org.jmol.viewer
Class JmolConstants
java.lang.Object
org.jmol.viewer.JmolConstants
public final class JmolConstants
- extends java.lang.Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
- 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 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
- See Also:
- Constant Field Values
GROUPID_WATER
private static final int GROUPID_WATER
- See Also:
- Constant Field Values
GROUPID_SOLVENT_MIN
private static final int GROUPID_SOLVENT_MIN
- See Also:
- Constant Field Values
GROUPID_ION_MIN
private static final int GROUPID_ION_MIN
- See Also:
- Constant Field Values
GROUPID_ION_MAX
private static final int GROUPID_ION_MAX
- See Also:
- Constant Field Values
predefinedGroup3Names
public static final java.lang.String[] predefinedGroup3Names
naNoH
private static final java.lang.String naNoH
- See Also:
- Constant Field Values
aaSp2
private static final java.lang.String aaSp2
- See Also:
- Constant Field Values
aaPlus
private static final java.lang.String aaPlus
- See Also:
- 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
- See Also:
- 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
- See Also:
- Constant Field Values
MODELKIT_ZAP_TITLE
public static final java.lang.String MODELKIT_ZAP_TITLE
- See Also:
- Constant Field Values
ADD_HYDROGEN_TITLE
public static final java.lang.String ADD_HYDROGEN_TITLE
- See Also:
- Constant Field Values
DEFAULT_FONTFACE
public static final java.lang.String DEFAULT_FONTFACE
- See Also:
- Constant Field Values
DEFAULT_FONTSTYLE
public static final java.lang.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_CONTACT
public static final int SHAPE_CONTACT
- 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 java.lang.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
CURSOR_DEFAULT
public static final int CURSOR_DEFAULT
- See Also:
- Constant Field Values
CURSOR_HAND
public static final int CURSOR_HAND
- See Also:
- Constant Field Values
CURSOR_CROSSHAIR
public static final int CURSOR_CROSSHAIR
- See Also:
- Constant Field Values
CURSOR_MOVE
public static final int CURSOR_MOVE
- See Also:
- Constant Field Values
CURSOR_WAIT
public static final int CURSOR_WAIT
- See Also:
- Constant Field Values
CURSOR_ZOOM
public static final int CURSOR_ZOOM
- See Also:
- Constant Field Values
JmolConstants
public JmolConstants()
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)