Also:
Constant Field Values

EXPORT_DRIVER_LIST

public static final java.lang.String EXPORT_DRIVER_LIST
See Also:
Constant Field Values

VdwPROBE

public static final java.lang.String VdwPROBE
See Also:
Constant Field Values

center

public static final javax.vecmath.Vector3f center

axisX

public static final javax.vecmath.Vector3f axisX

axisY

public static final javax.vecmath.Vector3f axisY

axisZ

public static final javax.vecmath.Vector3f axisZ

axisNX

public static final javax.vecmath.Vector3f axisNX

axisNY

public static final javax.vecmath.Vector3f axisNY

axisNZ

public static final javax.vecmath.Vector3f axisNZ

unitAxisVectors

public static final javax.vecmath.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

MOUSE_NONE

public static final int MOUSE_NONE
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

MAXIMUM_AUTO_BOND_COUNT

public static final int MAXIMUM_AUTO_BOND_COUNT
See Also:
Constant Field Values

madMultipleBondSmallMaximum

public static final short madMultipleBondSmallMaximum
See Also:
Constant Field Values

ANGSTROMS_PER_BOHR

public static final float ANGSTROMS_PER_BOHR
See Also:
Constant Field Values

altArgbsCpk

public static final int[] altArgbsCpk

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
See Also:
Constant Field Values

argbsIsosurfaceNegative

public static final int argbsIsosurfaceNegative
See Also:
Constant Field Values

specialAtomNames

private static final java.lang.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
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Constant Field Values

ATOMID_C4

public static final byte ATOMID_C4
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Constant Field Values

ATOMID_C5

public static final byte ATOMID_C5
See Also:
Constant Field Values

ATOMID_C6

public static final byte ATOMID_C6
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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
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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 java.util.Map<java.lang.String,java.lang.Integer> htSpecialAtoms

GROUPID_ARGININE

public static final int GROUPID_ARGININE
See Also:
Constant Field Values

GROUPID_ASPARAGINE

public static final int GROUPID_ASPARAGINE
See Also:
Constant Field Values

GROUPID_ASPARTATE

public static final int GROUPID_ASPARTATE
See Also:
Constant Field Values

GROUPID_CYSTEINE

public static final int GROUPID_CYSTEINE
See Also:
Constant Field Values

GROUPID_GLUTAMINE

public static final int GROUPID_GLUTAMINE
See Also:
Constant Field Values

GROUPID_GLUTAMATE

public static final int GROUPID_GLUTAMATE
See Also:
Constant Field Values

GROUPID_HISTIDINE

public static final int GROUPID_HISTIDINE
See Also:
Constant Field Values

GROUPID_LYSINE

public static final int GROUPID_LYSINE
See Also:
Constant Field Values

GROUPID_PROLINE

public static final int GROUPID_PROLINE
See Also:
Constant Field Values

GROUPID_TRYPTOPHAN

public static final int GROUPID_TRYPTOPHAN
See Also:
Constant Field Values

GROUPID_AMINO_MAX

public static final int GROUPID_AMINO_MAX
See Also:
Constant Field Values

GROUPID_NUCLEIC_MAX

public static final int GROUPID_NUCLEIC_MAX
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Constant Field Values

GROUPID_WATER

private static final int GROUPID_WATER
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Constant Field Values

GROUPID_SOLVENT_MIN

private static final int GROUPID_SOLVENT_MIN
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Constant Field Values

GROUPID_ION_MIN

private static final int GROUPID_ION_MIN
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Constant Field Values

GROUPID_ION_MAX

private static final int GROUPID_ION_MAX
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Constant Field Values

predefinedGroup3Names

public static final java.lang.String[] predefinedGroup3Names

naNoH

private static final java.lang.String naNoH
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Constant Field Values

aaSp2

private static final java.lang.String aaSp2
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Constant Field Values

aaPlus

private static final java.lang.String aaPlus
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Constant Field Values

pdbBondInfo

private static final java.lang.String[] pdbBondInfo

pdbHydrogenCount

private static final int[] pdbHydrogenCount

argbsShapely

public static final int[] argbsShapely

allCarbohydrates

private static final java.lang.String allCarbohydrates
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Constant Field Values

group3List

public static final java.lang.String group3List

group3Count

public static final int group3Count

predefinedGroup1Names

public static final char[] predefinedGroup1Names

predefinedVariable

public static java.lang.String[] predefinedVariable

predefinedStatic

public static java.lang.String[] predefinedStatic

MODELKIT_ZAP_STRING

public static final java.lang.String MODELKIT_ZAP_STRING
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Constant Field Values

MODELKIT_ZAP_TITLE

public static final java.lang.String MODELKIT_ZAP_TITLE
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Constant Field Values

ADD_HYDROGEN_TITLE

public static final java.lang.String ADD_HYDROGEN_TITLE
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Constant Field Values

DEFAULT_FONTFACE

public static final java.lang.String DEFAULT_FONTFACE
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Constant Field Values

DEFAULT_FONTSTYLE

public static final java.lang.String DEFAULT_FONTSTYLE
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Constant Field Values

LABEL_MINIMUM_FONTSIZE

public static final int LABEL_MINIMUM_FONTSIZE
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Constant Field Values

LABEL_MAXIMUM_FONTSIZE

public static final int LABEL_MAXIMUM_FONTSIZE
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Constant Field Values

LABEL_DEFAULT_FONTSIZE

public static final int LABEL_DEFAULT_FONTSIZE
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Constant Field Values

LABEL_DEFAULT_X_OFFSET

public static final int LABEL_DEFAULT_X_OFFSET
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Constant Field Values

LABEL_DEFAULT_Y_OFFSET

public static final int LABEL_DEFAULT_Y_OFFSET
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Constant Field Values

MEASURE_DEFAULT_FONTSIZE

public static final int MEASURE_DEFAULT_FONTSIZE
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Constant Field Values

AXES_DEFAULT_FONTSIZE

public static final int AXES_DEFAULT_FONTSIZE
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Constant Field Values

SHAPE_BALLS

public static final int SHAPE_BALLS
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Constant Field Values

SHAPE_STICKS

public static final int SHAPE_STICKS
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Constant Field Values

SHAPE_HSTICKS

public static final int SHAPE_HSTICKS
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Constant Field Values

SHAPE_SSSTICKS

public static final int SHAPE_SSSTICKS
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Constant Field Values

SHAPE_STRUTS

public static final int SHAPE_STRUTS
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Constant Field Values

SHAPE_LABELS

public static final int SHAPE_LABELS
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Constant Field Values

SHAPE_MEASURES

public static final int SHAPE_MEASURES
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Constant Field Values

SHAPE_STARS

public static final int SHAPE_STARS
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Constant Field Values

SHAPE_HALOS

public static final int SHAPE_HALOS
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Constant Field Values

SHAPE_MIN_SECONDARY

public static final int SHAPE_MIN_SECONDARY
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Constant Field Values

SHAPE_BACKBONE

public static final int SHAPE_BACKBONE
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Constant Field Values

SHAPE_TRACE

public static final int SHAPE_TRACE
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Constant Field Values

SHAPE_CARTOON

public static final int SHAPE_CARTOON
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Constant Field Values

SHAPE_STRANDS

public static final int SHAPE_STRANDS
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Constant Field Values

SHAPE_MESHRIBBON

public static final int SHAPE_MESHRIBBON
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Constant Field Values

SHAPE_RIBBONS

public static final int SHAPE_RIBBONS
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Constant Field Values

SHAPE_ROCKETS

public static final int SHAPE_ROCKETS
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Constant Field Values

SHAPE_MAX_SECONDARY

public static final int SHAPE_MAX_SECONDARY
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Constant Field Values

SHAPE_MIN_SPECIAL

public static final int SHAPE_MIN_SPECIAL
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Constant Field Values

SHAPE_DOTS

public static final int SHAPE_DOTS
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Constant Field Values

SHAPE_DIPOLES

public static final int SHAPE_DIPOLES
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Constant Field Values

SHAPE_VECTORS

public static final int SHAPE_VECTORS
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Constant Field Values

SHAPE_GEOSURFACE

public static final int SHAPE_GEOSURFACE
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Constant Field Values

SHAPE_ELLIPSOIDS

public static final int SHAPE_ELLIPSOIDS
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Constant Field Values

SHAPE_MAX_SIZE_ZERO_ON_RESTRICT

public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
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Constant Field Values

SHAPE_POLYHEDRA

public static final int SHAPE_POLYHEDRA
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Constant Field Values

SHAPE_MIN_HAS_ID

public static final int SHAPE_MIN_HAS_ID
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Constant Field Values

SHAPE_MIN_MESH_COLLECTION

public static final int SHAPE_MIN_MESH_COLLECTION
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Constant Field Values

SHAPE_DRAW

public static final int SHAPE_DRAW
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Constant Field Values

SHAPE_MAX_SPECIAL

public static final int SHAPE_MAX_SPECIAL
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Constant Field Values

SHAPE_MIN_SURFACE

public static final int SHAPE_MIN_SURFACE
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Constant Field Values

SHAPE_ISOSURFACE

public static final int SHAPE_ISOSURFACE
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Constant Field Values

SHAPE_CONTACT

public static final int SHAPE_CONTACT
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Constant Field Values

SHAPE_LCAOCARTOON

public static final int SHAPE_LCAOCARTOON
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Constant Field Values

SHAPE_MO

public static final int SHAPE_MO
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Constant Field Values

SHAPE_PMESH

public static final int SHAPE_PMESH
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Constant Field Values

SHAPE_PLOT3D

public static final int SHAPE_PLOT3D
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Constant Field Values

SHAPE_MAX_SURFACE

public static final int SHAPE_MAX_SURFACE
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Constant Field Values

SHAPE_MAX_MESH_COLLECTION

public static final int SHAPE_MAX_MESH_COLLECTION
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Constant Field Values

SHAPE_ECHO

public static final int SHAPE_ECHO
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Constant Field Values

SHAPE_MAX_HAS_ID

public static final int SHAPE_MAX_HAS_ID
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Constant Field Values

SHAPE_AXES

public static final int SHAPE_AXES
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Constant Field Values

SHAPE_BBCAGE

public static final int SHAPE_BBCAGE
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Constant Field Values

SHAPE_UCCAGE

public static final int SHAPE_UCCAGE
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Constant Field Values

SHAPE_HOVER

public static final int SHAPE_HOVER
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Constant Field Values

SHAPE_FRANK

public static final int SHAPE_FRANK
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Constant Field Values

SHAPE_MAX

public static final int SHAPE_MAX
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Constant Field Values

shapeClassBases

public static final java.lang.String[] shapeClassBases

ATOM_IN_FRAME

public static final int ATOM_IN_FRAME
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Constant Field Values

ATOM_SLABBED

public static final int ATOM_SLABBED
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Constant Field Values

CURSOR_DEFAULT

public static final int CURSOR_DEFAULT
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Constant Field Values

CURSOR_HAND

public static final int CURSOR_HAND
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Constant Field Values

CURSOR_CROSSHAIR

public static final int CURSOR_CROSSHAIR
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Constant Field Values

CURSOR_MOVE

public static final int CURSOR_MOVE
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Constant Field Values

CURSOR_WAIT

public static final int CURSOR_WAIT
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Constant Field Values

CURSOR_ZOOM

public static final int CURSOR_ZOOM
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Constant Field Values
Constructor Detail

JmolConstants

public JmolConstants()
Method Detail

embedScript

public static java.lang.String embedScript(java.lang.String s)

getSpecialAtomName

public static final java.lang.String getSpecialAtomName(int atomID)

lookupSpecialAtomID

public static byte lookupSpecialAtomID(java.lang.String atomName)

getAminoAcidValenceAndCharge

public static boolean getAminoAcidValenceAndCharge(java.lang.String res,
                                                   java.lang.String name,
                                                   int[] ret)
returns an array if we have special hybridization or charge

Parameters:
res -
name -
ret - [0] (target valence) may be reduced by one for sp2 for C or O only [1] will be set to 1 if positive (lysine or terminal N) or -1 if negative (OXT) [2] will be set to 2 if sp2 [3] is supplied covalent bond count
Returns:
true for special; false if not

getStandardPdbHydrogenCount

public static int getStandardPdbHydrogenCount(int pt)

getPdbBondInfo

public static java.lang.String[][] getPdbBondInfo(int pt)

checkCarbohydrate

public static final boolean checkCarbohydrate(java.lang.String group3)
Parameters:
group3 - a potential group3 name
Returns:
whether this is a carbohydrate from the list

getGroup3List

private static final java.lang.String getGroup3List()

isHetero

public static final boolean isHetero(java.lang.String group3)

getGroup3Pt

private static int getGroup3Pt(java.lang.String group3)

isShapeSecondary

public static final boolean isShapeSecondary(int i)

shapeTokenIndex

public static final int shapeTokenIndex(int tok)

getShapeClassName

public static final java.lang.String getShapeClassName(int shapeID)

getShapeVisibilityFlag

public static final int getShapeVisibilityFlag(int shapeID)