API for ChemmineR
Cheminformatics Toolkit for R

Global functions
.calc.distmat	Source code
.cluster_g	Source code
.cmp.similarity	Source code
.containedArom	Source code
.convertInput	Source code
.convertOutput	Source code
.cyclicCore	Source code
.data.frame.to.str	Source code
.ensureOB	Source code
.explain	Source code
.extract_single_sdf	Source code
.factor_to_vector	Source code
.gsubsdfsec	Source code
.haveOB	Source code
.interpret_atom	Source code
.is.arom	Source code
.is.file.backed.desc	Source code
.is.inner	Source code
.linearCon	Source code
.load.file.backed.desc	Source code
.neighbors	Source code
.onLoad	Source code
.parseV3000	Source code
.postToHost	Source code
.progress_bar	Source code
.read.one.sdf	Source code
.rings	Source code
.sdfDownload	Source code
.sdfParse	Source code
.search.nearest	Source code
.uniquifyAtomPairs	Source code
.update	Source code
AP-class	Man page
APset-class	Man page
DUD	Man page Source code
DrugBank	Man page Source code
ExtSDF-class	Man page
FP-class	Man page
FPset-class	Man page
MF	Man page Source code
MW	Man page Source code
RSWIG_createNewRef	Source code
R_SWIG_addCallbackFunctionStack	Source code
R_SWIG_getCallbackFunctionStack	Source code
SDF-class	Man page
SDF2apcmp	Man page Source code
SDFDataTable	Man page Source code
SDFset	Man page Source code
SDFset-class	Man page
SDFset2SDF	Man page
SDFset2SDF,SDFset-method	Man page
SDFset2SDF-methods	Man page
SDFset2SDF<-	Man page
SDFset2SDF<-,SDFset-method	Man page
SDFset2list	Man page
SDFset2list,SDFset-method	Man page
SDFset2list-methods	Man page
SDFstr-class	Man page
SMI-class	Man page
SMIset-class	Man page
[,APset-method	Man page
[,FPset-method	Man page
[,SDF-method	Man page
[,SDFset-method	Man page
[,SDFstr-method	Man page
[,SMIset-method	Man page
[<-,APset-method	Man page
[<-,FPset-method	Man page
[<-,SDF-method	Man page
[<-,SDFset-method	Man page
[<-,SDFstr-method	Man page
[<-,SMIset-method	Man page
[[,APset-method	Man page
[[,FPset-method	Man page
[[,SDF-method	Man page
[[,SDFset-method	Man page
[[,SDFstr-method	Man page
[[,SMIset-method	Man page
[[<-,APset-method	Man page
[[<-,SDF-method	Man page
[[<-,SDFset-method	Man page
[[<-,SDFstr-method	Man page
`Descriptors_get_descriptor`	Source code
`Descriptors_get_len`	Source code
`Descriptors_parse_sdf`	Source code
`Descriptors_parse_sdfile`	Source code
`Descriptors_parse_smiles`	Source code
`Descriptors`	Source code
`delete_Descriptors`	Source code
`similarity`	Source code
addDescriptorType	Man page Source code
addNeededFeatures	Source code
addNewFeatures	Man page Source code
ap	Man page
ap,AP-method	Man page
ap,APset-method	Man page
ap-methods	Man page
apfp	Man page
applyOptions	Source code
apset	Man page
apset2descdb	Man page Source code
as.character,FP-method	Man page
as.character,FPset-method	Man page
as.character,SMI-method	Man page
as.character,SMIset-method	Man page
as.matrix,FPset-method	Man page
as.numeric,FP-method	Man page
as.vector,FP-method	Man page
assert	Source code
atomblock	Man page
atomblock,SDF-method	Man page
atomblock,SDFset-method	Man page
atomblock-methods	Man page
atomblock<-	Man page
atomblock<-,SDFset-method	Man page
atomcount	Man page
atomcount,SDF-method	Man page
atomcount,SDFset-method	Man page
atomcountMA	Man page Source code
atomprop	Man page
atomsubset	Man page
attributesAsString	Source code
batchByIndex	Man page Source code
bondblock	Man page
bondblock,SDF-method	Man page
bondblock,SDFset-method	Man page
bondblock-methods	Man page
bondblock<-	Man page
bondblock<-,SDFset-method	Man page
bonds	Man page Source code
browseJob	Man page Source code
bufferLines	Man page Source code
bufferResultSet	Man page Source code
byCluster	Man page Source code
c,APset-method	Man page
c,FP-method	Man page
c,FPset-method	Man page
c,SDFset-method	Man page
c,SMIset-method	Man page
canonicalNumbering	Man page
canonicalNumberingOB	Source code
canonicalize	Man page
canonicalizeOB	Source code
cid	Man page
cid,APset-method	Man page
cid,FPset-method	Man page
cid,SDFset-method	Man page
cid,SMIset-method	Man page
cid<-	Man page
cid<-,APset-method	Man page
cid<-,FPset-method	Man page
cid<-,SDFset-method	Man page
cid<-,SMIset-method	Man page
cluster.sizestat	Man page Source code
cluster.visualize	Man page Source code
cmp.cluster	Man page Source code
cmp.duplicated	Man page Source code
cmp.parse	Man page Source code
cmp.parse1	Man page Source code
cmp.search	Man page Source code
cmp.similarity	Man page Source code
coerce,APset,AP-method	Man page
coerce,APset,list-method	Man page
coerce,FPset,FP-method	Man page Man page
coerce,SDF,SDFset-method	Man page
coerce,SDF,SDFstr-method	Man page
coerce,SDF,character-method	Man page
coerce,SDF,list-method	Man page
coerce,SDFset,SDF-method	Man page
coerce,SDFset,SDFstr-method	Man page
coerce,SDFset,list-method	Man page
coerce,SDFstr,SDFset-method	Man page
coerce,SDFstr,list-method	Man page
coerce,SMIset,SMI-method	Man page
coerce,character,FPset-method	Man page
coerce,character,SDF-method	Man page
coerce,character,SDFstr-method	Man page
coerce,character,SMI-method	Man page
coerce,character,SMIset-method	Man page
coerce,list,APset-method	Man page
coerce,list,SDF-method	Man page
coerce,list,SDFset-method	Man page
coerce,list,SDFstr-method	Man page
coerce,list,SMIset-method	Man page
coerce,matrix,FPset-method	Man page
coerce,numeric,FP-method	Man page
coerceIfNotSubclass	Source code
conMA	Man page Source code
concatenate_plots	Source code
createFeature	Source code
cstrsplit	Source code
datablock	Man page
datablock,SDF-method	Man page
datablock,SDFset-method	Man page
datablock-methods	Man page
datablock2ma	Man page Source code
datablock<-	Man page
datablock<-,SDFset-method	Man page
datablocktag	Man page
datablocktag,SDF-method	Man page
datablocktag,SDFset-method	Man page
db.explain	Man page Source code
db.subset	Man page Source code
dbGetQueryChecked	Source code
dbOp	Source code
dbTransaction	Man page Source code
default_edge_policy	Source code
default_node_policy	Source code
definition2SDFset	Source code
definitionChecksums	Source code
deleteCompounds	Source code
desc2fp	Man page Source code
descriptorTypes	Source code
draw_sdf	Man page Source code
enableForeignKeys	Source code
enumFromInteger	Source code
enumToInteger	Source code
ex2vec	Source code
exactMassOB	Man page Source code
featureDiff	Source code
findCompounds	Man page Source code
findCompoundsByChecksum	Source code
findCompoundsByName	Man page Source code
findCompoundsByX	Source code
findPositions	Source code
fingerprintOB	Man page Source code
fold	Man page
fold,FP-method	Man page
fold,FPset-method	Man page
foldCount	Man page
foldCount,FP-method	Man page
foldCount,FPset-method	Man page
foldVector	Source code
foldsNeeded	Source code
forestSizePriorities	Man page Source code
fp2bit	Man page Source code
fpSim	Man page Source code
fpSimOrig	Source code
fptype	Man page
fptype,FP-method	Man page
fptype,FPset-method	Man page
fromNNMatrix	Man page Source code
genAPDescriptors	Man page Source code
genParameters	Man page Source code
generate3DCoords	Man page
generate3DCoordsOB	Source code
getAllCompoundIds	Man page Source code
getAtomAttr,ExtSDF-method	Man page
getBondAttr,ExtSDF-method	Man page
getCompoundFeatures	Man page Source code
getCompoundNames	Man page Source code
getCompounds	Man page Source code
getDbConn	Source code
getIds	Man page Source code
getPreparedQuery	Source code
grepSDFset	Man page Source code
groups	Man page Source code
handle_raster	Source code
handle_segs	Source code
handle_text	Source code
header	Man page
header,SDF-method	Man page
header,SDFset-method	Man page
header-methods	Man page
header<-	Man page
header<-,SDFset-method	Man page
indexExistingCompounds	Source code
initDb	Man page Source code
insertDef	Source code
insertDescriptor	Source code
insertDescriptorType	Source code
insertFeature	Source code
insertNamedDef	Source code
insertUserFeatures	Source code
jarvisPatrick	Man page Source code
jarvisPatrick_c	Man page Source code
jobToken-class	Man page
largestComponent	Man page Source code
launchCMTool	Man page Source code
length,APset-method	Man page
length,FPset-method	Man page
length,SDFset-method	Man page
length,SDFstr-method	Man page
length,SMIset-method	Man page
listCMTools	Man page Source code
listFeatures	Man page Source code
loadDb	Source code
loadDescriptors	Source code
loadSdf	Man page Source code
loadSmiles	Man page Source code
makeUnique	Man page Source code
maximallyDissimilar	Man page Source code
nearestNeighbors	Man page Source code
numBits	Man page
numBits,FP-method	Man page
numBits,FPset-method	Man page
obmol	Man page
obmol,SDF-method	Man page
obmol,SDFset-method	Man page
obmol-methods	Man page
openBabelPlot	Man page Man page Source code
parBatchByIndex	Man page Source code
parseAttributes	Source code
plot	Man page
plot,SDF-method	Man page
plot,SDFset-method	Man page
plotStruc	Man page Source code
postgresqlWriteTable	Source code
processAndLoad	Source code
propOB	Man page Source code
pubchemCidToSDF	Man page Source code
pubchemFPencoding	Man page
pubchemName2CID	Man page Source code
pubchemSDF2PNG	Source code
pubchemSDFSearch	Man page Source code
pubchemSmilesSearch	Man page Source code
randomPriorities	Man page Source code
read.AP	Man page Source code
read.SDFindex	Man page Source code
read.SDFset	Man page Source code
read.SDFstr	Man page Source code
read.SMIset	Man page Source code
regenCoordsOB	Source code
regenerateCoords	Man page
result	Man page Source code
rings	Man page Source code
rmDups	Source code
sdf.subset	Man page Source code
sdf.visualize	Man page Source code
sdf2OBMol	Source code
sdf2ap	Man page Source code
sdf2image	Source code
sdf2list	Man page
sdf2list,SDF-method	Man page
sdf2smiles	Man page
sdf2smilesOB	Man page Source code
sdf2str	Man page
sdf2str,SDF-method	Man page
sdf2str-methods	Man page
sdfSet2definition	Source code
sdfStream	Man page Source code
sdfid	Man page
sdfid,SDF-method	Man page
sdfid,SDFset-method	Man page
sdfsample	Man page
sdfstr2list	Man page
sdfstr2list,SDFstr-method	Man page
sdfstr2list-methods	Man page
sdfstr2list<-	Man page
sdfstr2list<-,SDFstr-method	Man page
searchSim	Man page Source code
searchString	Man page Source code
selectInBatches	Man page Source code
setPriorities	Man page Source code
show,AP-method	Man page
show,APset-method	Man page
show,ExtSDF-method	Man page
show,FP-method	Man page
show,FPset-method	Man page
show,SDF-method	Man page
show,SDFset-method	Man page
show,SDFstr-method	Man page
show,SMI-method	Man page
show,SMIset-method	Man page
show,jobToken-method	Man page
smartsSearchOB	Man page Source code
smile2sdfFile	Source code
smiles2sdf	Man page
smiles2sdfOB	Man page Source code
smisample	Man page
splitNumChar	Man page Source code
status	Man page Source code
toolDetails	Man page Source code
trim	Source code
trimNeighbors	Man page Source code
updatePriorities	Source code
validSDF	Man page Source code
view	Man page
view,APset-method	Man page
view,FPset-method	Man page
view,SDFset-method	Man page
view,SMIset-method	Man page
view-methods	Man page
write.SDF	Man page Source code
write.SDFsplit	Man page Source code
write.SMI	Man page Source code
writeV3000	Source code