A B C D E F G H I J L M N O P R S T V W misc
addDescriptorType | Add Descriptor Type |
addNewFeatures | Add New Features |
ap | Return atom pair component of 'AP/APset' |
AP-class | Class "AP" |
ap-method | Class "AP" |
ap-method | Class "APset" |
ap-methods | Return atom pair component of 'AP/APset' |
apfp | Frequent Atom Pairs |
apset | Atom pairs stored in 'APset' object |
APset-class | Class "APset" |
apset2descdb | 'APset' to list-style AP database |
as.character-method | Class '"FP"' |
as.character-method | Class '"FPset"' |
as.character-method | Class '"SMI"' |
as.character-method | Class '"SMIset"' |
as.matrix-method | Class '"FPset"' |
as.numeric-method | Class '"FP"' |
as.vector-method | Class '"FP"' |
atomblock | Return atom block |
atomblock-method | Class "SDF" |
atomblock-method | Class "SDFset" |
atomblock-methods | Return atom block |
atomblock<- | Return atom block |
atomblock<--method | Class "SDFset" |
atomcount | Molecular property functions |
atomcount-method | Class "SDF" |
atomcount-method | Class "SDFset" |
atomcountMA | Molecular property functions |
atomprop | Standard atomic weights |
atomsubset | Subset SDF/SDFset Objects by Atom Index to Obtain Substructure |
batchByIndex | Batch by Index |
bondblock | Return bond block |
bondblock-method | Class "SDF" |
bondblock-method | Class "SDFset" |
bondblock-methods | Return bond block |
bondblock<- | Return bond block |
bondblock<--method | Class "SDFset" |
bonds | Bonds, charges and missing hydrogens |
browseJob | Open ChemMine Tools Job in Web Browser |
bufferLines | Buffer File Input |
bufferResultSet | Buffer Query Results |
byCluster | By Cluster |
c-method | Class "APset" |
c-method | Class '"FP"' |
c-method | Class '"FPset"' |
c-method | Class "SDFset" |
c-method | Class '"SMIset"' |
canonicalize | Canonicalize |
canonicalNumbering | Canonical Numbering |
cid | Return compound IDs |
cid-method | Class "APset" |
cid-method | Class '"FPset"' |
cid-method | Class "SDFset" |
cid-method | Class '"SMIset"' |
cid<- | Return compound IDs |
cid<--method | Class "APset" |
cid<--method | Class '"FPset"' |
cid<--method | Class "SDFset" |
cid<--method | Class '"SMIset"' |
cluster.sizestat | generate statistics on sizes of clusters |
cluster.visualize | visualize clustering result using multi-dimensional scaling |
cmp.cluster | cluster compounds using a descriptor database |
cmp.duplicated | quickly detect compound duplication in a descriptor database |
cmp.parse | Parse an SDF file and compute descriptors for all compounds |
cmp.parse1 | Parsing an SDF file and calculate the descriptor for one compound |
cmp.search | Search a descriptor database for compounds similar to query compound |
cmp.similarity | Compute similarity between two compounds using their descriptors |
coerce-method | Class "APset" |
coerce-method | Class '"FP"' |
coerce-method | Class '"FPset"' |
coerce-method | Class "SDF" |
coerce-method | Class "SDFset" |
coerce-method | Class "SDFstr" |
coerce-method | Class '"SMI"' |
coerce-method | Class '"SMIset"' |
conMA | Bond Matrices |
datablock | Return data block |
datablock-method | Class "SDF" |
datablock-method | Class "SDFset" |
datablock-methods | Return data block |
datablock2ma | SDF data blocks to matrix |
datablock<- | Return data block |
datablock<--method | Class "SDFset" |
datablocktag | Return data block |
datablocktag-method | Class "SDF" |
datablocktag-method | Class "SDFset" |
db.explain | Explain an atom-pair descriptor or an array of atom-pair descriptors |
db.subset | Subset a descriptor database and return a sub-database for the selected compounds |
dbTransaction | DB Transaction |
desc2fp | Fingerprints from descriptor vectors |
draw_sdf | draw_sdf |
DrugBank | Database Connections |
DUD | Database Connections |
exactMassOB | Exact Mass (Monoisotopic Mass) |
ExtSDF-class | Class "ExtSDF" |
findCompounds | Find Compounds in Database |
findCompoundsByName | Find compound by name |
fingerprintOB | Fingerprints from OpenBabel |
fold | Fold |
fold-method | Class '"FP"' |
fold-method | Class '"FPset"' |
foldCount | foldCount |
foldCount-method | Class '"FP"' |
foldCount-method | Class '"FPset"' |
forestSizePriorities | Set Priorities |
FP-class | Class '"FP"' |
fp2bit | Convert base 64 fingerprints to binary |
FPset-class | Class '"FPset"' |
fpSim | Fingerprint Search |
fptype | fptype |
fptype-method | Class '"FP"' |
fptype-method | Class '"FPset"' |
fromNNMatrix | From Nearest Neighbor Matrix |
genAPDescriptors | Generate AP Descriptors |
generate3DCoords | Generate 3D Coords |
genParameters | Generate Parameters |
getAllCompoundIds | Get ALl Compound Ids |
getAtomAttr | getAtomAttr |
getAtomAttr-method | Class "ExtSDF" |
getBondAttr | getBondAttr |
getBondAttr-method | Class "ExtSDF" |
getCompoundFeatures | Get Compound Features |
getCompoundNames | Get Compound Names |
getCompounds | Get Compounds From Database |
getIds | Import Compounds from PubChem |
grepSDFset | String search in 'SDFset' |
groups | Enumeration of Functional Groups and Atom Neighbors |
header | Return header block |
header-method | Class "SDF" |
header-method | Class "SDFset" |
header-methods | Return header block |
header<- | Return header block |
header<--method | Class "SDFset" |
initDb | Iinitialize SQL Database |
jarvisPatrick | Jarvis-Patrick Clustering |
jarvisPatrick_c | Jarvis Patrick Clustering in C code |
jobToken-class | Class '"jobToken"' |
largestComponent | Largest Component |
launchCMTool | Launch a Tool on ChemMine Tools |
length-method | Class "APset" |
length-method | Class '"FPset"' |
length-method | Class "SDFset" |
length-method | Class "SDFstr" |
length-method | Class '"SMIset"' |
listCMTools | List all available ChemMine Tools |
listFeatures | List Features |
loadSdf | Load SDF and SMILES Data |
loadSmiles | Load SDF and SMILES Data |
makeUnique | Uniquify CMP names |
maximallyDissimilar | Maximally Dissimilar |
MF | Molecular property functions |
MW | Molecular property functions |
nearestNeighbors | Nearest Neighbors |
numBits | numBits |
numBits-method | Class '"FP"' |
numBits-method | Class '"FPset"' |
obmol | obmol |
obmol-method | Class "SDF" |
obmol-method | Class "SDFset" |
obmol-methods | obmol |
openBabelPlot | Plot compound structures |
parBatchByIndex | Parallel Batch By Index |
plot | Plot compound structures |
plot-method | Class "SDF" |
plot-method | Class "SDFset" |
plotStruc | Plot compound structures |
propOB | Properties from OpenBabel |
pubchemCidToSDF | Import Compounds from PubChem |
pubchemFPencoding | Enncoding of PubChem Fingerprints |
pubchemInchi2cid | Query pubchem by InChI sttrings and return CIDs |
pubchemInchikey2sdf | Query pubchem by InChIKeys sttrings and get SDF back |
pubchemName2CID | Translate compound name to pubchem compound id |
pubchemSDFSearch | PubChem Similarity (Fingerprint) Search |
pubchemSmilesSearch | PubChem Similarity (Fingerprint) SMILES Search |
randomPriorities | Set Priorities |
read.AP | Read Atom Pair/Fingerprint Strings |
read.SDFindex | Extract Molecules from SD File by Line Index |
read.SDFset | SD file to 'SDFset' |
read.SDFstr | SD file to 'SDFstr' |
read.SMIset | SMILES file to 'SMIset' |
regenerateCoords | Re-generate 2D Coordinates |
result | Obtain the resulting output data from a ChemMine Tools Job |
rings | Ring and Aromaticity Perception |
SDF-class | Class "SDF" |
sdf.subset | Subset a SDF and return SDF segements for selected compounds |
sdf.visualize | Visualize an SDFset online using ChemMine Tools |
sdf2ap | Atom pair library |
SDF2apcmp | 'SDF' to 'list' for AP generation |
sdf2list | 'SDF' to 'list' |
sdf2list-method | Class "SDF" |
sdf2smiles | 'SDFset' to 'character' Convert 'SDFset' to SMILES ('character') |
sdf2smilesOB | 'SDFset' to 'character' Convert 'SDFset' to SMILES ('character') |
sdf2str | 'SDF' to 'SDFstr' |
sdf2str-method | Class "SDF" |
sdf2str-methods | 'SDF' to 'SDFstr' |
SDFDataTable | SDF Data Table |
sdfid | Return SDF compound IDs |
sdfid-method | Class "SDF" |
sdfid-method | Class "SDFset" |
sdfsample | SD file in 'SDFset' object |
SDFset | Class "SDFset" |
SDFset-class | Class "SDFset" |
SDFset2list | 'SDFset' to 'list' |
SDFset2list-method | Class "SDFset" |
SDFset2list-methods | 'SDFset' to 'list' |
SDFset2SDF | 'SDFset' to list with many 'SDF' |
SDFset2SDF-method | Class "SDFset" |
SDFset2SDF-methods | 'SDFset' to list with many 'SDF' |
SDFset2SDF<- | 'SDFset' to list with many 'SDF' |
SDFset2SDF<--method | Class "SDFset" |
SDFstr-class | Class "SDFstr" |
sdfstr2list | 'SDFstr' to 'list' |
sdfstr2list-method | Class "SDFstr" |
sdfstr2list-methods | 'SDFstr' to 'list' |
sdfstr2list<- | 'SDFstr' to 'list' |
sdfstr2list<--method | Class "SDFstr" |
sdfStream | Streaming through large SD files |
searchSim | PubChem Similarity (Fingerprint) Search |
searchString | PubChem Similarity (Fingerprint) SMILES Search |
selectInBatches | Select in Batches |
setPriorities | Set Priorities |
show-method | Class "AP" |
show-method | Class "APset" |
show-method | Class "ExtSDF" |
show-method | Class '"FP"' |
show-method | Class '"FPset"' |
show-method | Class "SDF" |
show-method | Class "SDFset" |
show-method | Class "SDFstr" |
show-method | Class '"SMI"' |
show-method | Class '"SMIset"' |
show-method | Class '"jobToken"' |
smartsSearchOB | SMARTS Search OB |
SMI-class | Class '"SMI"' |
smiles2sdf | Convert SMILES ('character') to 'SDFset' |
smiles2sdfOB | Convert SMILES ('character') to 'SDFset' |
smisample | SMILES file in 'SMIset' object |
SMIset-class | Class '"SMIset"' |
splitNumChar | SDF data blocks to matrix |
status | Get Status of a ChemMine Tools Job |
toolDetails | Detailed instructions for each ChemMine Tools web tool |
trimNeighbors | Trim Neighbors |
validSDF | Validity check of SDFset |
view | Viewing of complex objects |
view-method | Class "APset" |
view-method | Class '"FPset"' |
view-method | Class "SDFset" |
view-method | Class '"SMIset"' |
view-methods | Viewing of complex objects |
write.SDF | SDF export function |
write.SDFsplit | SDF split function |
write.SMI | SMI export function |
[-method | Class "APset" |
[-method | Class '"FPset"' |
[-method | Class "SDF" |
[-method | Class "SDFset" |
[-method | Class "SDFstr" |
[-method | Class '"SMIset"' |
[<--method | Class "APset" |
[<--method | Class '"FPset"' |
[<--method | Class "SDF" |
[<--method | Class "SDFset" |
[<--method | Class "SDFstr" |
[<--method | Class '"SMIset"' |
[[-method | Class "APset" |
[[-method | Class '"FPset"' |
[[-method | Class "SDF" |
[[-method | Class "SDFset" |
[[-method | Class "SDFstr" |
[[-method | Class '"SMIset"' |
[[<--method | Class "APset" |
[[<--method | Class "SDF" |
[[<--method | Class "SDFset" |
[[<--method | Class "SDFstr" |