Cheminformatics of Drug-like Small Molecule Data


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Documentation for package ‘ChemmineR’ version 2.12.3

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

-- A --

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.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
bufferLines Buffer File Input
bufferResultSet Buffer Query Results
byCluster By Cluster

-- C --

c-method Class "APset"
c-method Class '"FPset"'
c-method Class "SDFset"
cid Return compound IDs
cid-method Class "APset"
cid-method Class '"FPset"'
cid-method Class "SDFset"
cid<- Return compound IDs
cid<--method Class "APset"
cid<--method Class '"FPset"'
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 '"FP"'
coerce-method Class '"FPset"'
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
desc2fp Fingerprints from descriptor vectors

-- F --

findCompounds Find Compounds in Database
findCompoundsByName Find compound by name
FP-class Class '"FP"'
fp2bit Convert base 64 fingerprints to binary
FPset-class Class '"FPset"'
fpSim Fingerprint Search
fromNNMatrix From Nearest Neighbor Matrix

-- G --

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

-- L --

length-method Class "APset"
length-method Class '"FPset"'
length-method Class "SDFset"
length-method Class "SDFstr"
loadSdf Load SDF Data

-- M --

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

-- N --

nearestNeighbors Nearest Neighbors

-- P --

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

-- R --

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'
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"
sdfStream Streaming through large SD files
searchSim PubChem Similarity (Fingerprint) Search
searchString PubChem Similarity (Fingerprint) SMILES Search
selectInBatches Select in Batches
show-method Class "AP"
show-method Class "APset"
show-method Class '"FP"'
show-method Class '"FPset"'
show-method Class "SDF"
show-method Class "SDFset"
show-method Class "SDFstr"
smiles2sdf Convert SMILES ('character') to 'SDFset'
splitNumChar SDF data blocks to matrix

-- T --

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-methods Viewing of complex objects

-- W --

write.SDF SDF export function
write.SDFsplit SDF split function

-- misc --

[-method Class "APset"
[-method Class '"FPset"'
[-method Class "SDF"
[-method Class "SDFset"
[-method Class "SDFstr"
[<--method Class "APset"
[<--method Class '"FPset"'
[<--method Class "SDF"
[<--method Class "SDFset"
[<--method Class "SDFstr"
[[-method Class "APset"
[[-method Class '"FPset"'
[[-method Class "SDF"
[[-method Class "SDFset"
[[-method Class "SDFstr"
[[<--method Class "APset"
[[<--method Class "SDF"
[[<--method Class "SDFset"
[[<--method Class "SDFstr"