Package org.jmol.viewer
Class JC
- java.lang.Object
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- org.jmol.viewer.JC
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public final class JC extends Object
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Field Summary
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Constructor Summary
Constructors Constructor Description JC()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static String
embedScript(String s)
(package private) static String
fixProtocol(String name)
Check for databases that have changed from http:// to https:// over time.static int
getAlignment(int offset)
static int
getCIPChiralityCode(char c)
static String
getCIPChiralityName(int flags)
static String
getCIPRuleName(int i)
static String
getEchoName(int type)
static String
getHorizAlignmentName(int align)
static String
getMacro(String key)
static String
getMacroList()
static int
getNBOTypeFromName(String nboType)
static int
getOffset(int xOffset, int yOffset, boolean isAbsolute)
Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered".static int
getPointer(int offset)
static String
getPointerName(int pointer)
static int
getServiceCommand(String script)
static String
getShapeClassName(int shapeID, boolean isRenderer)
static int
getShapeVisibilityFlag(int shapeID)
static int
getUnitIDFlags(String type)
Get a unitID typestatic int
getXOffset(int offset)
X offset in pixels.static int
getYOffset(int offset)
Y offset in pixels; negative of this is the actual screen offsetstatic boolean
isOffsetAbsolute(int offset)
static boolean
isSmilesCanonical(String options)
(package private) static String
resolveDataBase(String database, String id, String format)
static int
setHorizAlignment(int offset, int hAlign)
static int
setPointer(int offset, int pointer)
static int
setZPosition(int offset, int pos)
static int
shapeTokenIndex(int tok)
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Field Detail
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NBO_TYPES
public static final String NBO_TYPES
- See Also:
- Constant Field Values
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CIP_CHIRALITY_UNKNOWN
public static final int CIP_CHIRALITY_UNKNOWN
- See Also:
- Constant Field Values
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CIP_CHIRALITY_R_FLAG
public static final int CIP_CHIRALITY_R_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_S_FLAG
public static final int CIP_CHIRALITY_S_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_CANTDETERMINE
public static final int CIP_CHIRALITY_CANTDETERMINE
- See Also:
- Constant Field Values
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CIP_CHIRALITY_NONE
public static final int CIP_CHIRALITY_NONE
- See Also:
- Constant Field Values
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CIP_CHIRALITY_EZ_FLAG
public static final int CIP_CHIRALITY_EZ_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_PSEUDO_FLAG
public static final int CIP_CHIRALITY_PSEUDO_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_AXIAL_FLAG
public static final int CIP_CHIRALITY_AXIAL_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_NAME_MASK
public static final int CIP_CHIRALITY_NAME_MASK
- See Also:
- Constant Field Values
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CIP_CHIRALITY_NAME_OFFSET
public static final int CIP_CHIRALITY_NAME_OFFSET
- See Also:
- Constant Field Values
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CIP_CHIRALITY_seqCis_FLAG
public static final int CIP_CHIRALITY_seqCis_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_seqTrans_FLAG
public static final int CIP_CHIRALITY_seqTrans_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_seqcis_FLAG
public static final int CIP_CHIRALITY_seqcis_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_seqtrans_FLAG
public static final int CIP_CHIRALITY_seqtrans_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_M_FLAG
public static final int CIP_CHIRALITY_M_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_P_FLAG
public static final int CIP_CHIRALITY_P_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_r_FLAG
public static final int CIP_CHIRALITY_r_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_s_FLAG
public static final int CIP_CHIRALITY_s_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_m_FLAG
public static final int CIP_CHIRALITY_m_FLAG
- See Also:
- Constant Field Values
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CIP_CHIRALITY_p_FLAG
public static final int CIP_CHIRALITY_p_FLAG
- See Also:
- Constant Field Values
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ruleNames
private static final String[] ruleNames
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PDB_ANNOTATIONS
public static final String PDB_ANNOTATIONS
- See Also:
- Constant Field Values
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CACTUS_FILE_TYPES
public static final String CACTUS_FILE_TYPES
- See Also:
- Constant Field Values
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defaultMacroDirectory
public static final String defaultMacroDirectory
- See Also:
- Constant Field Values
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databaseArray
public static String[] databaseArray
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macros
public static String[] macros
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copyright
public static final String copyright
- See Also:
- Constant Field Values
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version
public static final String version
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majorVersion
public static String majorVersion
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date
public static final String date
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versionInt
public static final int versionInt
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officialRelease
public static final boolean officialRelease
- See Also:
- Constant Field Values
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DEFAULT_HELP_PATH
public static final String DEFAULT_HELP_PATH
- See Also:
- Constant Field Values
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STATE_VERSION_STAMP
public static final String STATE_VERSION_STAMP
- See Also:
- Constant Field Values
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EMBEDDED_SCRIPT_TAG
public static final String EMBEDDED_SCRIPT_TAG
- See Also:
- Constant Field Values
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NOTE_SCRIPT_FILE
public static final String NOTE_SCRIPT_FILE
- See Also:
- Constant Field Values
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SCRIPT_EDITOR_IGNORE
public static final String SCRIPT_EDITOR_IGNORE
- See Also:
- Constant Field Values
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REPAINT_IGNORE
public static final String REPAINT_IGNORE
- See Also:
- Constant Field Values
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LOAD_ATOM_DATA_TYPES
public static final String LOAD_ATOM_DATA_TYPES
- See Also:
- Constant Field Values
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radiansPerDegree
public static final float radiansPerDegree
- See Also:
- Constant Field Values
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allowedQuaternionFrames
public static final String allowedQuaternionFrames
- See Also:
- Constant Field Values
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EXPORT_DRIVER_LIST
public static final String EXPORT_DRIVER_LIST
- See Also:
- Constant Field Values
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center
public static final javajs.util.V3 center
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axisX
public static final javajs.util.V3 axisX
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axisY
public static final javajs.util.V3 axisY
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axisZ
public static final javajs.util.V3 axisZ
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axisNX
public static final javajs.util.V3 axisNX
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axisNY
public static final javajs.util.V3 axisNY
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axisNZ
public static final javajs.util.V3 axisNZ
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unitAxisVectors
public static final javajs.util.V3[] unitAxisVectors
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XY_ZTOP
public static final int XY_ZTOP
- See Also:
- Constant Field Values
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DEFAULT_PERCENT_VDW_ATOM
public static final int DEFAULT_PERCENT_VDW_ATOM
- See Also:
- Constant Field Values
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DEFAULT_BOND_RADIUS
public static final float DEFAULT_BOND_RADIUS
- See Also:
- Constant Field Values
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DEFAULT_BOND_MILLIANGSTROM_RADIUS
public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS
- See Also:
- Constant Field Values
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DEFAULT_STRUT_RADIUS
public static final float DEFAULT_STRUT_RADIUS
- See Also:
- Constant Field Values
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DEFAULT_BOND_TOLERANCE
public static final float DEFAULT_BOND_TOLERANCE
- See Also:
- Constant Field Values
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DEFAULT_MIN_BOND_DISTANCE
public static final float DEFAULT_MIN_BOND_DISTANCE
- See Also:
- Constant Field Values
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DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MAX_CONNECT_DISTANCE
- See Also:
- Constant Field Values
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DEFAULT_MIN_CONNECT_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE
- See Also:
- Constant Field Values
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MINIMIZE_FIXED_RANGE
public static final float MINIMIZE_FIXED_RANGE
- See Also:
- Constant Field Values
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ENC_CALC_MAX_DIST
public static final float ENC_CALC_MAX_DIST
- See Also:
- Constant Field Values
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ENV_CALC_MAX_LEVEL
public static final int ENV_CALC_MAX_LEVEL
- See Also:
- Constant Field Values
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MOUSE_NONE
public static final int MOUSE_NONE
- See Also:
- Constant Field Values
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MULTIBOND_NEVER
public static final byte MULTIBOND_NEVER
- See Also:
- Constant Field Values
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MULTIBOND_WIREFRAME
public static final byte MULTIBOND_WIREFRAME
- See Also:
- Constant Field Values
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MULTIBOND_NOTSMALL
public static final byte MULTIBOND_NOTSMALL
- See Also:
- Constant Field Values
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MULTIBOND_ALWAYS
public static final byte MULTIBOND_ALWAYS
- See Also:
- Constant Field Values
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MAXIMUM_AUTO_BOND_COUNT
public static final int MAXIMUM_AUTO_BOND_COUNT
- See Also:
- Constant Field Values
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madMultipleBondSmallMaximum
public static final short madMultipleBondSmallMaximum
- See Also:
- Constant Field Values
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ANGSTROMS_PER_BOHR
public static final float ANGSTROMS_PER_BOHR
- See Also:
- Constant Field Values
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altArgbsCpk
public static final int[] altArgbsCpk
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argbsFormalCharge
public static final int[] argbsFormalCharge
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argbsRwbScale
public static final int[] argbsRwbScale
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FORMAL_CHARGE_COLIX_RED
public static final int FORMAL_CHARGE_COLIX_RED
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PARTIAL_CHARGE_COLIX_RED
public static final int PARTIAL_CHARGE_COLIX_RED
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PARTIAL_CHARGE_RANGE_SIZE
public static final int PARTIAL_CHARGE_RANGE_SIZE
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argbsRoygbScale
public static final int[] argbsRoygbScale
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argbsIsosurfacePositive
public static final int argbsIsosurfacePositive
- See Also:
- Constant Field Values
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argbsIsosurfaceNegative
public static final int argbsIsosurfaceNegative
- See Also:
- Constant Field Values
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ATOMID_AMINO_NITROGEN
public static final byte ATOMID_AMINO_NITROGEN
- See Also:
- Constant Field Values
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ATOMID_ALPHA_CARBON
public static final byte ATOMID_ALPHA_CARBON
- See Also:
- Constant Field Values
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ATOMID_CARBONYL_CARBON
public static final byte ATOMID_CARBONYL_CARBON
- See Also:
- Constant Field Values
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ATOMID_CARBONYL_OXYGEN
public static final byte ATOMID_CARBONYL_OXYGEN
- See Also:
- Constant Field Values
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ATOMID_O1
public static final byte ATOMID_O1
- See Also:
- Constant Field Values
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ATOMID_ALPHA_ONLY_MASK
public static final int ATOMID_ALPHA_ONLY_MASK
- See Also:
- Constant Field Values
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ATOMID_PROTEIN_MASK
public static final int ATOMID_PROTEIN_MASK
- See Also:
- Constant Field Values
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ATOMID_O5_PRIME
public static final byte ATOMID_O5_PRIME
- See Also:
- Constant Field Values
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ATOMID_C5_PRIME
public static final byte ATOMID_C5_PRIME
- See Also:
- Constant Field Values
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ATOMID_C4_PRIME
public static final byte ATOMID_C4_PRIME
- See Also:
- Constant Field Values
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ATOMID_C3_PRIME
public static final byte ATOMID_C3_PRIME
- See Also:
- Constant Field Values
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ATOMID_O3_PRIME
public static final byte ATOMID_O3_PRIME
- See Also:
- Constant Field Values
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ATOMID_C2_PRIME
public static final byte ATOMID_C2_PRIME
- See Also:
- Constant Field Values
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ATOMID_C1_PRIME
public static final byte ATOMID_C1_PRIME
- See Also:
- Constant Field Values
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ATOMID_O4_PRIME
public static final byte ATOMID_O4_PRIME
- See Also:
- Constant Field Values
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ATOMID_NUCLEIC_MASK
public static final int ATOMID_NUCLEIC_MASK
- See Also:
- Constant Field Values
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ATOMID_NUCLEIC_PHOSPHORUS
public static final byte ATOMID_NUCLEIC_PHOSPHORUS
- See Also:
- Constant Field Values
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ATOMID_PHOSPHORUS_ONLY_MASK
public static final int ATOMID_PHOSPHORUS_ONLY_MASK
- See Also:
- Constant Field Values
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ATOMID_DISTINGUISHING_ATOM_MAX
public static final int ATOMID_DISTINGUISHING_ATOM_MAX
- See Also:
- Constant Field Values
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ATOMID_CARBONYL_OD1
public static final byte ATOMID_CARBONYL_OD1
- See Also:
- Constant Field Values
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ATOMID_CARBONYL_OD2
public static final byte ATOMID_CARBONYL_OD2
- See Also:
- Constant Field Values
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ATOMID_CARBONYL_OE1
public static final byte ATOMID_CARBONYL_OE1
- See Also:
- Constant Field Values
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ATOMID_CARBONYL_OE2
public static final byte ATOMID_CARBONYL_OE2
- See Also:
- Constant Field Values
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ATOMID_N1
public static final byte ATOMID_N1
- See Also:
- Constant Field Values
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ATOMID_C2
public static final byte ATOMID_C2
- See Also:
- Constant Field Values
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ATOMID_N3
public static final byte ATOMID_N3
- See Also:
- Constant Field Values
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ATOMID_C4
public static final byte ATOMID_C4
- See Also:
- Constant Field Values
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ATOMID_C5
public static final byte ATOMID_C5
- See Also:
- Constant Field Values
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ATOMID_C6
public static final byte ATOMID_C6
- See Also:
- Constant Field Values
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ATOMID_O2
public static final byte ATOMID_O2
- See Also:
- Constant Field Values
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ATOMID_N7
public static final byte ATOMID_N7
- See Also:
- Constant Field Values
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ATOMID_C8
public static final byte ATOMID_C8
- See Also:
- Constant Field Values
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ATOMID_N9
public static final byte ATOMID_N9
- See Also:
- Constant Field Values
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ATOMID_N4
public static final byte ATOMID_N4
- See Also:
- Constant Field Values
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ATOMID_N2
public static final byte ATOMID_N2
- See Also:
- Constant Field Values
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ATOMID_N6
public static final byte ATOMID_N6
- See Also:
- Constant Field Values
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ATOMID_C5M
public static final byte ATOMID_C5M
- See Also:
- Constant Field Values
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ATOMID_O6
public static final byte ATOMID_O6
- See Also:
- Constant Field Values
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ATOMID_O4
public static final byte ATOMID_O4
- See Also:
- Constant Field Values
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ATOMID_S4
public static final byte ATOMID_S4
- See Also:
- Constant Field Values
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ATOMID_C7
public static final byte ATOMID_C7
- See Also:
- Constant Field Values
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ATOMID_TERMINATING_OXT
public static final byte ATOMID_TERMINATING_OXT
- See Also:
- Constant Field Values
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ATOMID_H5T_TERMINUS
public static final byte ATOMID_H5T_TERMINUS
- See Also:
- Constant Field Values
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ATOMID_O5T_TERMINUS
public static final byte ATOMID_O5T_TERMINUS
- See Also:
- Constant Field Values
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ATOMID_O1P
public static final byte ATOMID_O1P
- See Also:
- Constant Field Values
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ATOMID_OP1
public static final byte ATOMID_OP1
- See Also:
- Constant Field Values
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ATOMID_O2P
public static final byte ATOMID_O2P
- See Also:
- Constant Field Values
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ATOMID_OP2
public static final byte ATOMID_OP2
- See Also:
- Constant Field Values
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ATOMID_O2_PRIME
public static final byte ATOMID_O2_PRIME
- See Also:
- Constant Field Values
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ATOMID_H3T_TERMINUS
public static final byte ATOMID_H3T_TERMINUS
- See Also:
- Constant Field Values
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ATOMID_HO3_PRIME
public static final byte ATOMID_HO3_PRIME
- See Also:
- Constant Field Values
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ATOMID_HO5_PRIME
public static final byte ATOMID_HO5_PRIME
- See Also:
- Constant Field Values
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PURINE_MASK
public static final int PURINE_MASK
- See Also:
- Constant Field Values
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PYRIMIDINE_MASK
public static final int PYRIMIDINE_MASK
- See Also:
- Constant Field Values
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DNA_MASK
public static final int DNA_MASK
- See Also:
- Constant Field Values
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RNA_MASK
public static final int RNA_MASK
- See Also:
- Constant Field Values
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GROUPID_ARGININE
public static final int GROUPID_ARGININE
- See Also:
- Constant Field Values
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GROUPID_ASPARAGINE
public static final int GROUPID_ASPARAGINE
- See Also:
- Constant Field Values
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GROUPID_ASPARTATE
public static final int GROUPID_ASPARTATE
- See Also:
- Constant Field Values
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GROUPID_CYSTEINE
public static final int GROUPID_CYSTEINE
- See Also:
- Constant Field Values
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GROUPID_GLUTAMINE
public static final int GROUPID_GLUTAMINE
- See Also:
- Constant Field Values
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GROUPID_GLUTAMATE
public static final int GROUPID_GLUTAMATE
- See Also:
- Constant Field Values
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GROUPID_HISTIDINE
public static final int GROUPID_HISTIDINE
- See Also:
- Constant Field Values
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GROUPID_LYSINE
public static final int GROUPID_LYSINE
- See Also:
- Constant Field Values
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GROUPID_PROLINE
public static final int GROUPID_PROLINE
- See Also:
- Constant Field Values
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GROUPID_TRYPTOPHAN
public static final int GROUPID_TRYPTOPHAN
- See Also:
- Constant Field Values
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GROUPID_AMINO_MAX
public static final int GROUPID_AMINO_MAX
- See Also:
- Constant Field Values
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GROUPID_NUCLEIC_MAX
public static final int GROUPID_NUCLEIC_MAX
- See Also:
- Constant Field Values
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GROUPID_WATER
public static final int GROUPID_WATER
- See Also:
- Constant Field Values
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GROUPID_SOLVENT_MIN
public static final int GROUPID_SOLVENT_MIN
- See Also:
- Constant Field Values
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GROUPID_ION_MIN
private static final int GROUPID_ION_MIN
- See Also:
- Constant Field Values
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GROUPID_ION_MAX
private static final int GROUPID_ION_MAX
- See Also:
- Constant Field Values
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predefinedVariable
public static String[] predefinedVariable
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predefinedStatic
public static String[] predefinedStatic
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MODELKIT_ZAP_STRING
public static final String MODELKIT_ZAP_STRING
- See Also:
- Constant Field Values
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MODELKIT_ZAP_TITLE
public static final String MODELKIT_ZAP_TITLE
- See Also:
- Constant Field Values
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ZAP_TITLE
public static final String ZAP_TITLE
- See Also:
- Constant Field Values
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ADD_HYDROGEN_TITLE
public static final String ADD_HYDROGEN_TITLE
- See Also:
- Constant Field Values
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DEFAULT_FONTFACE
public static final String DEFAULT_FONTFACE
- See Also:
- Constant Field Values
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DEFAULT_FONTSTYLE
public static final String DEFAULT_FONTSTYLE
- See Also:
- Constant Field Values
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MEASURE_DEFAULT_FONTSIZE
public static final int MEASURE_DEFAULT_FONTSIZE
- See Also:
- Constant Field Values
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AXES_DEFAULT_FONTSIZE
public static final int AXES_DEFAULT_FONTSIZE
- See Also:
- Constant Field Values
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SHAPE_BALLS
public static final int SHAPE_BALLS
- See Also:
- Constant Field Values
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SHAPE_STICKS
public static final int SHAPE_STICKS
- See Also:
- Constant Field Values
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SHAPE_HSTICKS
public static final int SHAPE_HSTICKS
- See Also:
- Constant Field Values
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SHAPE_SSSTICKS
public static final int SHAPE_SSSTICKS
- See Also:
- Constant Field Values
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SHAPE_STRUTS
public static final int SHAPE_STRUTS
- See Also:
- Constant Field Values
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SHAPE_LABELS
public static final int SHAPE_LABELS
- See Also:
- Constant Field Values
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SHAPE_MEASURES
public static final int SHAPE_MEASURES
- See Also:
- Constant Field Values
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SHAPE_STARS
public static final int SHAPE_STARS
- See Also:
- Constant Field Values
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SHAPE_MIN_HAS_SETVIS
public static final int SHAPE_MIN_HAS_SETVIS
- See Also:
- Constant Field Values
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SHAPE_HALOS
public static final int SHAPE_HALOS
- See Also:
- Constant Field Values
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SHAPE_MIN_SECONDARY
public static final int SHAPE_MIN_SECONDARY
- See Also:
- Constant Field Values
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SHAPE_BACKBONE
public static final int SHAPE_BACKBONE
- See Also:
- Constant Field Values
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SHAPE_TRACE
public static final int SHAPE_TRACE
- See Also:
- Constant Field Values
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SHAPE_CARTOON
public static final int SHAPE_CARTOON
- See Also:
- Constant Field Values
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SHAPE_STRANDS
public static final int SHAPE_STRANDS
- See Also:
- Constant Field Values
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SHAPE_MESHRIBBON
public static final int SHAPE_MESHRIBBON
- See Also:
- Constant Field Values
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SHAPE_RIBBONS
public static final int SHAPE_RIBBONS
- See Also:
- Constant Field Values
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SHAPE_ROCKETS
public static final int SHAPE_ROCKETS
- See Also:
- Constant Field Values
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SHAPE_MAX_SECONDARY
public static final int SHAPE_MAX_SECONDARY
- See Also:
- Constant Field Values
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SHAPE_MIN_SPECIAL
public static final int SHAPE_MIN_SPECIAL
- See Also:
- Constant Field Values
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SHAPE_DOTS
public static final int SHAPE_DOTS
- See Also:
- Constant Field Values
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SHAPE_DIPOLES
public static final int SHAPE_DIPOLES
- See Also:
- Constant Field Values
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SHAPE_VECTORS
public static final int SHAPE_VECTORS
- See Also:
- Constant Field Values
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SHAPE_GEOSURFACE
public static final int SHAPE_GEOSURFACE
- See Also:
- Constant Field Values
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SHAPE_ELLIPSOIDS
public static final int SHAPE_ELLIPSOIDS
- See Also:
- Constant Field Values
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SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
- See Also:
- Constant Field Values
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SHAPE_MIN_HAS_ID
public static final int SHAPE_MIN_HAS_ID
- See Also:
- Constant Field Values
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SHAPE_POLYHEDRA
public static final int SHAPE_POLYHEDRA
- See Also:
- Constant Field Values
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SHAPE_DRAW
public static final int SHAPE_DRAW
- See Also:
- Constant Field Values
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SHAPE_MAX_SPECIAL
public static final int SHAPE_MAX_SPECIAL
- See Also:
- Constant Field Values
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SHAPE_CGO
public static final int SHAPE_CGO
- See Also:
- Constant Field Values
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SHAPE_MIN_SURFACE
public static final int SHAPE_MIN_SURFACE
- See Also:
- Constant Field Values
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SHAPE_ISOSURFACE
public static final int SHAPE_ISOSURFACE
- See Also:
- Constant Field Values
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SHAPE_CONTACT
public static final int SHAPE_CONTACT
- See Also:
- Constant Field Values
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SHAPE_LCAOCARTOON
public static final int SHAPE_LCAOCARTOON
- See Also:
- Constant Field Values
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SHAPE_LAST_ATOM_VIS_FLAG
private static final int SHAPE_LAST_ATOM_VIS_FLAG
- See Also:
- Constant Field Values
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SHAPE_MO
public static final int SHAPE_MO
- See Also:
- Constant Field Values
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SHAPE_NBO
public static final int SHAPE_NBO
- See Also:
- Constant Field Values
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SHAPE_PMESH
public static final int SHAPE_PMESH
- See Also:
- Constant Field Values
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SHAPE_PLOT3D
public static final int SHAPE_PLOT3D
- See Also:
- Constant Field Values
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SHAPE_MAX_SURFACE
public static final int SHAPE_MAX_SURFACE
- See Also:
- Constant Field Values
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SHAPE_MAX_MESH_COLLECTION
public static final int SHAPE_MAX_MESH_COLLECTION
- See Also:
- Constant Field Values
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SHAPE_ECHO
public static final int SHAPE_ECHO
- See Also:
- Constant Field Values
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SHAPE_MAX_HAS_ID
public static final int SHAPE_MAX_HAS_ID
- See Also:
- Constant Field Values
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SHAPE_BBCAGE
public static final int SHAPE_BBCAGE
- See Also:
- Constant Field Values
-
SHAPE_MAX_HAS_SETVIS
public static final int SHAPE_MAX_HAS_SETVIS
- See Also:
- Constant Field Values
-
SHAPE_UCCAGE
public static final int SHAPE_UCCAGE
- See Also:
- Constant Field Values
-
SHAPE_AXES
public static final int SHAPE_AXES
- 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
-
VIS_BOND_FLAG
public static final int VIS_BOND_FLAG
- See Also:
- Constant Field Values
-
VIS_BALLS_FLAG
public static final int VIS_BALLS_FLAG
- See Also:
- Constant Field Values
-
VIS_LABEL_FLAG
public static final int VIS_LABEL_FLAG
- See Also:
- Constant Field Values
-
VIS_BACKBONE_FLAG
public static final int VIS_BACKBONE_FLAG
- See Also:
- Constant Field Values
-
VIS_CARTOON_FLAG
public static final int VIS_CARTOON_FLAG
- See Also:
- Constant Field Values
-
ALPHA_CARBON_VISIBILITY_FLAG
public static final int ALPHA_CARBON_VISIBILITY_FLAG
- See Also:
- Constant Field Values
-
shapeClassBases
public static final String[] shapeClassBases
-
SCRIPT_COMPLETED
public static final String SCRIPT_COMPLETED
- See Also:
- Constant Field Values
-
JPEG_EXTENSIONS
public static final String JPEG_EXTENSIONS
- See Also:
- Constant Field Values
-
IMAGE_TYPES
public static final String IMAGE_TYPES
- See Also:
- Constant Field Values
-
IMAGE_OR_SCENE
public static final String IMAGE_OR_SCENE
- 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
-
LABEL_OFFSET_MAX
public static final int LABEL_OFFSET_MAX
- See Also:
- Constant Field Values
-
LABEL_OFFSET_MASK
private static final int LABEL_OFFSET_MASK
- See Also:
- Constant Field Values
-
LABEL_FLAGY_OFFSET_SHIFT
private static final int LABEL_FLAGY_OFFSET_SHIFT
- See Also:
- Constant Field Values
-
LABEL_FLAGX_OFFSET_SHIFT
private static final int LABEL_FLAGX_OFFSET_SHIFT
- See Also:
- Constant Field Values
-
LABEL_FLAGS
public static final int LABEL_FLAGS
- See Also:
- Constant Field Values
-
LABEL_POINTER_FLAGS
private static final int LABEL_POINTER_FLAGS
- See Also:
- Constant Field Values
-
LABEL_POINTER_NONE
public static final int LABEL_POINTER_NONE
- See Also:
- Constant Field Values
-
LABEL_POINTER_ON
public static final int LABEL_POINTER_ON
- See Also:
- Constant Field Values
-
LABEL_POINTER_BACKGROUND
public static final int LABEL_POINTER_BACKGROUND
- See Also:
- Constant Field Values
-
TEXT_ALIGN_SHIFT
private static final int TEXT_ALIGN_SHIFT
- See Also:
- Constant Field Values
-
TEXT_ALIGN_FLAGS
private static final int TEXT_ALIGN_FLAGS
- See Also:
- Constant Field Values
-
TEXT_ALIGN_NONE
public static final int TEXT_ALIGN_NONE
- See Also:
- Constant Field Values
-
TEXT_ALIGN_LEFT
public static final int TEXT_ALIGN_LEFT
- See Also:
- Constant Field Values
-
TEXT_ALIGN_CENTER
public static final int TEXT_ALIGN_CENTER
- See Also:
- Constant Field Values
-
TEXT_ALIGN_RIGHT
public static final int TEXT_ALIGN_RIGHT
- See Also:
- Constant Field Values
-
LABEL_ZPOS_FLAGS
private static final int LABEL_ZPOS_FLAGS
- See Also:
- Constant Field Values
-
LABEL_ZPOS_GROUP
public static final int LABEL_ZPOS_GROUP
- See Also:
- Constant Field Values
-
LABEL_ZPOS_FRONT
public static final int LABEL_ZPOS_FRONT
- See Also:
- Constant Field Values
-
LABEL_EXPLICIT
private static final int LABEL_EXPLICIT
- See Also:
- Constant Field Values
-
LABEL_CENTERED
private static final int LABEL_CENTERED
- See Also:
- Constant Field Values
-
LABEL_DEFAULT_OFFSET
public static int LABEL_DEFAULT_OFFSET
-
ECHO_TOP
public static final int ECHO_TOP
- See Also:
- Constant Field Values
-
ECHO_BOTTOM
public static final int ECHO_BOTTOM
- See Also:
- Constant Field Values
-
ECHO_MIDDLE
public static final int ECHO_MIDDLE
- See Also:
- Constant Field Values
-
ECHO_XY
public static final int ECHO_XY
- See Also:
- Constant Field Values
-
ECHO_XYZ
public static final int ECHO_XYZ
- See Also:
- Constant Field Values
-
echoNames
private static final String[] echoNames
-
hAlignNames
private static final String[] hAlignNames
-
SMILES_TYPE_SMILES
public static final int SMILES_TYPE_SMILES
- See Also:
- Constant Field Values
-
SMILES_TYPE_SMARTS
public static final int SMILES_TYPE_SMARTS
- See Also:
- Constant Field Values
-
SMILES_TYPE_OPENSMILES
public static final int SMILES_TYPE_OPENSMILES
- See Also:
- Constant Field Values
-
SMILES_TYPE_OPENSMARTS
public static final int SMILES_TYPE_OPENSMARTS
- See Also:
- Constant Field Values
-
SMILES_FIRST_MATCH_ONLY
public static final int SMILES_FIRST_MATCH_ONLY
- See Also:
- Constant Field Values
-
SMILES_NO_AROMATIC
public static final int SMILES_NO_AROMATIC
- See Also:
- Constant Field Values
-
SMILES_IGNORE_STEREOCHEMISTRY
public static final int SMILES_IGNORE_STEREOCHEMISTRY
- See Also:
- Constant Field Values
-
SMILES_INVERT_STEREOCHEMISTRY
public static final int SMILES_INVERT_STEREOCHEMISTRY
- See Also:
- Constant Field Values
-
SMILES_MAP_UNIQUE
public static final int SMILES_MAP_UNIQUE
- See Also:
- Constant Field Values
-
SMILES_AROMATIC_DEFINED
public static final int SMILES_AROMATIC_DEFINED
AROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.- See Also:
- Constant Field Values
-
SMILES_AROMATIC_STRICT
public static final int SMILES_AROMATIC_STRICT
AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds- See Also:
- Constant Field Values
-
SMILES_AROMATIC_DOUBLE
public static final int SMILES_AROMATIC_DOUBLE
AROMATIC_DOUBLE allows a distinction between single and double, as for example is necessary to distinguish between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing)- See Also:
- Constant Field Values
-
SMILES_AROMATIC_MMFF94
public static final int SMILES_AROMATIC_MMFF94
AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.- See Also:
- Constant Field Values
-
SMILES_AROMATIC_PLANAR
public static final int SMILES_AROMATIC_PLANAR
AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)- See Also:
- Constant Field Values
-
SMILES_IGNORE_ATOM_CLASS
public static final int SMILES_IGNORE_ATOM_CLASS
- See Also:
- Constant Field Values
-
SMILES_GEN_EXPLICIT_H
public static final int SMILES_GEN_EXPLICIT_H
- See Also:
- Constant Field Values
-
SMILES_GEN_TOPOLOGY
public static final int SMILES_GEN_TOPOLOGY
- See Also:
- Constant Field Values
-
SMILES_GEN_POLYHEDRAL
public static final int SMILES_GEN_POLYHEDRAL
- See Also:
- Constant Field Values
-
SMILES_GEN_ATOM_COMMENT
public static final int SMILES_GEN_ATOM_COMMENT
- See Also:
- Constant Field Values
-
SMILES_GEN_BIO
public static final int SMILES_GEN_BIO
- See Also:
- Constant Field Values
-
SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS
public static final int SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS
- See Also:
- Constant Field Values
-
SMILES_GEN_BIO_COV_CROSSLINK
public static final int SMILES_GEN_BIO_COV_CROSSLINK
- See Also:
- Constant Field Values
-
SMILES_GEN_BIO_HH_CROSSLINK
public static final int SMILES_GEN_BIO_HH_CROSSLINK
- See Also:
- Constant Field Values
-
SMILES_GEN_BIO_COMMENT
public static final int SMILES_GEN_BIO_COMMENT
- See Also:
- Constant Field Values
-
SMILES_GEN_BIO_NOCOMMENTS
public static final int SMILES_GEN_BIO_NOCOMMENTS
- See Also:
- Constant Field Values
-
SMILES_GROUP_BY_MODEL
public static final int SMILES_GROUP_BY_MODEL
- See Also:
- Constant Field Values
-
JSV_NOT
public static final int JSV_NOT
- See Also:
- Constant Field Values
-
JSV_SEND_JDXMOL
public static final int JSV_SEND_JDXMOL
- See Also:
- Constant Field Values
-
JSV_SETPEAKS
public static final int JSV_SETPEAKS
- See Also:
- Constant Field Values
-
JSV_SELECT
public static final int JSV_SELECT
- See Also:
- Constant Field Values
-
JSV_STRUCTURE
public static final int JSV_STRUCTURE
- See Also:
- Constant Field Values
-
JSV_SEND_H1SIMULATE
public static final int JSV_SEND_H1SIMULATE
- See Also:
- Constant Field Values
-
JSV_SEND_C13SIMULATE
public static final int JSV_SEND_C13SIMULATE
- See Also:
- Constant Field Values
-
NBO_MODEL
public static final int NBO_MODEL
- See Also:
- Constant Field Values
-
NBO_RUN
public static final int NBO_RUN
- See Also:
- Constant Field Values
-
NBO_VIEW
public static final int NBO_VIEW
- See Also:
- Constant Field Values
-
NBO_SEARCH
public static final int NBO_SEARCH
- See Also:
- Constant Field Values
-
NBO_CONFIG
public static final int NBO_CONFIG
- See Also:
- Constant Field Values
-
JSV_CLOSE
public static final int JSV_CLOSE
- See Also:
- Constant Field Values
-
READER_NOT_FOUND
public static String READER_NOT_FOUND
-
UNITID_MODEL
public static final int UNITID_MODEL
- See Also:
- Constant Field Values
-
UNITID_RESIDUE
public static final int UNITID_RESIDUE
- See Also:
- Constant Field Values
-
UNITID_ATOM
public static final int UNITID_ATOM
- See Also:
- Constant Field Values
-
UNITID_INSCODE
public static final int UNITID_INSCODE
- See Also:
- Constant Field Values
-
UNITID_TRIM
public static final int UNITID_TRIM
- See Also:
- Constant Field Values
-
DEFAULT_DRAG_DROP_SCRIPT
public static final String DEFAULT_DRAG_DROP_SCRIPT
- See Also:
- Constant Field Values
-
-
Method Detail
-
getNBOTypeFromName
public static int getNBOTypeFromName(String nboType)
-
getCIPChiralityName
public static String getCIPChiralityName(int flags)
-
getCIPRuleName
public static String getCIPRuleName(int i)
-
getCIPChiralityCode
public static int getCIPChiralityCode(char c)
-
fixProtocol
static String fixProtocol(String name)
Check for databases that have changed from http:// to https:// over time. We substitute https here in case this is from an old reference.- Parameters:
name
-- Returns:
- https protocol if necessary
-
getMacroList
public static String getMacroList()
-
getShapeVisibilityFlag
public static final int getShapeVisibilityFlag(int shapeID)
-
shapeTokenIndex
public static final int shapeTokenIndex(int tok)
-
getShapeClassName
public static final String getShapeClassName(int shapeID, boolean isRenderer)
-
getEchoName
public static String getEchoName(int type)
-
setZPosition
public static int setZPosition(int offset, int pos)
-
setPointer
public static int setPointer(int offset, int pointer)
-
getPointer
public static int getPointer(int offset)
-
getPointerName
public static String getPointerName(int pointer)
-
isOffsetAbsolute
public static boolean isOffsetAbsolute(int offset)
-
getOffset
public static int getOffset(int xOffset, int yOffset, boolean isAbsolute)
Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered". The non-exact default offset of [4,4] is represented as 0 so that new array elements do not have to be initialized.- Parameters:
xOffset
-yOffset
-isAbsolute
-- Returns:
- packed offset x and y with positioning flags
-
getXOffset
public static int getXOffset(int offset)
X offset in pixels. negative of this is the actual screen offset- Parameters:
offset
- 0 for an offset indicates "not set" and delivers the default offset- Returns:
- screen offset from left
-
getYOffset
public static int getYOffset(int offset)
Y offset in pixels; negative of this is the actual screen offset- Parameters:
offset
- 0 for an offset indicates "not set" and delivers the default offset- Returns:
- screen offset from bottom
-
getAlignment
public static int getAlignment(int offset)
-
setHorizAlignment
public static int setHorizAlignment(int offset, int hAlign)
-
getHorizAlignmentName
public static String getHorizAlignmentName(int align)
-
isSmilesCanonical
public static boolean isSmilesCanonical(String options)
-
getServiceCommand
public static int getServiceCommand(String script)
-
getUnitIDFlags
public static int getUnitIDFlags(String type)
Get a unitID type- Parameters:
type
- -mra (model name, residue, atom, and ins code), -mr (model and residue; no atom) -ra default - or -r just residue -t right-trim- Returns:
- coded type
-
-