addDescriptorType	addDescriptorType
addNewFeatures	addNewFeatures
ap	ap
ap,AP-method	AP-class
ap,APset-method	APset-class
AP-class	AP-class
ap-methods	ap
apfp	apfp
apset	apset
APset-class	APset-class
apset2descdb	apset2descdb
as.character,FP-method	FP-class
as.character,FPset-method	FPset-class
as.character,SMI-method	SMI-class
as.character,SMIset-method	SMIset-class
as.matrix,FPset-method	FPset-class
as.numeric,FP-method	FP-class
as.vector,FP-method	FP-class
atomblock	atomblock
atomblock,SDF-method	SDF-class
atomblock,SDFset-method	SDFset-class
atomblock-methods	atomblock
atomblock<-	atomblock
atomblock<-,SDFset-method	SDFset-class
atomcount	atomcount
atomcount,SDF-method	SDF-class
atomcount,SDFset-method	SDFset-class
atomcountMA	atomcount
atomprop	atomprop
atomsubset	atomsubset
batchByIndex	batchByIndex
bondblock	bondblock
bondblock,SDF-method	SDF-class
bondblock,SDFset-method	SDFset-class
bondblock-methods	bondblock
bondblock<-	bondblock
bondblock<-,SDFset-method	SDFset-class
bonds	bonds
browseJob	browseJob
bufferLines	bufferLines
bufferResultSet	bufferResultSet
byCluster	byCluster
c,APset-method	APset-class
c,FP-method	FP-class
c,FPset-method	FPset-class
c,SDFset-method	SDFset-class
c,SMIset-method	SMIset-class
canonicalize	canonicalize
canonicalNumbering	canonicalNumbering
cid	cid
cid,APset-method	APset-class
cid,FPset-method	FPset-class
cid,SDFset-method	SDFset-class
cid,SMIset-method	SMIset-class
cid<-	cid
cid<-,APset-method	APset-class
cid<-,FPset-method	FPset-class
cid<-,SDFset-method	SDFset-class
cid<-,SMIset-method	SMIset-class
cluster.sizestat	cluster.sizestat
cluster.visualize	cluster.visualize
cmp.cluster	cmp.cluster
cmp.duplicated	cmp.duplicated
cmp.parse	cmp.parse
cmp.parse1	cmp.parse1
cmp.search	cmp.search
cmp.similarity	cmp.similarity
coerce,APset,AP-method	APset-class
coerce,APset,list-method	APset-class
coerce,character,FPset-method	FPset-class
coerce,character,SDF-method	SDF-class
coerce,character,SDFstr-method	SDFstr-class
coerce,character,SMI-method	SMI-class
coerce,character,SMIset-method	SMIset-class
coerce,FPset,FP-method	FPset-class
coerce,list,APset-method	APset-class
coerce,list,SDF-method	SDF-class
coerce,list,SDFset-method	SDFset-class
coerce,list,SDFstr-method	SDFstr-class
coerce,list,SMIset-method	SMIset-class
coerce,matrix,FPset-method	FPset-class
coerce,numeric,FP-method	FP-class
coerce,SDF,character-method	SDF-class
coerce,SDF,list-method	SDF-class
coerce,SDF,SDFset-method	SDF-class
coerce,SDF,SDFstr-method	SDF-class
coerce,SDFset,list-method	SDFset-class
coerce,SDFset,SDF-method	SDFset-class
coerce,SDFset,SDFstr-method	SDFset-class
coerce,SDFstr,list-method	SDFstr-class
coerce,SDFstr,SDFset-method	SDFstr-class
coerce,SMIset,SMI-method	SMIset-class
conMA	conMA
datablock	datablock
datablock,SDF-method	SDF-class
datablock,SDFset-method	SDFset-class
datablock-methods	datablock
datablock2ma	datablock2ma
datablock<-	datablock
datablock<-,SDFset-method	SDFset-class
datablocktag	datablock
datablocktag,SDF-method	SDF-class
datablocktag,SDFset-method	SDFset-class
db.explain	db.explain
db.subset	db.subset
dbTransaction	dbTransaction
desc2fp	desc2fp
draw_sdf	draw_sdf
DrugBank	connections
DUD	connections
exactMassOB	exactMassOB
ExtSDF-class	ExtSDF-class
findCompounds	findCompounds
findCompoundsByName	findCompoundsByName
fingerprintOB	fingerprintOB
fold	fold
fold,FP-method	FP-class
fold,FPset-method	FPset-class
foldCount	foldCount
foldCount,FP-method	FP-class
foldCount,FPset-method	FPset-class
forestSizePriorities	setPriorities
FP-class	FP-class
fp2bit	fp2bit
FPset-class	FPset-class
fpSim	fpSim
fptype	fptype
fptype,FP-method	FP-class
fptype,FPset-method	FPset-class
fromNNMatrix	fromNNMatrix
genAPDescriptors	genAPDescriptors
generate3DCoords	generate3DCoords
genParameters	genParameters
getAllCompoundIds	getAllCompoundIds
getAtomAttr,ExtSDF-method	ExtSDF-class
getBondAttr,ExtSDF-method	ExtSDF-class
getCompoundFeatures	getCompoundFeatures
getCompoundNames	getCompoundNames
getCompounds	getCompounds
getIds	getIds
grepSDFset	grepSDFset
groups	groups
header	header
header,SDF-method	SDF-class
header,SDFset-method	SDFset-class
header-methods	header
header<-	header
header<-,SDFset-method	SDFset-class
initDb	initDb
jarvisPatrick	jarvisPatrick
jarvisPatrick_c	jarvisPatrick_c
jobToken-class	jobToken-class
largestComponent	largestComponent
launchCMTool	launchCMTool
length,APset-method	APset-class
length,FPset-method	FPset-class
length,SDFset-method	SDFset-class
length,SDFstr-method	SDFstr-class
length,SMIset-method	SMIset-class
listCMTools	listCMTools
listFeatures	listFeatures
loadSdf	loadSdf
loadSmiles	loadSdf
makeUnique	makeUnique
maximallyDissimilar	maximallyDissimilar
MF	atomcount
MW	atomcount
nearestNeighbors	nearestNeighbors
numBits	numBits
numBits,FP-method	FP-class
numBits,FPset-method	FPset-class
obmol	obmol
obmol,SDF-method	SDF-class
obmol,SDFset-method	SDFset-class
obmol-methods	obmol
openBabelPlot	openBabelPlot
parBatchByIndex	parBatchByIndex
plot	plotStruc
plot,SDF-method	SDF-class
plot,SDFset-method	SDFset-class
plotStruc	plotStruc
propOB	propOB
pubchemCidToSDF	pubchemCidToSDF
pubchemFPencoding	pubchemFPencoding
pubchemInchi2cid	pubchemInchi2cid
pubchemInchikey2sdf	pubchemInchikey2sdf
pubchemName2CID	pubchemName2CID
pubchemSDFSearch	pubchemSDFSearch
pubchemSmilesSearch	pubchemSmilesSearch
randomPriorities	setPriorities
read.AP	read.AP
read.SDFindex	read.SDFindex
read.SDFset	read.SDFset
read.SDFstr	read.SDFstr
read.SMIset	read.SMIset
regenerateCoords	regenerateCoords
result	result
rings	rings
SDF-class	SDF-class
sdf.subset	sdf.subset
sdf.visualize	sdf.visualize
sdf2ap	sdf2ap
SDF2apcmp	SDF2apcmp
sdf2list	sdf2list
sdf2list,SDF-method	SDF-class
sdf2smiles	sdf2smiles
sdf2smilesOB	sdf2smiles
sdf2str	sdf2str
sdf2str,SDF-method	SDF-class
sdf2str-methods	sdf2str
SDFDataTable	SDFDataTable
sdfid	sdfid
sdfid,SDF-method	SDF-class
sdfid,SDFset-method	SDFset-class
sdfsample	sdfsample
SDFset	SDFset-class
SDFset-class	SDFset-class
SDFset2list	SDFset2list
SDFset2list,SDFset-method	SDFset-class
SDFset2list-methods	SDFset2list
SDFset2SDF	SDFset2SDF
SDFset2SDF,SDFset-method	SDFset-class
SDFset2SDF-methods	SDFset2SDF
SDFset2SDF<-	SDFset2SDF
SDFset2SDF<-,SDFset-method	SDFset-class
SDFstr-class	SDFstr-class
sdfstr2list	sdfstr2list
sdfstr2list,SDFstr-method	SDFstr-class
sdfstr2list-methods	sdfstr2list
sdfstr2list<-	sdfstr2list
sdfstr2list<-,SDFstr-method	SDFstr-class
sdfStream	sdfStream
searchSim	searchSim
searchString	searchString
selectInBatches	selectInBatches
setPriorities	setPriorities
show,AP-method	AP-class
show,APset-method	APset-class
show,ExtSDF-method	ExtSDF-class
show,FP-method	FP-class
show,FPset-method	FPset-class
show,jobToken-method	jobToken-class
show,SDF-method	SDF-class
show,SDFset-method	SDFset-class
show,SDFstr-method	SDFstr-class
show,SMI-method	SMI-class
show,SMIset-method	SMIset-class
smartsSearchOB	smartsSearchOB
SMI-class	SMI-class
smiles2sdf	smiles2sdf
smiles2sdfOB	smiles2sdf
smisample	smisample
SMIset-class	SMIset-class
splitNumChar	datablock2ma
status	status
toolDetails	toolDetails
trimNeighbors	trimNeighbors
validSDF	validSDF
view	view
view,APset-method	APset-class
view,FPset-method	FPset-class
view,SDFset-method	SDFset-class
view,SMIset-method	SMIset-class
view-methods	view
write.SDF	write.SDF
write.SDFsplit	write.SDFsplit
write.SMI	write.SMI
[,APset-method	APset-class
[,FPset-method	FPset-class
[,SDF-method	SDF-class
[,SDFset-method	SDFset-class
[,SDFstr-method	SDFstr-class
[,SMIset-method	SMIset-class
[<-,APset-method	APset-class
[<-,FPset-method	FPset-class
[<-,SDF-method	SDF-class
[<-,SDFset-method	SDFset-class
[<-,SDFstr-method	SDFstr-class
[<-,SMIset-method	SMIset-class
[[,APset-method	APset-class
[[,FPset-method	FPset-class
[[,SDF-method	SDF-class
[[,SDFset-method	SDFset-class
[[,SDFstr-method	SDFstr-class
[[,SMIset-method	SMIset-class
[[<-,APset-method	APset-class
[[<-,SDF-method	SDF-class
[[<-,SDFset-method	SDFset-class
[[<-,SDFstr-method	SDFstr-class
