public final class JC
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
ADD_HYDROGEN_TITLE |
|
static java.lang.String |
allowedQuaternionFrames |
|
static int |
ALPHA_CARBON_VISIBILITY_FLAG |
|
static int[] |
altArgbsCpk |
|
static float |
ANGSTROMS_PER_BOHR |
|
static int[] |
argbsFormalCharge |
|
static int |
argbsIsosurfaceNegative |
|
static int |
argbsIsosurfacePositive |
|
static int[] |
argbsRoygbScale |
|
static int[] |
argbsRwbScale |
|
static byte |
ATOMID_ALPHA_CARBON |
|
static int |
ATOMID_ALPHA_ONLY_MASK |
|
static byte |
ATOMID_AMINO_NITROGEN |
|
static byte |
ATOMID_C1_PRIME |
|
static byte |
ATOMID_C2 |
|
static byte |
ATOMID_C2_PRIME |
|
static byte |
ATOMID_C3_PRIME |
|
static byte |
ATOMID_C4 |
|
static byte |
ATOMID_C4_PRIME |
|
static byte |
ATOMID_C5 |
|
static byte |
ATOMID_C5_PRIME |
|
static byte |
ATOMID_C5M |
|
static byte |
ATOMID_C6 |
|
static byte |
ATOMID_C7 |
|
static byte |
ATOMID_C8 |
|
static byte |
ATOMID_CARBONYL_CARBON |
|
static byte |
ATOMID_CARBONYL_OD1 |
|
static byte |
ATOMID_CARBONYL_OD2 |
|
static byte |
ATOMID_CARBONYL_OE1 |
|
static byte |
ATOMID_CARBONYL_OE2 |
|
static byte |
ATOMID_CARBONYL_OXYGEN |
|
static int |
ATOMID_DISTINGUISHING_ATOM_MAX |
|
static byte |
ATOMID_H3T_TERMINUS |
|
static byte |
ATOMID_H5T_TERMINUS |
|
static byte |
ATOMID_HO3_PRIME |
|
static byte |
ATOMID_HO5_PRIME |
|
static byte |
ATOMID_N1 |
|
static byte |
ATOMID_N2 |
|
static byte |
ATOMID_N3 |
|
static byte |
ATOMID_N4 |
|
static byte |
ATOMID_N6 |
|
static byte |
ATOMID_N7 |
|
static byte |
ATOMID_N9 |
|
static int |
ATOMID_NUCLEIC_MASK |
|
static byte |
ATOMID_NUCLEIC_PHOSPHORUS |
|
static byte |
ATOMID_O1 |
|
static byte |
ATOMID_O1P |
|
static byte |
ATOMID_O2 |
|
static byte |
ATOMID_O2_PRIME |
|
static byte |
ATOMID_O2P |
|
static byte |
ATOMID_O3_PRIME |
|
static byte |
ATOMID_O4 |
|
static byte |
ATOMID_O4_PRIME |
|
static byte |
ATOMID_O5_PRIME |
|
static byte |
ATOMID_O5T_TERMINUS |
|
static byte |
ATOMID_O6 |
|
static byte |
ATOMID_OP1 |
|
static byte |
ATOMID_OP2 |
|
static int |
ATOMID_PHOSPHORUS_ONLY_MASK |
|
static int |
ATOMID_PROTEIN_MASK |
|
static byte |
ATOMID_S4 |
|
static byte |
ATOMID_TERMINATING_OXT |
|
static int |
AXES_DEFAULT_FONTSIZE |
|
static javajs.util.V3 |
axisNX |
|
static javajs.util.V3 |
axisNY |
|
static javajs.util.V3 |
axisNZ |
|
static javajs.util.V3 |
axisX |
|
static javajs.util.V3 |
axisY |
|
static javajs.util.V3 |
axisZ |
|
static java.lang.String |
CACTUS_FILE_TYPES |
|
static javajs.util.V3 |
center |
|
static java.lang.String |
copyright |
|
static java.lang.String[] |
databases |
|
static java.lang.String |
date |
|
static short |
DEFAULT_BOND_MILLIANGSTROM_RADIUS |
|
static float |
DEFAULT_BOND_RADIUS |
|
static float |
DEFAULT_BOND_TOLERANCE |
|
static java.lang.String |
DEFAULT_FONTFACE |
|
static java.lang.String |
DEFAULT_FONTSTYLE |
|
static java.lang.String |
DEFAULT_HELP_PATH |
|
static float |
DEFAULT_MAX_CONNECT_DISTANCE |
|
static float |
DEFAULT_MIN_BOND_DISTANCE |
|
static float |
DEFAULT_MIN_CONNECT_DISTANCE |
|
static int |
DEFAULT_PERCENT_VDW_ATOM |
|
static float |
DEFAULT_STRUT_RADIUS |
|
static int |
DNA_MASK |
|
static int |
ECHO_BOTTOM |
|
static int |
ECHO_MIDDLE |
|
static int |
ECHO_TOP |
|
static int |
ECHO_XY |
|
static int |
ECHO_XYZ |
|
private static java.lang.String[] |
echoNames |
|
static java.lang.String |
EMBEDDED_SCRIPT_TAG |
|
static float |
ENC_CALC_MAX_DIST |
|
static int |
ENV_CALC_MAX_LEVEL |
|
static java.lang.String |
EXPORT_DRIVER_LIST |
|
static int |
FORMAL_CHARGE_COLIX_RED |
|
static int |
GROUPID_AMINO_MAX |
|
static int |
GROUPID_ARGININE |
|
static int |
GROUPID_ASPARAGINE |
|
static int |
GROUPID_ASPARTATE |
|
static int |
GROUPID_CYSTEINE |
|
static int |
GROUPID_GLUTAMATE |
|
static int |
GROUPID_GLUTAMINE |
|
static int |
GROUPID_HISTIDINE |
|
private static int |
GROUPID_ION_MAX |
|
private static int |
GROUPID_ION_MIN |
|
static int |
GROUPID_LYSINE |
|
static int |
GROUPID_NUCLEIC_MAX |
|
static int |
GROUPID_PROLINE |
|
static int |
GROUPID_SOLVENT_MIN |
|
static int |
GROUPID_TRYPTOPHAN |
|
static int |
GROUPID_WATER |
|
private static java.lang.String[] |
hAlignNames |
|
static java.lang.String |
IMAGE_OR_SCENE |
|
static java.lang.String |
IMAGE_TYPES |
|
static java.lang.String |
JPEG_EXTENSIONS |
|
static int |
JSV_CLOSE |
|
static int |
JSV_NOT |
|
static int |
JSV_SELECT |
|
static int |
JSV_SEND_C13SIMULATE |
|
static int |
JSV_SEND_H1SIMULATE |
|
static int |
JSV_SEND_JDXMOL |
|
static int |
JSV_SETPEAKS |
|
static int |
JSV_STRUCTURE |
|
private static int |
LABEL_CENTERED |
|
static int |
LABEL_DEFAULT_FONTSIZE |
|
static int |
LABEL_DEFAULT_OFFSET |
|
static int |
LABEL_DEFAULT_X_OFFSET |
|
static int |
LABEL_DEFAULT_Y_OFFSET |
|
private static int |
LABEL_EXPLICIT |
|
static int |
LABEL_FLAGS |
|
private static int |
LABEL_FLAGX_OFFSET_SHIFT |
|
private static int |
LABEL_FLAGY_OFFSET_SHIFT |
|
static int |
LABEL_MAXIMUM_FONTSIZE |
|
static int |
LABEL_MINIMUM_FONTSIZE |
|
private static int |
LABEL_OFFSET_MASK |
|
static int |
LABEL_OFFSET_MAX |
|
static int |
LABEL_POINTER_BACKGROUND |
|
private static int |
LABEL_POINTER_FLAGS |
|
static int |
LABEL_POINTER_NONE |
|
static int |
LABEL_POINTER_ON |
|
private static int |
LABEL_ZPOS_FLAGS |
|
static int |
LABEL_ZPOS_FRONT |
|
static int |
LABEL_ZPOS_GROUP |
|
static java.lang.String |
LOAD_ATOM_DATA_TYPES |
|
static java.lang.String[] |
macros |
|
static short |
madMultipleBondSmallMaximum |
|
static int |
MAXIMUM_AUTO_BOND_COUNT |
|
static int |
MEASURE_DEFAULT_FONTSIZE |
|
static int |
MINIMIZATION_ATOM_MAX |
|
static float |
MINIMIZE_FIXED_RANGE |
|
static java.lang.String |
MODELKIT_ZAP_STRING |
|
static java.lang.String |
MODELKIT_ZAP_TITLE |
|
static int |
MOUSE_NONE |
|
static byte |
MULTIBOND_ALWAYS |
|
static byte |
MULTIBOND_NEVER |
|
static byte |
MULTIBOND_NOTSMALL |
|
static byte |
MULTIBOND_WIREFRAME |
|
static int |
NBO_CONFIG |
|
static int |
NBO_MODEL |
|
static int |
NBO_RUN |
|
static int |
NBO_SEARCH |
|
static int |
NBO_VIEW |
|
static java.lang.String |
NOTE_SCRIPT_FILE |
|
static boolean |
officialRelease |
|
static int |
PARTIAL_CHARGE_COLIX_RED |
|
static int |
PARTIAL_CHARGE_RANGE_SIZE |
|
static java.lang.String |
PDB_ANNOTATIONS |
|
static java.lang.String[] |
predefinedStatic |
|
static java.lang.String[] |
predefinedVariable |
|
static int |
PURINE_MASK |
|
static int |
PYRIMIDINE_MASK |
|
static float |
radiansPerDegree |
|
static java.lang.String |
READER_NOT_FOUND |
|
static java.lang.String |
REPAINT_IGNORE |
|
static int |
RNA_MASK |
|
static java.lang.String |
SCRIPT_COMPLETED |
|
static java.lang.String |
SCRIPT_EDITOR_IGNORE |
|
static int |
SHAPE_AXES |
|
static int |
SHAPE_BACKBONE |
|
static int |
SHAPE_BALLS |
|
static int |
SHAPE_BBCAGE |
|
static int |
SHAPE_CARTOON |
|
static int |
SHAPE_CGO |
|
static int |
SHAPE_CONTACT |
|
static int |
SHAPE_DIPOLES |
|
static int |
SHAPE_DOTS |
|
static int |
SHAPE_DRAW |
|
static int |
SHAPE_ECHO |
|
static int |
SHAPE_ELLIPSOIDS |
|
static int |
SHAPE_FRANK |
|
static int |
SHAPE_GEOSURFACE |
|
static int |
SHAPE_HALOS |
|
static int |
SHAPE_HOVER |
|
static int |
SHAPE_HSTICKS |
|
static int |
SHAPE_ISOSURFACE |
|
static int |
SHAPE_LABELS |
|
private static int |
SHAPE_LAST_ATOM_VIS_FLAG |
|
static int |
SHAPE_LCAOCARTOON |
|
static int |
SHAPE_MAX |
|
static int |
SHAPE_MAX_HAS_ID |
|
static int |
SHAPE_MAX_HAS_SETVIS |
|
static int |
SHAPE_MAX_MESH_COLLECTION |
|
static int |
SHAPE_MAX_SECONDARY |
|
static int |
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT |
|
static int |
SHAPE_MAX_SPECIAL |
|
static int |
SHAPE_MAX_SURFACE |
|
static int |
SHAPE_MEASURES |
|
static int |
SHAPE_MESHRIBBON |
|
static int |
SHAPE_MIN_HAS_ID |
|
static int |
SHAPE_MIN_HAS_SETVIS |
|
static int |
SHAPE_MIN_SECONDARY |
|
static int |
SHAPE_MIN_SPECIAL |
|
static int |
SHAPE_MIN_SURFACE |
|
static int |
SHAPE_MO |
|
static int |
SHAPE_NBO |
|
static int |
SHAPE_PLOT3D |
|
static int |
SHAPE_PMESH |
|
static int |
SHAPE_POLYHEDRA |
|
static int |
SHAPE_RIBBONS |
|
static int |
SHAPE_ROCKETS |
|
static int |
SHAPE_SSSTICKS |
|
static int |
SHAPE_STARS |
|
static int |
SHAPE_STICKS |
|
static int |
SHAPE_STRANDS |
|
static int |
SHAPE_STRUTS |
|
static int |
SHAPE_TRACE |
|
static int |
SHAPE_UCCAGE |
|
static int |
SHAPE_VECTORS |
|
static java.lang.String[] |
shapeClassBases |
|
static int |
SMILES_AROMATIC_DEFINED |
AROMATIC_DEFINED draws all aromatic bonds from connection definitions
It is deprecated, because a=a will set it by itself.
|
static 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)
|
static 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.
|
static int |
SMILES_AROMATIC_PLANAR |
AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)
|
static int |
SMILES_AROMATIC_STRICT |
AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds
|
static int |
SMILES_FIRST_MATCH_ONLY |
|
static int |
SMILES_GEN_ATOM_COMMENT |
|
static int |
SMILES_GEN_BIO |
|
static int |
SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS |
|
static int |
SMILES_GEN_BIO_COMMENT |
|
static int |
SMILES_GEN_BIO_COV_CROSSLINK |
|
static int |
SMILES_GEN_BIO_HH_CROSSLINK |
|
static int |
SMILES_GEN_BIO_NOCOMMENTS |
|
static int |
SMILES_GEN_EXPLICIT_H |
|
static int |
SMILES_GEN_POLYHEDRAL |
|
static int |
SMILES_GEN_TOPOLOGY |
|
static int |
SMILES_GROUP_BY_MODEL |
|
static int |
SMILES_IGNORE_ATOM_CLASS |
|
static int |
SMILES_IGNORE_STEREOCHEMISTRY |
|
static int |
SMILES_INVERT_STEREOCHEMISTRY |
|
static int |
SMILES_NO_AROMATIC |
|
static int |
SMILES_TYPE_OPENSMARTS |
|
static int |
SMILES_TYPE_OPENSMILES |
|
static int |
SMILES_TYPE_SMARTS |
|
static int |
SMILES_TYPE_SMILES |
|
static java.lang.String |
STATE_VERSION_STAMP |
|
static int |
TEXT_ALIGN_CENTER |
|
private static int |
TEXT_ALIGN_FLAGS |
|
static int |
TEXT_ALIGN_LEFT |
|
static int |
TEXT_ALIGN_NONE |
|
static int |
TEXT_ALIGN_RIGHT |
|
private static int |
TEXT_ALIGN_SHIFT |
|
static javajs.util.V3[] |
unitAxisVectors |
|
static int |
UNITID_ATOM |
|
static int |
UNITID_INSCODE |
|
static int |
UNITID_MODEL |
|
static int |
UNITID_RESIDUE |
|
static int |
UNITID_TRIM |
|
static java.lang.String |
version |
|
static int |
versionInt |
|
static int |
VIS_BACKBONE_FLAG |
|
static int |
VIS_BALLS_FLAG |
|
static int |
VIS_BOND_FLAG |
|
static int |
VIS_CARTOON_FLAG |
|
static int |
VIS_LABEL_FLAG |
|
static int |
XY_ZTOP |
|
static java.lang.String |
ZAP_TITLE |
Constructor | Description |
---|---|
JC() |
Modifier and Type | Method | Description |
---|---|---|
static java.lang.String |
embedScript(java.lang.String s) |
|
static java.lang.String |
fixProtocol(java.lang.String name) |
Check for databases that have changed from http:// to https:// over time.
|
static int |
getAlignment(int offset) |
|
static java.lang.String |
getEchoName(int type) |
|
static java.lang.String |
getHorizAlignmentName(int align) |
|
static java.lang.String |
getMacro(java.lang.String key) |
|
static java.lang.String |
getMacroList() |
|
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 java.lang.String |
getPointerName(int pointer) |
|
static int |
getServiceCommand(java.lang.String script) |
|
static java.lang.String |
getShapeClassName(int shapeID,
boolean isRenderer) |
|
static int |
getShapeVisibilityFlag(int shapeID) |
|
static int |
getUnitIDFlags(java.lang.String type) |
Get a unitID type
|
static int |
getXOffset(int offset) |
X offset in pixels.
|
static int |
getYOffset(int offset) |
Y offset in pixels; negative of this is the actual screen offset
|
static boolean |
isOffsetAbsolute(int offset) |
|
static boolean |
isSmilesCanonical(java.lang.String options) |
|
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) |
public static final java.lang.String PDB_ANNOTATIONS
public static final java.lang.String CACTUS_FILE_TYPES
public static java.lang.String[] databases
public static java.lang.String[] macros
public static final java.lang.String copyright
public static final java.lang.String version
public static final java.lang.String date
public static final int versionInt
public static final boolean officialRelease
public static final java.lang.String DEFAULT_HELP_PATH
public static final java.lang.String STATE_VERSION_STAMP
public static final java.lang.String EMBEDDED_SCRIPT_TAG
public static final java.lang.String NOTE_SCRIPT_FILE
public static final java.lang.String SCRIPT_EDITOR_IGNORE
public static final java.lang.String REPAINT_IGNORE
public static final java.lang.String LOAD_ATOM_DATA_TYPES
public static final float radiansPerDegree
public static final java.lang.String allowedQuaternionFrames
public static final java.lang.String EXPORT_DRIVER_LIST
public static final javajs.util.V3 center
public static final javajs.util.V3 axisX
public static final javajs.util.V3 axisY
public static final javajs.util.V3 axisZ
public static final javajs.util.V3 axisNX
public static final javajs.util.V3 axisNY
public static final javajs.util.V3 axisNZ
public static final javajs.util.V3[] unitAxisVectors
public static final int XY_ZTOP
public static final int DEFAULT_PERCENT_VDW_ATOM
public static final float DEFAULT_BOND_RADIUS
public static final short DEFAULT_BOND_MILLIANGSTROM_RADIUS
public static final float DEFAULT_STRUT_RADIUS
public static final float DEFAULT_BOND_TOLERANCE
public static final float DEFAULT_MIN_BOND_DISTANCE
public static final float DEFAULT_MAX_CONNECT_DISTANCE
public static final float DEFAULT_MIN_CONNECT_DISTANCE
public static final int MINIMIZATION_ATOM_MAX
public static final float MINIMIZE_FIXED_RANGE
public static final float ENC_CALC_MAX_DIST
public static final int ENV_CALC_MAX_LEVEL
public static final int MOUSE_NONE
public static final byte MULTIBOND_NEVER
public static final byte MULTIBOND_WIREFRAME
public static final byte MULTIBOND_NOTSMALL
public static final byte MULTIBOND_ALWAYS
public static final int MAXIMUM_AUTO_BOND_COUNT
public static final short madMultipleBondSmallMaximum
public static final float ANGSTROMS_PER_BOHR
public static final int[] altArgbsCpk
public static final int[] argbsFormalCharge
public static final int[] argbsRwbScale
public static final int FORMAL_CHARGE_COLIX_RED
public static final int PARTIAL_CHARGE_COLIX_RED
public static final int PARTIAL_CHARGE_RANGE_SIZE
public static final int[] argbsRoygbScale
public static final int argbsIsosurfacePositive
public static final int argbsIsosurfaceNegative
public static final byte ATOMID_AMINO_NITROGEN
public static final byte ATOMID_ALPHA_CARBON
public static final byte ATOMID_CARBONYL_CARBON
public static final byte ATOMID_CARBONYL_OXYGEN
public static final byte ATOMID_O1
public static final int ATOMID_ALPHA_ONLY_MASK
public static final int ATOMID_PROTEIN_MASK
public static final byte ATOMID_O5_PRIME
public static final byte ATOMID_C5_PRIME
public static final byte ATOMID_C4_PRIME
public static final byte ATOMID_C3_PRIME
public static final byte ATOMID_O3_PRIME
public static final byte ATOMID_C2_PRIME
public static final byte ATOMID_C1_PRIME
public static final byte ATOMID_O4_PRIME
public static final int ATOMID_NUCLEIC_MASK
public static final byte ATOMID_NUCLEIC_PHOSPHORUS
public static final int ATOMID_PHOSPHORUS_ONLY_MASK
public static final int ATOMID_DISTINGUISHING_ATOM_MAX
public static final byte ATOMID_CARBONYL_OD1
public static final byte ATOMID_CARBONYL_OD2
public static final byte ATOMID_CARBONYL_OE1
public static final byte ATOMID_CARBONYL_OE2
public static final byte ATOMID_N1
public static final byte ATOMID_C2
public static final byte ATOMID_N3
public static final byte ATOMID_C4
public static final byte ATOMID_C5
public static final byte ATOMID_C6
public static final byte ATOMID_O2
public static final byte ATOMID_N7
public static final byte ATOMID_C8
public static final byte ATOMID_N9
public static final byte ATOMID_N4
public static final byte ATOMID_N2
public static final byte ATOMID_N6
public static final byte ATOMID_C5M
public static final byte ATOMID_O6
public static final byte ATOMID_O4
public static final byte ATOMID_S4
public static final byte ATOMID_C7
public static final byte ATOMID_TERMINATING_OXT
public static final byte ATOMID_H5T_TERMINUS
public static final byte ATOMID_O5T_TERMINUS
public static final byte ATOMID_O1P
public static final byte ATOMID_OP1
public static final byte ATOMID_O2P
public static final byte ATOMID_OP2
public static final byte ATOMID_O2_PRIME
public static final byte ATOMID_H3T_TERMINUS
public static final byte ATOMID_HO3_PRIME
public static final byte ATOMID_HO5_PRIME
public static final int PURINE_MASK
public static final int PYRIMIDINE_MASK
public static final int DNA_MASK
public static final int RNA_MASK
public static final int GROUPID_ARGININE
public static final int GROUPID_ASPARAGINE
public static final int GROUPID_ASPARTATE
public static final int GROUPID_CYSTEINE
public static final int GROUPID_GLUTAMINE
public static final int GROUPID_GLUTAMATE
public static final int GROUPID_HISTIDINE
public static final int GROUPID_LYSINE
public static final int GROUPID_PROLINE
public static final int GROUPID_TRYPTOPHAN
public static final int GROUPID_AMINO_MAX
public static final int GROUPID_NUCLEIC_MAX
public static final int GROUPID_WATER
public static final int GROUPID_SOLVENT_MIN
private static final int GROUPID_ION_MIN
private static final int GROUPID_ION_MAX
public static java.lang.String[] predefinedVariable
public static java.lang.String[] predefinedStatic
public static final java.lang.String MODELKIT_ZAP_STRING
public static final java.lang.String MODELKIT_ZAP_TITLE
public static final java.lang.String ZAP_TITLE
public static final java.lang.String ADD_HYDROGEN_TITLE
public static final java.lang.String DEFAULT_FONTFACE
public static final java.lang.String DEFAULT_FONTSTYLE
public static final int MEASURE_DEFAULT_FONTSIZE
public static final int AXES_DEFAULT_FONTSIZE
public static final int SHAPE_BALLS
public static final int SHAPE_STICKS
public static final int SHAPE_HSTICKS
public static final int SHAPE_SSSTICKS
public static final int SHAPE_STRUTS
public static final int SHAPE_LABELS
public static final int SHAPE_MEASURES
public static final int SHAPE_STARS
public static final int SHAPE_MIN_HAS_SETVIS
public static final int SHAPE_HALOS
public static final int SHAPE_MIN_SECONDARY
public static final int SHAPE_BACKBONE
public static final int SHAPE_TRACE
public static final int SHAPE_CARTOON
public static final int SHAPE_STRANDS
public static final int SHAPE_MESHRIBBON
public static final int SHAPE_RIBBONS
public static final int SHAPE_ROCKETS
public static final int SHAPE_MAX_SECONDARY
public static final int SHAPE_MIN_SPECIAL
public static final int SHAPE_DOTS
public static final int SHAPE_DIPOLES
public static final int SHAPE_VECTORS
public static final int SHAPE_GEOSURFACE
public static final int SHAPE_ELLIPSOIDS
public static final int SHAPE_MAX_SIZE_ZERO_ON_RESTRICT
public static final int SHAPE_MIN_HAS_ID
public static final int SHAPE_POLYHEDRA
public static final int SHAPE_DRAW
public static final int SHAPE_MAX_SPECIAL
public static final int SHAPE_CGO
public static final int SHAPE_MIN_SURFACE
public static final int SHAPE_ISOSURFACE
public static final int SHAPE_CONTACT
public static final int SHAPE_LCAOCARTOON
private static final int SHAPE_LAST_ATOM_VIS_FLAG
public static final int SHAPE_MO
public static final int SHAPE_NBO
public static final int SHAPE_PMESH
public static final int SHAPE_PLOT3D
public static final int SHAPE_MAX_SURFACE
public static final int SHAPE_MAX_MESH_COLLECTION
public static final int SHAPE_ECHO
public static final int SHAPE_MAX_HAS_ID
public static final int SHAPE_BBCAGE
public static final int SHAPE_MAX_HAS_SETVIS
public static final int SHAPE_UCCAGE
public static final int SHAPE_AXES
public static final int SHAPE_HOVER
public static final int SHAPE_FRANK
public static final int SHAPE_MAX
public static final int VIS_BOND_FLAG
public static final int VIS_BALLS_FLAG
public static final int VIS_LABEL_FLAG
public static final int VIS_BACKBONE_FLAG
public static final int VIS_CARTOON_FLAG
public static final int ALPHA_CARBON_VISIBILITY_FLAG
public static final java.lang.String[] shapeClassBases
public static final java.lang.String SCRIPT_COMPLETED
public static final java.lang.String JPEG_EXTENSIONS
public static final java.lang.String IMAGE_TYPES
public static final java.lang.String IMAGE_OR_SCENE
public static final int LABEL_MINIMUM_FONTSIZE
public static final int LABEL_MAXIMUM_FONTSIZE
public static final int LABEL_DEFAULT_FONTSIZE
public static final int LABEL_DEFAULT_X_OFFSET
public static final int LABEL_DEFAULT_Y_OFFSET
public static final int LABEL_OFFSET_MAX
private static final int LABEL_OFFSET_MASK
private static final int LABEL_FLAGY_OFFSET_SHIFT
private static final int LABEL_FLAGX_OFFSET_SHIFT
public static final int LABEL_FLAGS
private static final int LABEL_POINTER_FLAGS
public static final int LABEL_POINTER_NONE
public static final int LABEL_POINTER_ON
public static final int LABEL_POINTER_BACKGROUND
private static final int TEXT_ALIGN_SHIFT
private static final int TEXT_ALIGN_FLAGS
public static final int TEXT_ALIGN_NONE
public static final int TEXT_ALIGN_LEFT
public static final int TEXT_ALIGN_CENTER
public static final int TEXT_ALIGN_RIGHT
private static final int LABEL_ZPOS_FLAGS
public static final int LABEL_ZPOS_GROUP
public static final int LABEL_ZPOS_FRONT
private static final int LABEL_EXPLICIT
private static final int LABEL_CENTERED
public static int LABEL_DEFAULT_OFFSET
public static final int ECHO_TOP
public static final int ECHO_BOTTOM
public static final int ECHO_MIDDLE
public static final int ECHO_XY
public static final int ECHO_XYZ
private static final java.lang.String[] echoNames
private static final java.lang.String[] hAlignNames
public static final int SMILES_TYPE_SMILES
public static final int SMILES_TYPE_SMARTS
public static final int SMILES_TYPE_OPENSMILES
public static final int SMILES_TYPE_OPENSMARTS
public static final int SMILES_FIRST_MATCH_ONLY
public static final int SMILES_NO_AROMATIC
public static final int SMILES_IGNORE_STEREOCHEMISTRY
public static final int SMILES_INVERT_STEREOCHEMISTRY
public static final int SMILES_AROMATIC_DEFINED
public static final int SMILES_AROMATIC_STRICT
public static final int SMILES_AROMATIC_DOUBLE
public static final int SMILES_AROMATIC_MMFF94
public static final int SMILES_AROMATIC_PLANAR
public static final int SMILES_IGNORE_ATOM_CLASS
public static final int SMILES_GEN_EXPLICIT_H
public static final int SMILES_GEN_TOPOLOGY
public static final int SMILES_GEN_POLYHEDRAL
public static final int SMILES_GEN_ATOM_COMMENT
public static final int SMILES_GEN_BIO
public static final int SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS
public static final int SMILES_GEN_BIO_COV_CROSSLINK
public static final int SMILES_GEN_BIO_HH_CROSSLINK
public static final int SMILES_GEN_BIO_COMMENT
public static final int SMILES_GEN_BIO_NOCOMMENTS
public static final int SMILES_GROUP_BY_MODEL
public static final int JSV_NOT
public static final int JSV_SEND_JDXMOL
public static final int JSV_SETPEAKS
public static final int JSV_SELECT
public static final int JSV_STRUCTURE
public static final int JSV_SEND_H1SIMULATE
public static final int JSV_SEND_C13SIMULATE
public static final int NBO_MODEL
public static final int NBO_RUN
public static final int NBO_VIEW
public static final int NBO_SEARCH
public static final int NBO_CONFIG
public static final int JSV_CLOSE
public static java.lang.String READER_NOT_FOUND
public static final int UNITID_MODEL
public static final int UNITID_RESIDUE
public static final int UNITID_ATOM
public static final int UNITID_INSCODE
public static final int UNITID_TRIM
public static java.lang.String fixProtocol(java.lang.String name)
name
- public static java.lang.String getMacroList()
public static java.lang.String getMacro(java.lang.String key)
public static java.lang.String embedScript(java.lang.String s)
public static final int getShapeVisibilityFlag(int shapeID)
public static final int shapeTokenIndex(int tok)
public static final java.lang.String getShapeClassName(int shapeID, boolean isRenderer)
public static java.lang.String getEchoName(int type)
public static int setZPosition(int offset, int pos)
public static int setPointer(int offset, int pointer)
public static int getPointer(int offset)
public static java.lang.String getPointerName(int pointer)
public static boolean isOffsetAbsolute(int offset)
public static int getOffset(int xOffset, int yOffset, boolean isAbsolute)
xOffset
- yOffset
- isAbsolute
- public static int getXOffset(int offset)
offset
- 0 for an offset indicates "not set" and delivers the default offsetpublic static int getYOffset(int offset)
offset
- 0 for an offset indicates "not set" and delivers the default offsetpublic static int getAlignment(int offset)
public static int setHorizAlignment(int offset, int hAlign)
public static java.lang.String getHorizAlignmentName(int align)
public static boolean isSmilesCanonical(java.lang.String options)
public static int getServiceCommand(java.lang.String script)
public static int getUnitIDFlags(java.lang.String type)
type
- -mra (model name, residue, atom, and ins code),
-mr (model and residue; no atom)
-ra default
- or -r just residue
-t right-trim