Package org.jmol.viewer
Class JC
java.lang.Object
org.jmol.viewer.JC
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
static final String
static final int
static final int[]
static final float
static final int[]
static final int
static final int
static final int[]
static final int[]
static final byte
static final int
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final int
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final int
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final byte
static final int
static final int
static final byte
static final byte
static final int
static final javajs.util.V3
static final javajs.util.V3
static final javajs.util.V3
static final javajs.util.V3
static final javajs.util.V3
static final javajs.util.V3
static final String
static final javajs.util.V3
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final String
private static final String[]
static final String
static final short
static final float
static final float
static final String
static final String
static final String
static final String
static final float
static final float
static final float
static final int
static final float
static final String
private static final String
static final int
static final float
static final int
static final int
static final int
static final int
static final int
private static final String[]
static final String
static final float
static final int
static final String
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final String[]
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
private static final int
private static final int
static final int
static final int
static final int
static final int
static final int
static final int
private static final String[]
static final String
static final String
static final String
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
private static final int
static final int
static int
static final int
static final int
static final int
static final int
private static final int
private static final int
static final int
static final int
private static final int
static final int
static final int
private static final int
static final int
static final int
private static final int
static final int
static final int
(package private) static final String
static final String
static String[]
static final short
static String
static final int
static final int
static final float
static final String
static final String
static final int
static final byte
static final byte
static final byte
static final byte
static final int
static final int
static final int
static final int
static final String
static final int
static final String
static final boolean
static final int
static final int
static final String
static String[]
static String[]
static final int
static final int
static final float
static String
static final String
static final int
private static final String[]
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
private static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final String[]
static final int
static final int
AROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.static final int
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)static final int
AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.static final int
AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)static final int
AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bondsstatic final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final String
static final int
private static final int
static final int
static final int
static final int
private static final int
static final float
static final javajs.util.V3[]
static final int
static final int
static final int
static final int
static final int
static final String
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final String
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic String
(package private) static String
fixOptimadeCall
(String url) Get all necessary response fields if an optimade call.(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 String
getBoolName
(int g) 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 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 final String
getShapeClassName
(int shapeID, boolean isRenderer) static final 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 final int
shapeTokenIndex
(int tok)
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Field Details
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NBO_TYPES
- See Also:
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CIP_CHIRALITY_UNKNOWN
public static final int CIP_CHIRALITY_UNKNOWN- See Also:
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CIP_CHIRALITY_R_FLAG
public static final int CIP_CHIRALITY_R_FLAG- See Also:
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CIP_CHIRALITY_S_FLAG
public static final int CIP_CHIRALITY_S_FLAG- See Also:
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CIP_CHIRALITY_CANTDETERMINE
public static final int CIP_CHIRALITY_CANTDETERMINE- See Also:
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CIP_CHIRALITY_NONE
public static final int CIP_CHIRALITY_NONE- See Also:
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CIP_CHIRALITY_EZ_FLAG
public static final int CIP_CHIRALITY_EZ_FLAG- See Also:
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CIP_CHIRALITY_PSEUDO_FLAG
public static final int CIP_CHIRALITY_PSEUDO_FLAG- See Also:
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CIP_CHIRALITY_AXIAL_FLAG
public static final int CIP_CHIRALITY_AXIAL_FLAG- See Also:
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CIP_CHIRALITY_NAME_MASK
public static final int CIP_CHIRALITY_NAME_MASK- See Also:
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CIP_CHIRALITY_NAME_OFFSET
public static final int CIP_CHIRALITY_NAME_OFFSET- See Also:
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CIP_CHIRALITY_seqCis_FLAG
public static final int CIP_CHIRALITY_seqCis_FLAG- See Also:
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CIP_CHIRALITY_seqTrans_FLAG
public static final int CIP_CHIRALITY_seqTrans_FLAG- See Also:
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CIP_CHIRALITY_seqcis_FLAG
public static final int CIP_CHIRALITY_seqcis_FLAG- See Also:
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CIP_CHIRALITY_seqtrans_FLAG
public static final int CIP_CHIRALITY_seqtrans_FLAG- See Also:
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CIP_CHIRALITY_M_FLAG
public static final int CIP_CHIRALITY_M_FLAG- See Also:
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CIP_CHIRALITY_P_FLAG
public static final int CIP_CHIRALITY_P_FLAG- See Also:
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CIP_CHIRALITY_r_FLAG
public static final int CIP_CHIRALITY_r_FLAG- See Also:
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CIP_CHIRALITY_s_FLAG
public static final int CIP_CHIRALITY_s_FLAG- See Also:
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CIP_CHIRALITY_m_FLAG
public static final int CIP_CHIRALITY_m_FLAG- See Also:
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CIP_CHIRALITY_p_FLAG
public static final int CIP_CHIRALITY_p_FLAG- See Also:
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ruleNames
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PDB_ANNOTATIONS
- See Also:
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CACTUS_FILE_TYPES
- See Also:
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defaultMacroDirectory
- See Also:
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databaseArray
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legacyResolver
- See Also:
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databases
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defaultOptimadeFieldsStr
- See Also:
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macros
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copyright
- See Also:
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version
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majorVersion
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date
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versionInt
public static final int versionInt -
officialRelease
public static final boolean officialRelease- See Also:
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DEFAULT_HELP_PATH
- See Also:
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STATE_VERSION_STAMP
- See Also:
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EMBEDDED_SCRIPT_TAG
- See Also:
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NOTE_SCRIPT_FILE
- See Also:
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SCRIPT_EXT
- See Also:
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SCRIPT_STEP
- See Also:
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SCRIPT_START
- See Also:
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SCRIPT_NOENDCHECK
- See Also:
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SCRIPT_ISEDITOR
- See Also:
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SCRIPT_EDITOR_IGNORE
- See Also:
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REPAINT_IGNORE
- See Also:
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SCRIPT_GUI
- See Also:
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LOAD_ATOM_DATA_TYPES
- See Also:
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radiansPerDegree
public static final float radiansPerDegree- See Also:
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allowedQuaternionFrames
- See Also:
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EXPORT_DRIVER_LIST
- See Also:
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center
public static final javajs.util.V3 center -
axisX
public static final javajs.util.V3 axisX -
axisY
public static final javajs.util.V3 axisY -
axisZ
public static final javajs.util.V3 axisZ -
axisNX
public static final javajs.util.V3 axisNX -
axisNY
public static final javajs.util.V3 axisNY -
axisNZ
public static final javajs.util.V3 axisNZ -
unitAxisVectors
public static final javajs.util.V3[] unitAxisVectors -
XY_ZTOP
public static final int XY_ZTOP- See Also:
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DEFAULT_PERCENT_VDW_ATOM
public static final int DEFAULT_PERCENT_VDW_ATOM- See Also:
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DEFAULT_BOND_RADIUS
public static final float DEFAULT_BOND_RADIUS- See Also:
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DEFAULT_BOND_MILLIANGSTROM_RADIUS
public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS- See Also:
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DEFAULT_STRUT_RADIUS
public static final float DEFAULT_STRUT_RADIUS- See Also:
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DEFAULT_BOND_TOLERANCE
public static final float DEFAULT_BOND_TOLERANCE- See Also:
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DEFAULT_MIN_BOND_DISTANCE
public static final float DEFAULT_MIN_BOND_DISTANCE- See Also:
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DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MAX_CONNECT_DISTANCE- See Also:
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DEFAULT_MIN_CONNECT_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE- See Also:
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MINIMIZE_FIXED_RANGE
public static final float MINIMIZE_FIXED_RANGE- See Also:
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ENC_CALC_MAX_DIST
public static final float ENC_CALC_MAX_DIST- See Also:
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ENV_CALC_MAX_LEVEL
public static final int ENV_CALC_MAX_LEVEL- See Also:
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MOUSE_NONE
public static final int MOUSE_NONE- See Also:
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MULTIBOND_NEVER
public static final byte MULTIBOND_NEVER- See Also:
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MULTIBOND_WIREFRAME
public static final byte MULTIBOND_WIREFRAME- See Also:
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MULTIBOND_NOTSMALL
public static final byte MULTIBOND_NOTSMALL- See Also:
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MULTIBOND_ALWAYS
public static final byte MULTIBOND_ALWAYS- See Also:
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MAXIMUM_AUTO_BOND_COUNT
public static final int MAXIMUM_AUTO_BOND_COUNT- See Also:
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madMultipleBondSmallMaximum
public static final short madMultipleBondSmallMaximum- See Also:
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ANGSTROMS_PER_BOHR
public static final float ANGSTROMS_PER_BOHR- See Also:
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altArgbsCpk
public static final int[] altArgbsCpk -
argbsFormalCharge
public static final int[] argbsFormalCharge -
argbsRwbScale
public static final int[] argbsRwbScale -
FORMAL_CHARGE_COLIX_RED
public static final int FORMAL_CHARGE_COLIX_RED -
PARTIAL_CHARGE_COLIX_RED
public static final int PARTIAL_CHARGE_COLIX_RED -
PARTIAL_CHARGE_RANGE_SIZE
public static final int PARTIAL_CHARGE_RANGE_SIZE -
argbsRoygbScale
public static final int[] argbsRoygbScale -
argbsIsosurfacePositive
public static final int argbsIsosurfacePositive- See Also:
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argbsIsosurfaceNegative
public static final int argbsIsosurfaceNegative- See Also:
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ATOMID_AMINO_NITROGEN
public static final byte ATOMID_AMINO_NITROGEN- See Also:
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ATOMID_ALPHA_CARBON
public static final byte ATOMID_ALPHA_CARBON- See Also:
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ATOMID_CARBONYL_CARBON
public static final byte ATOMID_CARBONYL_CARBON- See Also:
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ATOMID_CARBONYL_OXYGEN
public static final byte ATOMID_CARBONYL_OXYGEN- See Also:
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ATOMID_O1
public static final byte ATOMID_O1- See Also:
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ATOMID_ALPHA_ONLY_MASK
public static final int ATOMID_ALPHA_ONLY_MASK- See Also:
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ATOMID_PROTEIN_MASK
public static final int ATOMID_PROTEIN_MASK- See Also:
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ATOMID_O5_PRIME
public static final byte ATOMID_O5_PRIME- See Also:
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ATOMID_C5_PRIME
public static final byte ATOMID_C5_PRIME- See Also:
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ATOMID_C4_PRIME
public static final byte ATOMID_C4_PRIME- See Also:
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ATOMID_C3_PRIME
public static final byte ATOMID_C3_PRIME- See Also:
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ATOMID_O3_PRIME
public static final byte ATOMID_O3_PRIME- See Also:
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ATOMID_C2_PRIME
public static final byte ATOMID_C2_PRIME- See Also:
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ATOMID_C1_PRIME
public static final byte ATOMID_C1_PRIME- See Also:
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ATOMID_O4_PRIME
public static final byte ATOMID_O4_PRIME- See Also:
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ATOMID_NUCLEIC_MASK
public static final int ATOMID_NUCLEIC_MASK- See Also:
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ATOMID_NUCLEIC_PHOSPHORUS
public static final byte ATOMID_NUCLEIC_PHOSPHORUS- See Also:
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ATOMID_PHOSPHORUS_ONLY_MASK
public static final int ATOMID_PHOSPHORUS_ONLY_MASK- See Also:
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ATOMID_DISTINGUISHING_ATOM_MAX
public static final int ATOMID_DISTINGUISHING_ATOM_MAX- See Also:
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ATOMID_CARBONYL_OD1
public static final byte ATOMID_CARBONYL_OD1- See Also:
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ATOMID_CARBONYL_OD2
public static final byte ATOMID_CARBONYL_OD2- See Also:
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ATOMID_CARBONYL_OE1
public static final byte ATOMID_CARBONYL_OE1- See Also:
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ATOMID_CARBONYL_OE2
public static final byte ATOMID_CARBONYL_OE2- See Also:
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ATOMID_N1
public static final byte ATOMID_N1- See Also:
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ATOMID_C2
public static final byte ATOMID_C2- See Also:
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ATOMID_N3
public static final byte ATOMID_N3- See Also:
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ATOMID_C4
public static final byte ATOMID_C4- See Also:
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ATOMID_C5
public static final byte ATOMID_C5- See Also:
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ATOMID_C6
public static final byte ATOMID_C6- See Also:
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ATOMID_O2
public static final byte ATOMID_O2- See Also:
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ATOMID_N7
public static final byte ATOMID_N7- See Also:
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ATOMID_C8
public static final byte ATOMID_C8- See Also:
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ATOMID_N9
public static final byte ATOMID_N9- See Also:
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ATOMID_N4
public static final byte ATOMID_N4- See Also:
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ATOMID_N2
public static final byte ATOMID_N2- See Also:
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ATOMID_N6
public static final byte ATOMID_N6- See Also:
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ATOMID_C5M
public static final byte ATOMID_C5M- See Also:
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ATOMID_O6
public static final byte ATOMID_O6- See Also:
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ATOMID_O4
public static final byte ATOMID_O4- See Also:
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ATOMID_S4
public static final byte ATOMID_S4- See Also:
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ATOMID_C7
public static final byte ATOMID_C7- See Also:
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ATOMID_TERMINATING_OXT
public static final byte ATOMID_TERMINATING_OXT- See Also:
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ATOMID_H5T_TERMINUS
public static final byte ATOMID_H5T_TERMINUS- See Also:
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ATOMID_O5T_TERMINUS
public static final byte ATOMID_O5T_TERMINUS- See Also:
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ATOMID_O1P
public static final byte ATOMID_O1P- See Also:
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ATOMID_OP1
public static final byte ATOMID_OP1- See Also:
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ATOMID_O2P
public static final byte ATOMID_O2P- See Also:
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ATOMID_OP2
public static final byte ATOMID_OP2- See Also:
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ATOMID_O2_PRIME
public static final byte ATOMID_O2_PRIME- See Also:
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ATOMID_H3T_TERMINUS
public static final byte ATOMID_H3T_TERMINUS- See Also:
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ATOMID_HO3_PRIME
public static final byte ATOMID_HO3_PRIME- See Also:
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ATOMID_HO5_PRIME
public static final byte ATOMID_HO5_PRIME- See Also:
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PURINE_MASK
public static final int PURINE_MASK- See Also:
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PYRIMIDINE_MASK
public static final int PYRIMIDINE_MASK- See Also:
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DNA_MASK
public static final int DNA_MASK- See Also:
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RNA_MASK
public static final int RNA_MASK- See Also:
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GROUPID_ARGININE
public static final int GROUPID_ARGININE- See Also:
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GROUPID_ASPARAGINE
public static final int GROUPID_ASPARAGINE- See Also:
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GROUPID_ASPARTATE
public static final int GROUPID_ASPARTATE- See Also:
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GROUPID_CYSTEINE
public static final int GROUPID_CYSTEINE- See Also:
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GROUPID_GLUTAMINE
public static final int GROUPID_GLUTAMINE- See Also:
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GROUPID_GLUTAMATE
public static final int GROUPID_GLUTAMATE- See Also:
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GROUPID_HISTIDINE
public static final int GROUPID_HISTIDINE- See Also:
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GROUPID_LYSINE
public static final int GROUPID_LYSINE- See Also:
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GROUPID_PROLINE
public static final int GROUPID_PROLINE- See Also:
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GROUPID_TRYPTOPHAN
public static final int GROUPID_TRYPTOPHAN- See Also:
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GROUPID_AMINO_MAX
public static final int GROUPID_AMINO_MAX- See Also:
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GROUPID_NUCLEIC_MAX
public static final int GROUPID_NUCLEIC_MAX- See Also:
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GROUPID_WATER
public static final int GROUPID_WATER- See Also:
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GROUPID_SOLVENT_MIN
public static final int GROUPID_SOLVENT_MIN- See Also:
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GROUPID_ION_MIN
private static final int GROUPID_ION_MIN- See Also:
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GROUPID_ION_MAX
private static final int GROUPID_ION_MAX- See Also:
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predefinedVariable
-
predefinedStatic
-
MODELKIT_ZAP_STRING
- See Also:
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MODELKIT_ZAP_TITLE
- See Also:
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ZAP_TITLE
- See Also:
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ADD_HYDROGEN_TITLE
- See Also:
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DEFAULT_FONTFACE
- See Also:
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DEFAULT_FONTSTYLE
- See Also:
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MEASURE_DEFAULT_FONTSIZE
public static final int MEASURE_DEFAULT_FONTSIZE- See Also:
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AXES_DEFAULT_FONTSIZE
public static final int AXES_DEFAULT_FONTSIZE- See Also:
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DRAW_DEFAULT_FONTSIZE
public static final float DRAW_DEFAULT_FONTSIZE- See Also:
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SHAPE_BALLS
public static final int SHAPE_BALLS- See Also:
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SHAPE_STICKS
public static final int SHAPE_STICKS- See Also:
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SHAPE_HSTICKS
public static final int SHAPE_HSTICKS- See Also:
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SHAPE_SSSTICKS
public static final int SHAPE_SSSTICKS- See Also:
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SHAPE_STRUTS
public static final int SHAPE_STRUTS- See Also:
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SHAPE_LABELS
public static final int SHAPE_LABELS- See Also:
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SHAPE_MEASURES
public static final int SHAPE_MEASURES- See Also:
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SHAPE_STARS
public static final int SHAPE_STARS- See Also:
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SHAPE_MIN_HAS_SETVIS
public static final int SHAPE_MIN_HAS_SETVIS- See Also:
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SHAPE_HALOS
public static final int SHAPE_HALOS- See Also:
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SHAPE_MIN_SECONDARY
public static final int SHAPE_MIN_SECONDARY- See Also:
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SHAPE_BACKBONE
public static final int SHAPE_BACKBONE- See Also:
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SHAPE_TRACE
public static final int SHAPE_TRACE- See Also:
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SHAPE_CARTOON
public static final int SHAPE_CARTOON- See Also:
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SHAPE_STRANDS
public static final int SHAPE_STRANDS- See Also:
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SHAPE_MESHRIBBON
public static final int SHAPE_MESHRIBBON- See Also:
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SHAPE_RIBBONS
public static final int SHAPE_RIBBONS- See Also:
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SHAPE_ROCKETS
public static final int SHAPE_ROCKETS- See Also:
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SHAPE_MAX_SECONDARY
public static final int SHAPE_MAX_SECONDARY- See Also:
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SHAPE_MIN_SPECIAL
public static final int SHAPE_MIN_SPECIAL- See Also:
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SHAPE_DOTS
public static final int SHAPE_DOTS- See Also:
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SHAPE_DIPOLES
public static final int SHAPE_DIPOLES- See Also:
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SHAPE_VECTORS
public static final int SHAPE_VECTORS- See Also:
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SHAPE_GEOSURFACE
public static final int SHAPE_GEOSURFACE- See Also:
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SHAPE_ELLIPSOIDS
public static final int SHAPE_ELLIPSOIDS- See Also:
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SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT- See Also:
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SHAPE_MIN_HAS_ID
public static final int SHAPE_MIN_HAS_ID- See Also:
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SHAPE_POLYHEDRA
public static final int SHAPE_POLYHEDRA- See Also:
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SHAPE_DRAW
public static final int SHAPE_DRAW- See Also:
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SHAPE_MAX_SPECIAL
public static final int SHAPE_MAX_SPECIAL- See Also:
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SHAPE_CGO
public static final int SHAPE_CGO- See Also:
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SHAPE_MIN_SURFACE
public static final int SHAPE_MIN_SURFACE- See Also:
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SHAPE_ISOSURFACE
public static final int SHAPE_ISOSURFACE- See Also:
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SHAPE_CONTACT
public static final int SHAPE_CONTACT- See Also:
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SHAPE_LCAOCARTOON
public static final int SHAPE_LCAOCARTOON- See Also:
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SHAPE_LAST_ATOM_VIS_FLAG
private static final int SHAPE_LAST_ATOM_VIS_FLAG- See Also:
-
SHAPE_MO
public static final int SHAPE_MO- See Also:
-
SHAPE_NBO
public static final int SHAPE_NBO- See Also:
-
SHAPE_PMESH
public static final int SHAPE_PMESH- See Also:
-
SHAPE_PLOT3D
public static final int SHAPE_PLOT3D- See Also:
-
SHAPE_MAX_SURFACE
public static final int SHAPE_MAX_SURFACE- See Also:
-
SHAPE_MAX_MESH_COLLECTION
public static final int SHAPE_MAX_MESH_COLLECTION- See Also:
-
SHAPE_ECHO
public static final int SHAPE_ECHO- See Also:
-
SHAPE_MAX_HAS_ID
public static final int SHAPE_MAX_HAS_ID- See Also:
-
SHAPE_BBCAGE
public static final int SHAPE_BBCAGE- See Also:
-
SHAPE_MAX_HAS_SETVIS
public static final int SHAPE_MAX_HAS_SETVIS- See Also:
-
SHAPE_UCCAGE
public static final int SHAPE_UCCAGE- See Also:
-
SHAPE_AXES
public static final int SHAPE_AXES- See Also:
-
SHAPE_HOVER
public static final int SHAPE_HOVER- See Also:
-
SHAPE_FRANK
public static final int SHAPE_FRANK- See Also:
-
SHAPE_MAX
public static final int SHAPE_MAX- See Also:
-
VIS_BOND_FLAG
public static final int VIS_BOND_FLAG- See Also:
-
VIS_BALLS_FLAG
public static final int VIS_BALLS_FLAG- See Also:
-
VIS_LABEL_FLAG
public static final int VIS_LABEL_FLAG- See Also:
-
VIS_BACKBONE_FLAG
public static final int VIS_BACKBONE_FLAG- See Also:
-
VIS_CARTOON_FLAG
public static final int VIS_CARTOON_FLAG- See Also:
-
ALPHA_CARBON_VISIBILITY_FLAG
public static final int ALPHA_CARBON_VISIBILITY_FLAG- See Also:
-
shapeClassBases
-
SCRIPT_COMPLETED
- See Also:
-
JPEG_EXTENSIONS
- See Also:
-
IMAGE_TYPES
- See Also:
-
IMAGE_OR_SCENE
- See Also:
-
LABEL_MINIMUM_FONTSIZE
public static final int LABEL_MINIMUM_FONTSIZE- See Also:
-
LABEL_MAXIMUM_FONTSIZE
public static final int LABEL_MAXIMUM_FONTSIZE- See Also:
-
LABEL_DEFAULT_FONTSIZE
public static final int LABEL_DEFAULT_FONTSIZE- See Also:
-
LABEL_DEFAULT_X_OFFSET
public static final int LABEL_DEFAULT_X_OFFSET- See Also:
-
LABEL_DEFAULT_Y_OFFSET
public static final int LABEL_DEFAULT_Y_OFFSET- See Also:
-
LABEL_OFFSET_MAX
public static final int LABEL_OFFSET_MAX- See Also:
-
LABEL_OFFSET_MASK
private static final int LABEL_OFFSET_MASK- See Also:
-
LABEL_FLAGY_OFFSET_SHIFT
private static final int LABEL_FLAGY_OFFSET_SHIFT- See Also:
-
LABEL_FLAGX_OFFSET_SHIFT
private static final int LABEL_FLAGX_OFFSET_SHIFT- See Also:
-
LABEL_FLAGS
public static final int LABEL_FLAGS- See Also:
-
LABEL_POINTER_FLAGS
private static final int LABEL_POINTER_FLAGS- See Also:
-
LABEL_POINTER_NONE
public static final int LABEL_POINTER_NONE- See Also:
-
LABEL_POINTER_ON
public static final int LABEL_POINTER_ON- See Also:
-
LABEL_POINTER_BACKGROUND
public static final int LABEL_POINTER_BACKGROUND- See Also:
-
TEXT_ALIGN_SHIFT
private static final int TEXT_ALIGN_SHIFT- See Also:
-
TEXT_ALIGN_FLAGS
private static final int TEXT_ALIGN_FLAGS- See Also:
-
TEXT_ALIGN_NONE
public static final int TEXT_ALIGN_NONE- See Also:
-
TEXT_ALIGN_LEFT
public static final int TEXT_ALIGN_LEFT- See Also:
-
TEXT_ALIGN_CENTER
public static final int TEXT_ALIGN_CENTER- See Also:
-
TEXT_ALIGN_RIGHT
public static final int TEXT_ALIGN_RIGHT- See Also:
-
LABEL_ZPOS_FLAGS
private static final int LABEL_ZPOS_FLAGS- See Also:
-
LABEL_ZPOS_GROUP
public static final int LABEL_ZPOS_GROUP- See Also:
-
LABEL_ZPOS_FRONT
public static final int LABEL_ZPOS_FRONT- See Also:
-
LABEL_EXPLICIT
public static final int LABEL_EXPLICIT- See Also:
-
LABEL_CENTERED
private static final int LABEL_CENTERED- See Also:
-
LABEL_DEFAULT_OFFSET
public static int LABEL_DEFAULT_OFFSET -
ECHO_TOP
public static final int ECHO_TOP- See Also:
-
ECHO_BOTTOM
public static final int ECHO_BOTTOM- See Also:
-
ECHO_MIDDLE
public static final int ECHO_MIDDLE- See Also:
-
ECHO_XY
public static final int ECHO_XY- See Also:
-
ECHO_XYZ
public static final int ECHO_XYZ- See Also:
-
echoNames
-
hAlignNames
-
SMILES_TYPE_SMILES
public static final int SMILES_TYPE_SMILES- See Also:
-
SMILES_TYPE_SMARTS
public static final int SMILES_TYPE_SMARTS- See Also:
-
SMILES_TYPE_OPENSMILES
public static final int SMILES_TYPE_OPENSMILES- See Also:
-
SMILES_TYPE_OPENSMARTS
public static final int SMILES_TYPE_OPENSMARTS- See Also:
-
SMILES_FIRST_MATCH_ONLY
public static final int SMILES_FIRST_MATCH_ONLY- See Also:
-
SMILES_NO_AROMATIC
public static final int SMILES_NO_AROMATIC- See Also:
-
SMILES_IGNORE_STEREOCHEMISTRY
public static final int SMILES_IGNORE_STEREOCHEMISTRY- See Also:
-
SMILES_INVERT_STEREOCHEMISTRY
public static final int SMILES_INVERT_STEREOCHEMISTRY- See Also:
-
SMILES_MAP_UNIQUE
public static final int SMILES_MAP_UNIQUE- See Also:
-
SMILES_AROMATIC_DEFINED
public static final int SMILES_AROMATIC_DEFINEDAROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.- See Also:
-
SMILES_AROMATIC_STRICT
public static final int SMILES_AROMATIC_STRICTAROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds- See Also:
-
SMILES_AROMATIC_DOUBLE
public static final int SMILES_AROMATIC_DOUBLEAROMATIC_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:
-
SMILES_AROMATIC_MMFF94
public static final int SMILES_AROMATIC_MMFF94AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.- See Also:
-
SMILES_AROMATIC_PLANAR
public static final int SMILES_AROMATIC_PLANARAROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)- See Also:
-
SMILES_IGNORE_ATOM_CLASS
public static final int SMILES_IGNORE_ATOM_CLASS- See Also:
-
SMILES_GEN_EXPLICIT_H_ALL
public static final int SMILES_GEN_EXPLICIT_H_ALL- See Also:
-
SMILES_GEN_EXPLICIT_H2_ONLY
public static final int SMILES_GEN_EXPLICIT_H2_ONLY- See Also:
-
SMILES_GEN_TOPOLOGY
public static final int SMILES_GEN_TOPOLOGY- See Also:
-
SMILES_GEN_POLYHEDRAL
public static final int SMILES_GEN_POLYHEDRAL- See Also:
-
SMILES_GEN_ATOM_COMMENT
public static final int SMILES_GEN_ATOM_COMMENT- See Also:
-
SMILES_GEN_NO_BRANCHES
public static final int SMILES_GEN_NO_BRANCHES- See Also:
-
SMILES_GEN_BIO
public static final int SMILES_GEN_BIO- See Also:
-
SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS
public static final int SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS- See Also:
-
SMILES_GEN_BIO_COV_CROSSLINK
public static final int SMILES_GEN_BIO_COV_CROSSLINK- See Also:
-
SMILES_GEN_BIO_HH_CROSSLINK
public static final int SMILES_GEN_BIO_HH_CROSSLINK- See Also:
-
SMILES_GEN_BIO_COMMENT
public static final int SMILES_GEN_BIO_COMMENT- See Also:
-
SMILES_GEN_BIO_NOCOMMENTS
public static final int SMILES_GEN_BIO_NOCOMMENTS- See Also:
-
SMILES_GROUP_BY_MODEL
public static final int SMILES_GROUP_BY_MODEL- See Also:
-
SMILES_2D
public static final int SMILES_2D- See Also:
-
JSV_NOT
public static final int JSV_NOT- See Also:
-
JSV_SEND_JDXMOL
public static final int JSV_SEND_JDXMOL- See Also:
-
JSV_SETPEAKS
public static final int JSV_SETPEAKS- See Also:
-
JSV_SELECT
public static final int JSV_SELECT- See Also:
-
JSV_STRUCTURE
public static final int JSV_STRUCTURE- See Also:
-
JSV_SEND_H1SIMULATE
public static final int JSV_SEND_H1SIMULATE- See Also:
-
JSV_SEND_C13SIMULATE
public static final int JSV_SEND_C13SIMULATE- See Also:
-
NBO_MODEL
public static final int NBO_MODEL- See Also:
-
NBO_RUN
public static final int NBO_RUN- See Also:
-
NBO_VIEW
public static final int NBO_VIEW- See Also:
-
NBO_SEARCH
public static final int NBO_SEARCH- See Also:
-
NBO_CONFIG
public static final int NBO_CONFIG- See Also:
-
JSV_CLOSE
public static final int JSV_CLOSE- See Also:
-
READER_NOT_FOUND
-
UNITID_MODEL
public static final int UNITID_MODEL- See Also:
-
UNITID_RESIDUE
public static final int UNITID_RESIDUE- See Also:
-
UNITID_ATOM
public static final int UNITID_ATOM- See Also:
-
UNITID_INSCODE
public static final int UNITID_INSCODE- See Also:
-
UNITID_TRIM
public static final int UNITID_TRIM- See Also:
-
DEFAULT_DRAG_DROP_SCRIPT
- See Also:
-
UC_TOLERANCE2
public static final float UC_TOLERANCE2- See Also:
-
globalBooleans
-
GLOBAL_FRACTCOORD
public static final int GLOBAL_FRACTCOORD- See Also:
-
GLOBAL_SYMMETRY
public static final int GLOBAL_SYMMETRY- See Also:
-
GLOBAL_UNITCELLS
public static final int GLOBAL_UNITCELLS- See Also:
-
GLOBAL_CONECT
public static final int GLOBAL_CONECT- See Also:
-
GLOBAL_ISPDB
public static final int GLOBAL_ISPDB- See Also:
-
GLOBAL_DOMAINS
public static final int GLOBAL_DOMAINS- See Also:
-
GLOBAL_VALIDATIONS
public static final int GLOBAL_VALIDATIONS- See Also:
-
GLOBAL_SUPERCELL
public static final int GLOBAL_SUPERCELL- See Also:
-
GLOBAL_AROMATICBONDS
public static final int GLOBAL_AROMATICBONDS- See Also:
-
GLOBAL_MODULATED
public static final int GLOBAL_MODULATED- See Also:
-
-
Constructor Details
-
JC
public JC()
-
-
Method Details
-
getNBOTypeFromName
-
getCIPChiralityName
-
getCIPRuleName
-
getCIPChiralityCode
public static int getCIPChiralityCode(char c) -
resolveDataBase
-
fixProtocol
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
-
fixOptimadeCall
Get all necessary response fields if an optimade call. Note that the only conditions we have here is that this is http and "optimade" is in the URL. Obviously not exactly correct.- Parameters:
url
-- Returns:
- call with added necessary response_fields
-
embedScript
-
getShapeVisibilityFlag
public static final int getShapeVisibilityFlag(int shapeID) -
shapeTokenIndex
public static final int shapeTokenIndex(int tok) -
getShapeClassName
-
getEchoName
-
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
-
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
-
isSmilesCanonical
-
getServiceCommand
-
getUnitIDFlags
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
-
getBoolName
-