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
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
parBatchByIndex	parBatchByIndex
plot	plotStruc
plot,SDF-method	SDF-class
plot,SDFset-method	SDFset-class
plotStruc	plotStruc
propOB	propOB
pubchemFPencoding	pubchemFPencoding
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
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
