# Analysis of Small Molecule and Screening Data

## Documentation for package ‘ChemmineR’ version 2.6.1

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

A B C D F G H L M P R S V W misc

## -- 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 --

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"

## -- L --

length-method | Class "APset"
length-method | Class "SDFset"
length-method | Class "SDFstr"

## -- 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 --

validSDF | Validity check of SDFset
view | Viewing of complex objects
view-method | Class "APset"
view-method | Class "SDFset"
view-methods | Viewing of complex objects

## -- W --

write.SDF | SDF export function

## -- misc --

[-method | Class "APset"
[-method | Class "SDF"
[-method | Class "SDFset"
[-method | Class "SDFstr"
[<--method | Class "APset"
[<--method | Class "SDF"
[<--method | Class "SDFset"
[<--method | Class "SDFstr"
[[-method | Class "APset"
[[-method | Class "SDF"
[[-method | Class "SDFset"
[[-method | Class "SDFstr"
[[<--method | Class "APset"
[[<--method | Class "SDF"
[[<--method | Class "SDFset"
[[<--method | Class "SDFstr"