Analysis of Small Molecule and Screening Data

Documentation for package ‘ChemmineR’ version 2.8.1

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-- A --

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'
apset	Atom pairs stored in 'APset' object
APset-class	Class "APset"
apset2descdb	'APset' to list-style AP database
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 --

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

-- C --

c-method	Class "APset"
c-method	Class "SDFset"
cid	Return compound IDs
cid-method	Class "APset"
cid-method	Class "SDFset"
cid<-	Return compound IDs
cid<--method	Class "APset"
cid<--method	Class "SDFset"
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 "SDF"
coerce-method	Class "SDFset"
coerce-method	Class "SDFstr"
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

-- F --

fp2bit	Convert base 64 fingerprints to binary
fpSim	PubChem Fingerprint Search

-- G --

getIds	Import Compounds from PubChem
grepSDFset	String search in 'SDFset'
groups	Enumeration of Functional Groups and Atom Neighbors

-- H --

-- L --

-- M --

makeUnique	Uniquify CMP names
MF	Molecular property functions
MW	Molecular property functions

-- P --

plot	Plot compound structures
plot-method	Class "SDF"
plot-method	Class "SDFset"
plotStruc	Plot compound structures
pubchemFPencoding	Enncoding of PubChem Fingerprints

-- R --

read.SDFset	SD file to 'SDFset'
read.SDFstr	SD file to 'SDFstr'
rings	Ring and Aromaticity Perception

-- S --

SDF-class	Class "SDF"
sdf.subset	Subset a SDF and return SDF segements for selected compounds
sdf.visualize	Subset a SDFset and visualize selected compounds in a webpage
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')
sdf2str	'SDF' to 'SDFstr'
sdf2str-method	Class "SDF"
sdf2str-methods	'SDF' to 'SDFstr'
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"
searchSim	PubChem Similarity (Fingerprint) Search
searchString	PubChem Similarity (Fingerprint) SMILES Search
show-method	Class "AP"
show-method	Class "APset"
show-method	Class "SDF"
show-method	Class "SDFset"
show-method	Class "SDFstr"
smiles2sdf	Convert SMILES ('character') to 'SDFset'
splitNumChar	SDF data blocks to matrix

-- V --

-- W --

SDF export function

-- misc --