A

add(Atom) - Method in class com.daylight.PathSet

from dt_add.

add(Bond) - Method in class com.daylight.PathSet

from dt_add.

add(Atom) - Method in class com.daylight.Set

from dt_add.

add(Bond) - Method in class com.daylight.Set

from dt_add.

addAtom(int, int) - Method in class com.daylight.Molecule

from dt_addatom.

addBond(Atom, BondType) - Method in class com.daylight.Atom

from dt_addbond.

addComponent(Molecule, Role) - Method in class com.daylight.Reaction

from dt_addcomponent.

addImplicitHydrogens(boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_addh.

append(DaylightObject) - Method in class com.daylight.Sequence

from dt_append.

append(String) - Method in class com.daylight.Sequence

from dt_append.

appendStringProperty(String, String) - Method in class com.daylight.DaylightObject

from dt_appendstring.

appendValue(String) - Method in class com.daylight.DayString

from dt_appendstringvalue.

asciiToBinary(String) - Static method in class com.daylight.DayString

from dt_stringvalue.

atEnd() - Method in class com.daylight.Sequence

from dt_atend.

atEnd() - Method in class com.daylight.Stream

from dt_atend.

Atom - Class in com.daylight

Object representing an Atom

Atom() - Constructor for class com.daylight.Atom

 

AtomBondCollection - Class in com.daylight

Base class for for any object for which object.stream(DaylightObject::Atom) and object.stream(DaylightObject::Bond) will return a stream of atoms and bonds, respectively.

AtomBondCollection() - Constructor for class com.daylight.AtomBondCollection

implicit superconstructor.

atStart() - Method in class com.daylight.Sequence

from dt_atstart.

B

binaryToAscii(String) - Static method in class com.daylight.DayString

from dt_binary2ascii.

Bond - Class in com.daylight

Object representing a bond

Bond() - Constructor for class com.daylight.Bond

 

BondOrder - Enum in com.daylight.enumtype

Bond Order values are 'Unknown', 'Single', 'Double' and 'Triple'

BondStyle - Enum in com.daylight.enumtype

BondStyle values are 'EdgeReset', 'EdgeSimple', 'EdgeTee', 'EdgeTeeIn', 'EdgeTeeOut', 'EdgeTri', 'EdgeTriIn', 'EdgeTriOut', 'EdgeHash', 'EdgeDative', 'EdgeTri_TriIn', 'EdgeTri_TriOut', 'EdgeTee_TeeIn', or 'EdgeTee_TeeOut'

BondType - Enum in com.daylight.enumtype

Bond type values are 'Unknown', 'Single', 'Double', 'Triple', 'Aromatic' and 'Wild'

C

calculateCoordinates() - Method in class com.daylight.Depiction

from dt_calcxy.

checkJavaLicense() - Static method in class com.daylight.WrapperLicense

 

checkProgramLicense(String) - Static method in class com.daylight.DaylightObject

from dt_check_license.

checkToolkitLicense(String) - Static method in class com.daylight.DaylightObject

from dt_check_license.

ChiralValue - Enum in com.daylight.enumtype

Chiral value values are 'None', 'Tetrahedral', 'TetrahedralAl', 'SquarePlanar', 'TrigonalBipyramidal', 'Octahedral', 'TetrahedralAnticlockwise', and 'TetrahedralClockwise'

clearErrors() - Static method in class com.daylight.DaylightObject

from dt_errorclear.

com.daylight - package com.daylight

 

com.daylight.enumtype - package com.daylight.enumtype

 

com.daylight.exception - package com.daylight.exception

 

commonSubstruct(Sequence, int, CommonSubstructFlags) - Static method in class com.daylight.Pattern

from dt_common_substruct

CommonSubstructFlags - Enum in com.daylight.enumtype

Common substructure flags values are 'Default', 'SimpleTopology', 'UseOneAtomPaths', 'UseTorderOnly'

Conformation - Class in com.daylight

Object representing a conformation object

Conformation(ConnectedAtomCollection) - Constructor for class com.daylight.Conformation

from dt_alloc_conformation.

ConnectedAtomCollection - Class in com.daylight

A collection of atoms joined by bonds

ConnectedAtomCollection() - Constructor for class com.daylight.ConnectedAtomCollection

implicit superconstructor.

convertToGraphRepresentation() - Method in class com.daylight.ConnectedAtomCollection

from dt_molgraph.

copy() - Method in class com.daylight.Conformation

from dt_copy.

copy() - Method in class com.daylight.DayString

from dt_copy.

copy() - Method in class com.daylight.Depiction

from dt_copy.

copy() - Method in class com.daylight.Fingerprint

from dt_copy.

copy() - Method in class com.daylight.Integer

from dt_copy.

copy() - Method in class com.daylight.Molecule

from dt_copy.

copy() - Method in class com.daylight.Path

from dt_copy.

copy() - Method in class com.daylight.PathSet

from dt_copy.

copy() - Method in class com.daylight.Pattern

from dt_copy.

copy() - Method in class com.daylight.Reaction

from dt_copy.

copy() - Method in class com.daylight.Real

from dt_copy.

copy() - Method in class com.daylight.Sequence

from dt_copy.

copy() - Method in class com.daylight.Stream

from dt_copy.

copy() - Method in class com.daylight.Substructure

from dt_copy.

copy() - Method in class com.daylight.Transform

from dt_copy.

createConformation() - Method in class com.daylight.ConnectedAtomCollection

from dt_alloc_conformation.

createDepiction() - Method in class com.daylight.ConnectedAtomCollection

from dt_alloc_depiction.

Cycle - Class in com.daylight

Object representing a cycle

Cycle() - Constructor for class com.daylight.Cycle

implicit superconstructor.

D

DaylightCppObject - Class in com.daylight

 

DaylightCppObject() - Constructor for class com.daylight.DaylightCppObject

 

DaylightErrorType - Enum in com.daylight.enumtype

Daylight error type, values are 'None', 'Note', 'Warning' , 'Error' and 'Fatal'

DaylightException - Exception in com.daylight.exception

Daylight Exception

DaylightObject - Class in com.daylight

Base class for all Daylight Objects

DaylightObject() - Constructor for class com.daylight.DaylightObject

 

DaylightObjectType - Enum in com.daylight.enumtype

Daylight Object type values are 'Any', 'Integer', 'Real', 'String', 'Molecule', 'Conformation', 'Depiction', 'Atom', 'Bond', 'Cycle', 'Stream', 'Sequence', 'Substructure', 'Path', 'Pattern', 'VectorBinding', 'PathSet', 'Fingerprint', 'Program', 'Reaction', 'Transform' and 'Conversion'

DayString - Class in com.daylight

Object representing a Daylight string

DayString() - Constructor for class com.daylight.DayString

from dt_alloc_string.

DayString(String) - Constructor for class com.daylight.DayString

from dt_alloc_string.

deallocateContents() - Method in class com.daylight.Sequence

deallocates all objects contained by the sequence.

deleteCurrent() - Method in class com.daylight.Sequence

from dt_delete.

depict(Depictor) - Method in class com.daylight.Depiction

from dt_depict - draw a two-dimensional rendition of a molecule or reaction.

Depiction - Class in com.daylight

Object representing 2-D coordinates, atom visibilities and bond styles of a molecule or reaction.

Depiction(ConnectedAtomCollection) - Constructor for class com.daylight.Depiction

from dt_alloc_depiction.

DepictionLabel - Class in com.daylight

Object representing a depiction label

DepictionLabel(String, int) - Constructor for class com.daylight.DepictionLabel

 

DepictionOrientation - Enum in com.daylight.enumtype

Depiction orientation values are 'None', 'Auto', and 'Wild'

Depictor - Interface in com.daylight

Abstract base class for depiction classes which implement the drawing library interface

DepictorText - Class in com.daylight

Object representing depictor text

DepictorText() - Constructor for class com.daylight.DepictorText

 

disableVirtualHandles() - Static method in class com.daylight.DaylightObject

from dt_vh_disable.

DoubleBondOrientation - Enum in com.daylight.enumtype

Double bond orientation, values are 'Cis', 'Trans' and 'Unspecified'

drawBox(Rectangle2D.Float) - Method in interface com.daylight.Depictor

dl_drawbox.

drawLabel(DepictorText) - Method in interface com.daylight.Depictor

dl_drawlabel.

drawOval(Rectangle2D.Float) - Method in interface com.daylight.Depictor

dl_drawoval.

drawTo(Point2D.Float) - Method in interface com.daylight.Depictor

dl_drawto.

E

equals(Object) - Method in class com.daylight.DaylightObject

 

exclusiveMatch(ConnectedAtomCollection, int) - Method in class com.daylight.Pattern

from dt_xmatch.

exclusiveTransform(Molecule, TransformDirection, int) - Method in class com.daylight.Transform

from dt_xtransform.

exclusiveTransform(Sequence, TransformDirection, int) - Method in class com.daylight.Transform

from dt_xtransform.

F

finalize() - Method in class com.daylight.Atom

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.AtomBondCollection

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Bond

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Conformation

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.ConnectedAtomCollection

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Cycle

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.DaylightObject

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.DayString

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Depiction

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.DepictionLabel

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.DepictorText

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Fingerprint

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Integer

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Molecule

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Path

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.PathSet

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Pattern

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Reaction

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Real

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Sequence

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Set

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Stream

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Substructure

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.Transform

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

finalize() - Method in class com.daylight.VectorBinding

Called by the garbage collector on an object when garbage collection determines that there are no more references to the object.

Fingerprint - Class in com.daylight

Object representing a Daylight fingerprint

Fingerprint(int) - Constructor for class com.daylight.Fingerprint

Allocate a new fingerprint.

FingerprintOperation - Enum in com.daylight.enumtype

fingerprint operation, values are 'Set', 'Or', 'Not', 'And', 'Not', and 'Xor'

fingerTest(Fingerprint) - Method in class com.daylight.Fingerprint

from dt_fp_fingertest.

fitLabel(DepictorText, Rectangle2D.Float) - Method in interface com.daylight.Depictor

dl_fitlabel.

flush() - Method in interface com.daylight.Depictor

dl_flush.

fold(int, float) - Method in class com.daylight.Fingerprint

from dt_fp_foldfp.

G

generateFingerprint(int, int, int) - Method in class com.daylight.AtomBondCollection

from dt_fp_generatefp.

getAdjunct() - Method in class com.daylight.DaylightObject

from dt_adjunct.

getAncestor() - Method in class com.daylight.DaylightObject

 

getAngleInRadians() - Method in class com.daylight.DepictorText

The desired angle in radians of text to the horizontal baseline.

getArbitraryOrder() - Method in class com.daylight.Atom

from dt_arborder.

getArbitrarySmiles(boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_arbsmiles.

getArbitraryStream(DaylightObjectType, boolean, boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_arbstream.

getAspectRatio() - Method in interface com.daylight.Depictor

dl_paspect.

getAtomCount() - Method in class com.daylight.AtomBondCollection

from dt_count.

getAtomicNumber() - Method in class com.daylight.Atom

from dt_number.

getAtomicWeight() - Method in class com.daylight.Atom

from dt_weight.

getBase() - Method in class com.daylight.DaylightObject

from dt_base.

getBaseSize() - Method in class com.daylight.DepictorText

The vertical size of the text in the units of the depiction coordinate space.

getBitOnCount() - Method in class com.daylight.Fingerprint

from dt_fp_bitcount.

getBitValue(int) - Method in class com.daylight.Fingerprint

from dt_fp_bitvalue.

getBond(Atom) - Method in class com.daylight.Atom

from dt_bond.

getBondOrder() - Method in class com.daylight.Bond

from dt_bondorder.

getBondStyle(Atom, Bond) - Method in class com.daylight.Depiction

from dt_bondstyle.

getBondType() - Method in class com.daylight.Bond

from dt_bondtype.

getBooleanProperty(String) - Method in class com.daylight.DaylightObject

from dt_boolean.

getBounds() - Method in interface com.daylight.Depictor

dl_bounds.

getCanonicalSmiles(boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_cansmiles.

getCanonicalStream(DaylightObjectType, boolean, boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_canstream.

getChiralBonds(ChiralValue) - Method in class com.daylight.Atom

from dt_chiseq.

getChiralClass(ChiralValue) - Static method in class com.daylight.DaylightObject

from dt_chiclass.

getChiralOrder(ChiralValue) - Static method in class com.daylight.DaylightObject

from dt_chiorder.

getChiralValue(Sequence) - Method in class com.daylight.Atom

from dt_chival.

getCommonBitOnCount(Fingerprint) - Method in class com.daylight.Fingerprint

from dt_fp_commonbitcount.

getConnectedAtom(Bond) - Method in class com.daylight.Atom

from dt_xatom.

getCoordinate(Atom) - Method in class com.daylight.Conformation

from dt_getcoord.

getCoordinate(Atom) - Method in class com.daylight.Depiction

from dt_getcoord.

getCount(DaylightObjectType) - Method in class com.daylight.DaylightObject

from dt_count.

getDifferenceFingerprint(int, int, int) - Method in class com.daylight.Reaction

from dt_fp_differencefp.

getDoubleBondOrientation(Bond, Bond) - Method in class com.daylight.Bond

from dt_dbo.

getDoubleBondOrientation(Bond, boolean) - Method in class com.daylight.Bond

from dt_dbo.

getDoubleBondOrientation() - Method in class com.daylight.Bond

from dt_dbo.

getErrors(DaylightErrorType) - Static method in class com.daylight.DaylightObject

from dt_errors.

getEuclidianDistance(Fingerprint) - Method in class com.daylight.Fingerprint

from dt_fp_euclid.

getExchangeSmiles(boolean, boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_xsmiles.

getExistingObjectCount() - Static method in class com.daylight.DaylightObject

gets the count of existing daylight objects.

getFormalCharge() - Method in class com.daylight.Atom

from dt_charge.

getFrameGraphicsAttribute() - Method in class com.daylight.Depiction

from dt_framega.

getFunction() - Method in exception com.daylight.exception.DaylightException

 

getGraphicsAttribute(Atom) - Method in class com.daylight.Depiction

from dt_ga.

getGraphicsAttribute(Bond) - Method in class com.daylight.Depiction

from dt_ga.

getGraphicsAttribute(Cycle) - Method in class com.daylight.Depiction

from dt_ga.

getGraphicsAttribute() - Method in class com.daylight.DepictionLabel

gets the graphics attribute.

getHandleProperty(String) - Method in class com.daylight.DaylightObject

from dt_gethandle.

getHorizontalJustification() - Method in class com.daylight.DepictorText

The horizontal justification for the text.

getHydrogenCount() - Method in class com.daylight.Atom

from dt_hcount.

getImplicitHydrogenCount() - Method in class com.daylight.Atom

from dt_imp_hcount.

getIntegerProperty(String) - Method in class com.daylight.DaylightObject

from dt_integer.

getIsomericHydrogen() - Static method in class com.daylight.Atom

from dt_isohydro.

getLabel1(Atom) - Method in class com.daylight.Depiction

from dt_label1.

getLabel1(Bond) - Method in class com.daylight.Depiction

from dt_label1.

getLabel1(Cycle) - Method in class com.daylight.Depiction

from dt_label1.

getLabel1(Molecule) - Method in class com.daylight.Depiction

from dt_label1.

getLabel2(Atom) - Method in class com.daylight.Depiction

from dt_label2.

getLabel2(Bond) - Method in class com.daylight.Depiction

from dt_label2.

getLabel2(Cycle) - Method in class com.daylight.Depiction

from dt_label2.

getLabel2(Molecule) - Method in class com.daylight.Depiction

from dt_label2.

getLabelBounds(DepictorText) - Method in interface com.daylight.Depictor

dl_labelbounds.

getLocation() - Method in class com.daylight.DepictorText

The desired location of the text in the depiction coordinate space.

getName() - Method in class com.daylight.VectorBinding

from dt_name.

getOrientation() - Method in class com.daylight.Depiction

from dt_orient.

getOriginalBitOnCount() - Method in class com.daylight.Fingerprint

from dt_fp_obitcount.

getOriginalSize() - Method in class com.daylight.Fingerprint

from dt_fp_obits.

getOriginalStream(DaylightObjectType) - Method in class com.daylight.ConnectedAtomCollection

from dt_origstream.

getOriginatingSmiles() - Method in class com.daylight.ConnectedAtomCollection

from dt_info.

getOriginatingSmirks() - Method in class com.daylight.Transform

from dt_info.

getParent() - Method in class com.daylight.DaylightObject

from dt_parent.

getPattern(Role) - Method in class com.daylight.Transform

from dt_pattern.

getPropertyNames() - Method in class com.daylight.DaylightObject

from dt_propnames.

getPropertyType(String) - Method in class com.daylight.DaylightObject

from dt_proptype.

getRange(int, int) - Method in class com.daylight.Fingerprint

from dt_fp_range.

getRangeSourceOffset(int, int) - Method in class com.daylight.Fingerprint

from dt_fp_range.

getReactionMapSet() - Method in class com.daylight.Atom

from dt_getmap.

getRealProperty(String) - Method in class com.daylight.DaylightObject

from dt_real.

getRole(Atom) - Method in class com.daylight.Reaction

from dt_getrole.

getRole(Bond) - Method in class com.daylight.Reaction

from dt_getrole.

getRole(Cycle) - Method in class com.daylight.Reaction

from dt_getrole.

getRole(Molecule) - Method in class com.daylight.Reaction

from dt_getrole.

getRuntimeLibraryCreationDate() - Static method in class com.daylight.DaylightObject

from dt_info.

getRuntimeLibraryVersion() - Static method in class com.daylight.DaylightObject

from dt_info.

getSimilarity(Fingerprint, String) - Method in class com.daylight.Fingerprint

from dt_fp_similarity.

getSize() - Method in class com.daylight.Fingerprint

from dt_fp_nbits.

getSizes() - Method in class com.daylight.DepictorText

The size of each letter of text as an array.

getStream(DaylightObjectType) - Method in class com.daylight.DaylightObject

from dt_stream.

getStringProperty(String) - Method in class com.daylight.DaylightObject

from dt_string.

getStringValue() - Method in class com.daylight.Fingerprint

from dt_stringvalue.

getSuperSubscripts() - Method in class com.daylight.DepictorText

the superscript or subscript indication for each letter of text as an array.

getSymbol() - Method in class com.daylight.Atom

from dt_symbol.

getSymmetryClass(boolean) - Method in class com.daylight.Atom

from dt_symclass.

getSymmetryOrder(boolean) - Method in class com.daylight.Atom

from dt_symorder.

getTanimotoDistance(Fingerprint) - Method in class com.daylight.Fingerprint

from dt_fp_tanimoto.

getText() - Method in class com.daylight.DepictionLabel

gets the label text.

getText() - Method in class com.daylight.DepictorText

The text to be displayed.

getTverskyDistance(Fingerprint, float, float) - Method in class com.daylight.Fingerprint

from dt_fp_tversky.

getType() - Method in class com.daylight.DaylightObject

from dt_type.

getTypename() - Method in class com.daylight.DaylightObject

from dt_typename.

getUniqueId() - Method in class com.daylight.DaylightObject

from dt_uid.

getUniqueIdRange(DaylightObjectType) - Method in class com.daylight.DaylightObject

from dt_uidrange.

getValue() - Method in class com.daylight.DayString

from dt_stringvalue.

getValue() - Method in class com.daylight.Integer

from dt_integervalue.

getValue() - Method in class com.daylight.Real

from dt_realvalue.

getValue() - Method in class com.daylight.VectorBinding

from dt_getval.

getVerticalJustification() - Method in class com.daylight.DepictorText

The vertical justification for the text.

getWorstErrorType() - Static method in class com.daylight.DaylightObject

from dt_errorworst.

H

hashCode() - Method in class com.daylight.DaylightObject

 

HorizontalJustification - Enum in com.daylight.enumtype

Horizontal justification, values are 'Left', 'Center', 'Right'

I

inSameReactionMap(Atom) - Method in class com.daylight.Atom

from dt_mapped.

insert(DaylightObject) - Method in class com.daylight.Sequence

from dt_insert.

Integer - Class in com.daylight

Object representing an integer

Integer() - Constructor for class com.daylight.Integer

from dt_alloc_integer.

Integer(int) - Constructor for class com.daylight.Integer

from dt_alloc_integer.

InvalidLicenseException - Exception in com.daylight.exception

Invalid license exception

InvalidReactionException - Exception in com.daylight.exception

Invalid Reaction exception

InvalidSmartsException - Exception in com.daylight.exception

Invalid Smarts exception

InvalidSmilesException - Exception in com.daylight.exception

Invalid Smiles exception

InvalidTypeException - Exception in com.daylight.exception

Invalid type exception

isAromatic() - Method in class com.daylight.Atom

from dt_aromatic.

isAromatic() - Method in class com.daylight.Bond

from dt_aromatic.

isAromatic() - Method in class com.daylight.Cycle

from dt_aromatic.

isChiral() - Method in class com.daylight.Atom

from dt_ischiral.

isCompressed() - Method in class com.daylight.Depiction

from dt_compressed.

isDrawingIsomerics() - Method in class com.daylight.Depiction

from dt_isomeric.

isFramed() - Method in class com.daylight.Depiction

from dt_frame.

isMember(DaylightObject) - Method in class com.daylight.Set

from dt_member.

isModifiable() - Method in class com.daylight.ConnectedAtomCollection

from dt_mod_is_on.

isNullObject() - Method in class com.daylight.DaylightObject

returns true if the object is the NULL_OB.

isSchematic() - Method in class com.daylight.Depiction

from dt_schematic.

isVisible(Atom) - Method in class com.daylight.Depiction

from dt_visible.

M

makeReactionMapSeparate() - Method in class com.daylight.Atom

from dt_setmap.

match(ConnectedAtomCollection, boolean) - Method in class com.daylight.Pattern

from dt_match.

Molecule - Class in com.daylight

Object representing a molecule

Molecule() - Constructor for class com.daylight.Molecule

from dt_allocmol.

Molecule(String) - Constructor for class com.daylight.Molecule

from dt_smilein.

Molecule(String, boolean) - Constructor for class com.daylight.Molecule

from dt_smilin_addh.

MoleculeModifiableException - Exception in com.daylight.exception

Molecule modifiable exception

MoleculeNotModifiableException - Exception in com.daylight.exception

Molecule not modifiable exception

moveTo(Point2D.Float) - Method in interface com.daylight.Depictor

dl_moveto.

mpInitialize() - Static method in class com.daylight.DaylightObject

from dt_mp_initialize

mpLock(DaylightObject) - Static method in class com.daylight.DaylightObject

from dt_mp_lock

mpTrylock(DaylightObject) - Static method in class com.daylight.DaylightObject

from dt_mp_trylock

mpUnlock(DaylightObject) - Static method in class com.daylight.DaylightObject

from dt_mp_unlock

N

next() - Method in class com.daylight.Sequence

from dt_next.

next() - Method in class com.daylight.Stream

from dt_next.

O

optimizeSmarts(String, boolean) - Static method in class com.daylight.Pattern

from dt_smarts_opt.

P

partialFingerprint(Atom, int, int, int) - Method in class com.daylight.AtomBondCollection

from dt_fp_partfp.

partialFingerprint(Bond, int, int, int) - Method in class com.daylight.AtomBondCollection

from dt_fp_partfp.

Path - Class in com.daylight

Object representing a path

Path(ConnectedAtomCollection) - Constructor for class com.daylight.Path

from dt_alloc_path.

PathSet - Class in com.daylight

 

PathSet() - Constructor for class com.daylight.PathSet

implicit superconstructor.

PathSet(ConnectedAtomCollection) - Constructor for class com.daylight.PathSet

from dt_alloc_pathset.

Pattern - Class in com.daylight

Object representing SMARTS

Pattern() - Constructor for class com.daylight.Pattern

implicit superconstructor.

Pattern(String) - Constructor for class com.daylight.Pattern

from dt_smartin.

permuteToFirstInSequence(Sequence, ChiralValue) - Method in class com.daylight.Bond

from dt_chiperm.

Point3D - Class in com.daylight

Object representing a 3D point.

Point3D() - Constructor for class com.daylight.Point3D

 

ProgramDelimiter - Enum in com.daylight.enumtype

Program delimiter, values are 'None' and 'CarriageReturn'

projectOnto(Depiction) - Method in class com.daylight.Conformation

from dt_project.

PropertyType - Enum in com.daylight.enumtype

Property type, values are 'Boolean', 'Handle', 'Integer', 'Real', 'String' and 'None'

R

Reaction - Class in com.daylight

Object representing a reaction

Reaction() - Constructor for class com.daylight.Reaction

from dt_alloc_reaction.

Reaction(String) - Constructor for class com.daylight.Reaction

from dt_smilin.

Real - Class in com.daylight

Object representing a real number

Real() - Constructor for class com.daylight.Real

from dt_alloc_real.

Real(float) - Constructor for class com.daylight.Real

from dt_alloc_real.

Real(DaylightObject) - Constructor for class com.daylight.Real

for conversion *

ref - Variable in class com.daylight.DaylightCppObject

 

remove() - Method in class com.daylight.Atom

 

remove() - Method in class com.daylight.Bond

from dt_dealloc.

remove(Atom) - Method in class com.daylight.Set

from dt_remove.

remove(Bond) - Method in class com.daylight.Set

from dt_remove.

reset() - Method in class com.daylight.Sequence

from dt_reset.

reset() - Method in class com.daylight.Stream

from dt_reset.

Role - Enum in com.daylight.enumtype

Reaction role, values are 'Reactant', 'Agent', 'Product', and 'Any'

rotate(float, float, float, float) - Method in class com.daylight.Conformation

from dt_rotate.

rotate(float) - Method in class com.daylight.Depiction

from dt_rotate.

S

saveError(String, DaylightErrorType, String) - Static method in class com.daylight.DaylightObject

from dt_errorsave.

scale(float, float, float) - Method in class com.daylight.Conformation

from dt_scale.

scale(float, float) - Method in class com.daylight.Depiction

from dt_scale.

Sequence - Class in com.daylight

Object representing a sequence

Sequence() - Constructor for class com.daylight.Sequence

from dt_alloc_seq.

Set - Class in com.daylight

Object representing a set

Set() - Constructor for class com.daylight.Set

implicit superconstructor.

setAdjunct(DaylightObject) - Method in class com.daylight.DaylightObject

from dt_setadjunct.

setArbitraryOrder(int) - Method in class com.daylight.Atom

from dt_setarborder.

setAromatic(boolean) - Method in class com.daylight.Atom

from dt_setaromatic.

setAtomicNumber(int) - Method in class com.daylight.Atom

from dt_setnumber.

setAtomicWeight(int) - Method in class com.daylight.Atom

from dt_setweight.

setBitValue(int, int) - Method in class com.daylight.Fingerprint

from dt_fp_setbitvalue.

setBondOrder(BondType) - Method in class com.daylight.Bond

from dt_setbondorder.

setBondStyle(Atom, Bond, BondStyle) - Method in class com.daylight.Depiction

from dt_setbondstyle.

setBondType(BondType) - Method in class com.daylight.Bond

from dt_setbondtype.

setBooleanProperty(String, boolean) - Method in class com.daylight.DaylightObject

from dt_setboolean.

setBounds(Rectangle2D.Float) - Method in interface com.daylight.Depictor

dl_fitbounds.

setChiralValue(Sequence, ChiralValue) - Method in class com.daylight.Atom

from dt_setchival.

setCompressed(boolean) - Method in class com.daylight.Depiction

from dt_setcompressed.

setCoordinate(Atom, float, float, float) - Method in class com.daylight.Conformation

from dt_setcoord.

setCoordinate(Atom, float, float) - Method in class com.daylight.Depiction

from dt_setcoord.

setCurrentGraphicsAttribute(int) - Method in interface com.daylight.Depictor

dl_setga.

setDefaultBondStyles() - Method in class com.daylight.Depiction

from dt_setbondstyles.

setDoubleBondOrientation(Bond, Bond, DoubleBondOrientation) - Method in class com.daylight.Bond

from dt_setdbo.

setDoubleBondOrientation(Bond, boolean, DoubleBondOrientation) - Method in class com.daylight.Bond

from dt_setdbo.

setDoubleBondOrientation(DoubleBondOrientation) - Method in class com.daylight.Bond

from dt_setdbo.

setDrawingIsomerics(boolean) - Method in class com.daylight.Depiction

from dt_setisomeric.

setFormalCharge(int) - Method in class com.daylight.Atom

from dt_setcharge.

setFramed(boolean) - Method in class com.daylight.Depiction

from dt_setframe.

setFrameGraphicsAttribute(int) - Method in class com.daylight.Depiction

from dt_setframega.

setGraphicsAttribute(Atom, int) - Method in class com.daylight.Depiction

from dt_setga.

setGraphicsAttribute(Bond, int) - Method in class com.daylight.Depiction

from dt_setga.

setGraphicsAttribute(Cycle, int) - Method in class com.daylight.Depiction

from dt_setga.

setGraphicsAttribute(int) - Method in class com.daylight.DepictionLabel

sets the graphics attribute.

setHandleProperty(String, DaylightObject) - Method in class com.daylight.DaylightObject

from dt_setHandle.

setImplicitHydrogenCount(int) - Method in class com.daylight.Atom

from dt_setimp_hcount.

setIntegerProperty(String, int) - Method in class com.daylight.DaylightObject

from dt_setinteger.

setLabel1(Atom, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel1.

setLabel1(Bond, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel1.

setLabel1(Cycle, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel1.

setLabel1(Molecule, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel1.

setLabel2(Atom, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel2.

setLabel2(Bond, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel2.

setLabel2(Cycle, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel2.

setLabel2(Molecule, DepictionLabel) - Method in class com.daylight.Depiction

from dt_setlabel2.

setModifiable(boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_mod_off and dt_mod_on.

setOrientation(DepictionOrientation) - Method in class com.daylight.Depiction

from dt_setorient.

setOriginalBitOnCount(int) - Method in class com.daylight.Fingerprint

from dt_fp_setobitcount.

setOriginalSize(int) - Method in class com.daylight.Fingerprint

from dt_fp_setobits.

setRange(int, int, byte[], int, FingerprintOperation) - Method in class com.daylight.Fingerprint

from dt_fp_setrange.

setRealProperty(String, float) - Method in class com.daylight.DaylightObject

from dt_setreal.

setSameReactionMap(Atom) - Method in class com.daylight.Atom

from dt_setmap.

setSchematic(boolean) - Method in class com.daylight.Depiction

from dt_setschematic.

setStringProperty(String, String) - Method in class com.daylight.DaylightObject

from dt_setstring.

setStringValue(String) - Method in class com.daylight.Fingerprint

from dt_setstringvalue.

setText(String) - Method in class com.daylight.DepictionLabel

sets the label text.

setValue(String) - Method in class com.daylight.DayString

from dt_setstringvalue.

setValue(int) - Method in class com.daylight.Integer

from dt_setintegervalue.

setValue(float) - Method in class com.daylight.Real

from dt_setrealvalue.

setValue(Pattern) - Method in class com.daylight.VectorBinding

from dt_setval.

setValue(PathSet) - Method in class com.daylight.VectorBinding

from dt_setval.

setVisible(Atom, boolean) - Method in class com.daylight.Depiction

from dt_setvisible.

size() - Method in class com.daylight.Sequence

returns number of objects in the sequence.

SmilesGenerationException - Exception in com.daylight.exception

Smiles Generation exception

sort() - Method in class com.daylight.Sequence

from dt_seqsort.

Stream - Class in com.daylight

Object representing a Stream

Stream() - Constructor for class com.daylight.Stream

 

Substructure - Class in com.daylight

Object representing a Substructure

Substructure(ConnectedAtomCollection) - Constructor for class com.daylight.Substructure

dt_alloc_substruct.

suppressImplicitHydrogens(boolean) - Method in class com.daylight.ConnectedAtomCollection

from dt_suppressh.

T

toEnd() - Method in class com.daylight.Sequence

from dt_toend.

Toolkit - Enum in com.daylight.enumtype

Daylight toolkits, values are 'Depict', 'Fingerprint', 'Http', 'Merlin', 'ProgramObject', 'Reaction', 'Smarts', and 'Smiles'

Transform - Class in com.daylight

Object representing a transform

Transform(String) - Constructor for class com.daylight.Transform

from dt_smirkin.

transform(Molecule, TransformDirection, boolean) - Method in class com.daylight.Transform

from dt_transform.

transform(Sequence, TransformDirection, boolean) - Method in class com.daylight.Transform

from dt_transform.

TransformDirection - Enum in com.daylight.enumtype

Transform direction, values are 'Forward' and 'Reverse'

translate(float, float, float) - Method in class com.daylight.Conformation

from dt_translate.

translate(float, float) - Method in class com.daylight.Depiction

from dt_translate.

U

UnimplementedException - Exception in com.daylight.exception

Unimplemented exception

uniqueMatch(ConnectedAtomCollection, boolean) - Method in class com.daylight.Pattern

from dt_umatch.

uniqueTransform(Molecule, TransformDirection, boolean) - Method in class com.daylight.Transform

from dt_utransform.

uniqueTransform(Sequence, TransformDirection, boolean) - Method in class com.daylight.Transform

from dt_utransform.

V

valueOf(String) - Static method in enum com.daylight.enumtype.BondOrder

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.BondStyle

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.BondType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.ChiralValue

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.CommonSubstructFlags

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.DaylightErrorType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.DaylightObjectType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.DepictionOrientation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.DoubleBondOrientation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.FingerprintOperation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.HorizontalJustification

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.ProgramDelimiter

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.PropertyType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.Role

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.Toolkit

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.TransformDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.daylight.enumtype.VerticalJustification

Returns the enum constant of this type with the specified name.

values() - Static method in enum com.daylight.enumtype.BondOrder

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.BondStyle

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.BondType

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.ChiralValue

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.CommonSubstructFlags

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.DaylightErrorType

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.DaylightObjectType

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.DepictionOrientation

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.DoubleBondOrientation

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.FingerprintOperation

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.HorizontalJustification

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.ProgramDelimiter

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.PropertyType

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.Role

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.Toolkit

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.TransformDirection

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum com.daylight.enumtype.VerticalJustification

Returns an array containing the constants of this enum type, in the order they're declared.

VectorBinding - Class in com.daylight

Object representing a vector binding

VectorBinding(String) - Constructor for class com.daylight.VectorBinding

from dt_alloc_vbind.

vectorMatch(ConnectedAtomCollection, boolean) - Method in class com.daylight.Pattern

from dt_vmatch.

VerticalJustification - Enum in com.daylight.enumtype

Vertical justification, values are 'Upper', 'Center', 'Lower', 'Top', 'Middle', and 'Bottom'

W

WrapperLicense - Class in com.daylight

 

WrapperLicense() - Constructor for class com.daylight.WrapperLicense

 

X

x - Variable in class com.daylight.Point3D

 

Y

y - Variable in class com.daylight.Point3D

 

Z

z - Variable in class com.daylight.Point3D

 

zeroCoordinates() - Method in class com.daylight.Conformation

from dt_zerocoord.

zeroCoordinates() - Method in class com.daylight.Depiction

from dt_zerocoord.