# Cheminformatics Toolkit for R

## Documentation for package ‘ChemmineR’ version 3.54.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N O P R S T V W misc

## -- A --

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

## -- B --

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 --

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

## -- D --

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

## -- E --

exactMassOB | Exact Mass (Monoisotopic Mass)
ExtSDF-class | Class "ExtSDF"

## -- F --

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

## -- G --

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

## -- H --

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"

## -- I --

initDb | Iinitialize SQL Database

## -- J --

jarvisPatrick | Jarvis-Patrick Clustering
jarvisPatrick_c | Jarvis Patrick Clustering in C code
jobToken-class | Class '"jobToken"'

## -- L --

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

## -- M --

makeUnique | Uniquify CMP names
maximallyDissimilar | Maximally Dissimilar
MF | Molecular property functions
MW | Molecular property functions

## -- N --

nearestNeighbors | Nearest Neighbors
numBits | numBits
numBits-method | Class '"FP"'
numBits-method | Class '"FPset"'

## -- O --

obmol | obmol
obmol-method | Class "SDF"
obmol-method | Class "SDFset"
obmol-methods | obmol
openBabelPlot | Plot compound structures

## -- P --

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

## -- R --

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

## -- S --

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

## -- T --

toolDetails | Detailed instructions for each ChemMine Tools web tool
trimNeighbors | Trim Neighbors

## -- V --

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

## -- W --

write.SDF | SDF export function
write.SDFsplit | SDF split function
write.SMI | SMI export function

## -- misc --

[-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"