Cheminformatics Toolkit for R


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Documentation for package ‘ChemmineR’ version 3.56.0

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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"