All Methods Instance Methods Concrete Methods Deprecated Methods
| Modifier and Type |
Method and Description |
IndigoObject |
addAtom(String symbol) |
IndigoObject |
addBond(IndigoObject atom,
int order) |
void |
addCatalyst(IndigoObject molecule) |
void |
addConstraint(String type,
String value) |
void |
addConstraintNot(String type,
String value) |
void |
addConstraintOr(String type,
String value) |
IndigoObject |
addDataSGroup(Collection<Integer> atoms,
Collection<Integer> bonds,
String description,
String data) |
IndigoObject |
addDataSGroup(int[] atoms,
int[] bonds,
String description,
String data) |
void |
addDecomposition(IndigoObject q_match) |
void |
addProduct(IndigoObject molecule) |
void |
addReactant(IndigoObject molecule) |
IndigoObject |
addRSite(String name) |
int |
addSGroupAttachmentPoint(int aidx,
int lvidx,
String apid) |
void |
addStereocenter(int type,
int v1,
int v2,
int v3) |
void |
addStereocenter(int type,
int v1,
int v2,
int v3,
int v4) |
int |
addTemplate(IndigoObject templates,
String name) |
float |
alignAtoms(Collection<Integer> atom_ids,
Collection<Float> desired_xyz) |
float |
alignAtoms(int[] atom_ids,
float[] desired_xyz) |
IndigoObject |
allScaffolds() |
void |
append(IndigoObject obj) |
void |
aromatize() |
int |
arrayAdd(IndigoObject other) |
IndigoObject |
at(int idx) |
int |
atomicNumber() |
int |
atomMappingNumber(IndigoObject reaction_atom) |
void |
automap() |
void |
automap(String mode) |
String |
b64cdx() |
IndigoObject |
bond() |
int |
bondOrder() |
int |
bondStereo() |
String |
canonicalSmarts() |
String |
canonicalSmiles() |
String |
cdxml() |
void |
changeStereocenterType(int type) |
Integer |
charge() |
String |
check() |
String |
check(String type) |
int |
check3DStereo() |
String |
checkAmbiguousH() |
String |
checkBadValence() |
int |
checkChirality() |
int |
checkQuery() |
int |
checkRGroups() |
int |
checkStereo() |
int |
checkValence() |
void |
clean2d() |
void |
clear() |
void |
clearAAM() |
void |
clearAlleneCenters() |
void |
clearAttachmentPoints() |
void |
clearCisTrans() |
void |
clearProperties() |
void |
clearStereocenters() |
void |
clearXYZ() |
IndigoObject |
clone() |
void |
close() |
String |
cml() |
void |
cmlAppend(IndigoObject item) |
void |
cmlFooter() |
void |
cmlHeader() |
IndigoObject |
component(int index) |
int |
componentIndex() |
int |
copyRGroups(IndigoObject other) |
void |
correctReactingCenters() |
int |
count() |
int |
countAlleneCenters() |
int |
countAtoms() |
int |
countAttachmentPoints() |
int |
countBits() |
int |
countBonds() |
int |
countCatalysts() |
int |
countComponents() |
int |
countDataSGroups() |
int |
countGenericSGroups() |
int |
countHeavyAtoms() |
Integer |
countHydrogens() |
int |
countImplicitHydrogens() |
int |
countMatches(IndigoObject query) |
int |
countMatchesWithLimit(IndigoObject query,
int embeddings_limit) |
int |
countMolecules() |
int |
countMultipleGroups() |
int |
countProducts() |
int |
countPseudoatoms() |
int |
countReactants() |
int |
countRepeatingUnits() |
int |
countRGroups() |
int |
countRSites() |
int |
countSSSR() |
int |
countStereocenters() |
int |
countSuperatoms() |
IndigoObject |
createEdgeSubmolecule(Collection<Integer> vertices,
Collection<Integer> edges) |
IndigoObject |
createEdgeSubmolecule(int[] vertices,
int[] edges) |
IndigoObject |
createSGroup(String type,
IndigoObject mapping,
String name) |
IndigoObject |
createSubmolecule(Collection<Integer> vertices) |
IndigoObject |
createSubmolecule(int[] vertices) |
String |
data() |
String |
dbgInternalType() |
void |
dearomatize() |
IndigoObject |
decomposedMoleculeHighlighted() |
IndigoObject |
decomposedMoleculeScaffold() |
IndigoObject |
decomposedMoleculeWithRGroups() |
IndigoObject |
decomposeMolecule(IndigoObject mol) |
int |
degree() |
int |
deleteSGroupAttachmentPoint(int apidx) |
String |
description() |
IndigoObject |
destination() |
void |
dispose() |
int |
expandAbbreviations() |
Integer |
explicitValence() |
String |
fasta(IndigoObject library) |
protected void |
finalize() |
IndigoObject |
findSGroups(String property,
String value) |
int |
findTemplate(String name) |
IndigoObject |
fingerprint() |
IndigoObject |
fingerprint(String type) |
void |
foldHydrogens() |
void |
foldUnfoldHydrogens() |
float |
getAcidPkaValue(IndigoObject atom,
int level,
int min_level) |
IndigoObject |
getAtom(int idx) |
float |
getBasicPkaValue(IndigoObject atom,
int level,
int min_level) |
IndigoObject |
getBond(int idx) |
IndigoObject |
getDataSGroup(int index) |
IndigoObject |
getGenericSGroup(int index) |
Hybridization |
getHybridization() |
String |
getHybridizationStr() |
Indigo |
getIndigo() |
IndigoObject |
getMolecule(int idx) |
IndigoObject |
getMultipleGroup(int index) |
String |
getOriginalFormat() |
String |
getProperty(String prop) |
IndigoObject |
getRepeatingUnit(int index) |
int |
getRepeatingUnitConnectivity() |
String |
getRepeatingUnitSubscript() |
String |
getSGroupClass() |
float[] |
getSGroupCoords() |
int |
getSGroupDisplayOption() |
int |
getSGroupIndex() |
int |
getSGroupMultiplier() |
String |
getSGroupName() |
int |
getSGroupNumCrossBonds() |
int |
getSGroupOriginalId() |
int |
getSGroupParentId() |
int |
getSGroupSeqId() |
int |
getSGroupType() |
IndigoObject |
getSubmolecule(Collection<Integer> vertices) |
IndigoObject |
getSubmolecule(int[] vertices) |
IndigoObject |
getSuperatom(int index) |
String |
getTemplateAtomClass() |
String |
getTGroupAlias() |
String |
getTGroupClass() |
String |
getTGroupName() |
String |
grossFormula() |
boolean |
hasCoord() |
long |
hash() |
boolean |
hasNext() |
boolean |
hasProperty(String prop) |
boolean |
hasZCoord() |
String |
helm(IndigoObject library) |
void |
highlight() |
IndigoObject |
highlightedTarget() |
String |
idt(IndigoObject library) |
void |
ignoreAtom(IndigoObject atom) |
int |
index() |
void |
invertStereo() |
void |
ionize(float pH,
float pHToll) |
boolean |
isChiral() |
boolean |
isHighlighted() |
int |
isotope() |
boolean |
isPossibleFischerProjection(String options) |
boolean |
isPseudoatom() |
boolean |
isRSite() |
boolean |
isTemplateAtom() |
IndigoObject |
iterateAlleneCenters() |
IndigoObject |
iterateArray() |
IndigoObject |
iterateAtoms() |
IndigoObject |
iterateAttachmentPoints(int order) |
IndigoObject |
iterateBonds() |
IndigoObject |
iterateCatalysts() |
IndigoObject |
iterateComponents() |
IndigoObject |
iterateDataSGroups() |
IndigoObject |
iterateDecomposedMolecules()
Deprecated.
|
IndigoObject |
iterateDecompositions() |
IndigoObject |
iterateEdgeSubmolecules(int min_edges,
int max_edges) |
IndigoObject |
iterateGenericSGroups() |
IndigoObject |
iterateMatches(IndigoObject query) |
IndigoObject |
iterateMolecules() |
IndigoObject |
iterateMultipleGroups() |
IndigoObject |
iterateNeighbors() |
IndigoObject |
iterateProducts() |
IndigoObject |
iterateProperties() |
IndigoObject |
iteratePseudoatoms() |
IndigoObject |
iterateReactants() |
IndigoObject |
iterateReactions() |
IndigoObject |
iterateRepeatingUnits() |
IndigoObject |
iterateRGroupFragments() |
IndigoObject |
iterateRGroups() |
IndigoObject |
iterateRings(int min_vertices,
int max_vertices) |
IndigoObject |
iterateRSites() |
IndigoObject |
iterateSGroups() |
IndigoObject |
iterateSSSR() |
IndigoObject |
iterateStereocenters() |
IndigoObject |
iterateSubtrees(int min_vertices,
int max_vertices) |
IndigoObject |
iterateSuperatoms() |
IndigoObject |
iterateTGroups() |
Iterator<IndigoObject> |
iterator() |
String |
json() |
String |
layeredCode() |
void |
layout() |
double |
logP() |
String |
macroProperties(float upc,
float nac) |
IndigoObject |
mapAtom(IndigoObject query_atom) |
IndigoObject |
mapBond(IndigoObject query_bond) |
IndigoObject |
mapMolecule(IndigoObject query_reaction_molecule) |
int |
markEitherCisTrans() |
int |
markStereobonds() |
String |
massComposition() |
IndigoObject |
match(IndigoObject query) |
byte[] |
mdlct() |
IndigoObject |
merge(IndigoObject other) |
double |
molarRefractivity() |
double |
molecularWeight() |
String |
molfile() |
double |
monoisotopicMass() |
double |
mostAbundantMass() |
String |
name() |
IndigoObject |
next() |
boolean |
normalize() |
boolean |
normalize(String options) |
int |
numHydrogenBondAcceptors() |
int |
numHydrogenBondDonors() |
int |
numRotatableBonds() |
String |
oneBitsList() |
void |
optimize() |
void |
optimize(String options) |
double |
pKa() |
Integer |
radical() |
Integer |
radicalElectrons() |
String |
rawData() |
void |
rdfAppend(IndigoObject item) |
void |
rdfHeader() |
int |
reactingCenter(IndigoObject bond) |
void |
remove() |
void |
removeAtoms(Collection<Integer> vertices) |
void |
removeAtoms(int[] vertices) |
void |
removeBonds(Collection<Integer> bonds) |
void |
removeBonds(int[] bonds) |
void |
removeConstraints(String type) |
void |
removeProperty(String prop) |
int |
removeTemplate(String name) |
IndigoObject |
resetAtom(String symbol) |
void |
resetCharge() |
void |
resetExplicitValence() |
void |
resetIsotope() |
void |
resetRadical() |
void |
resetStereo() |
int |
resetSymmetricCisTrans() |
int |
resetSymmetricStereocenters() |
String |
rxnfile() |
void |
saveCdxml(String filename) |
void |
saveCml(String filename) |
void |
saveFastaToFile(String filename) |
void |
saveMolfile(String filename) |
void |
saveRxnfile(String filename) |
void |
saveSequence3LetterToFile(String filename,
IndigoObject library) |
void |
saveSequenceToFile(String filename,
IndigoObject library) |
void |
sdfAppend(IndigoObject item) |
String |
sequence(IndigoObject library) |
String |
sequence3Letter(IndigoObject library) |
byte[] |
serialize() |
void |
setAtomMappingNumber(IndigoObject reaction_atom,
int number) |
void |
setAttachmentPoint(int order) |
void |
setBondOrder(int order) |
void |
setCharge(int charge) |
void |
setDataSGroupXY(float x,
float y) |
void |
setDataSGroupXY(float x,
float y,
String options) |
void |
setExplicitValence(int valence) |
void |
setImplicitHCount(int hcount) |
void |
setIsotope(int isotope) |
void |
setName(String name) |
void |
setProperty(String prop,
String value) |
void |
setRadical(int radical) |
void |
setReactingCenter(IndigoObject bond,
int type) |
IndigoObject |
setRSite(String name) |
int |
setSGroupBrackets(int brk_style,
float x1,
float y1,
float x2,
float y2,
float x3,
float y3,
float x4,
float y4) |
void |
setSGroupClass(String sgclass) |
int |
setSGroupCoords(float x,
float y) |
int |
setSGroupData(String data) |
int |
setSGroupDataType(String data_type) |
int |
setSGroupDescription(String description) |
int |
setSGroupDisplay(String option) |
int |
setSGroupDisplayOption(int option) |
int |
setSGroupFieldName(String name) |
int |
setSGroupLocation(String option) |
int |
setSGroupMultiplier(int mult) |
void |
setSGroupName(String sgname) |
int |
setSGroupOriginalId(int original) |
int |
setSGroupParentId(int parent) |
int |
setSGroupQueryCode(String querycode) |
int |
setSGroupQueryOper(String queryoper) |
int |
setSGroupTag(String tag) |
int |
setSGroupTagAlign(int tag_align) |
int |
setSGroupXCoord(float x) |
int |
setSGroupYCoord(float y) |
void |
setStereocenterGroup(int group) |
int |
setTemplateAtomClass(String name) |
void |
setXYZ(float[] xyz) |
void |
setXYZ(float x,
float y,
float z) |
int |
singleAllowedRGroup() |
String |
smarts() |
String |
smiles() |
void |
smilesAppend(IndigoObject item) |
IndigoObject |
source() |
void |
standardize() |
int |
stereocenterGroup() |
int[] |
stereocenterPyramid() |
int |
stereocenterType() |
String |
symbol() |
int[] |
symmetryClasses() |
int |
tell() |
byte[] |
toBuffer() |
int |
topology() |
String |
toString() |
double |
tpsa() |
double |
tpsa(boolean includeSP) |
int |
transformCTABtoSCSR(IndigoObject templates) |
int |
transformSCSRtoCTAB() |
void |
unfoldHydrogens() |
void |
unhighlight() |
void |
unignoreAllAtoms() |
void |
unignoreAtom(IndigoObject atom) |
int |
valence() |
int |
validateChirality() |
float[] |
xyz() |