Man pages for girke-lab/ChemmineR
Cheminformatics Toolkit for R

addDescriptorTypeAdd Descriptor Type
addNewFeaturesAdd New Features
apReturn atom pair component of 'AP/APset'
AP-classClass "AP"
apfpFrequent Atom Pairs
apsetAtom pairs stored in 'APset' object
apset2descdb'APset' to list-style AP database
APset-classClass "APset"
atomblockReturn atom block
atomcountMolecular property functions
atompropStandard atomic weights
atomsubsetSubset SDF/SDFset Objects by Atom Index to Obtain...
batchByIndexBatch by Index
bondblockReturn bond block
bondsBonds, charges and missing hydrogens
browseJobOpen ChemMine Tools Job in Web Browser
bufferLinesBuffer File Input
bufferResultSetBuffer Query Results
byClusterBy Cluster
canonicalNumberingCanonical Numbering
cidReturn compound IDs
cluster.sizestatgenerate statistics on sizes of clusters
cluster.visualizevisualize clustering result using multi-dimensional scaling
cmp.clustercluster compounds using a descriptor database
cmp.duplicatedquickly detect compound duplication in a descriptor database
cmp.parseParse an SDF file and compute descriptors for all compounds
cmp.parse1Parsing an SDF file and calculate the descriptor for one...
cmp.searchSearch a descriptor database for compounds similar to query...
cmp.similarityCompute similarity between two compounds using their...
conMABond Matrices
connectionsDatabase Connections
datablockReturn data block
datablock2maSDF data blocks to matrix
db.explainExplain an atom-pair descriptor or an array of atom-pair...
db.subsetSubset a descriptor database and return a sub-database for...
dbTransactionDB Transaction
desc2fpFingerprints from descriptor vectors
exactMassOBExact Mass (Monoisotopic Mass)
ExtSDF-classClass "ExtSDF"
findCompoundsFind Compounds in Database
findCompoundsByNameFind compound by name
fingerprintOBFingerprints from OpenBabel
fp2bitConvert base 64 fingerprints to binary
FP-classClass '"FP"'
FPset-classClass '"FPset"'
fpSimFingerprint Search
fromNNMatrixFrom Nearest Neighbor Matrix
genAPDescriptorsGenerate AP Descriptors
generate3DCoordsGenerate 3D Coords
genParametersGenerate Parameters
getAllCompoundIdsGet ALl Compound Ids
getCompoundFeaturesGet Compound Features
getCompoundNamesGet Compound Names
getCompoundsGet Compounds From Database
getIdsImport Compounds from PubChem
grepSDFsetString search in 'SDFset'
groupsEnumeration of Functional Groups and Atom Neighbors
headerReturn header block
initDbIinitialize SQL Database
jarvisPatrickJarvis-Patrick Clustering
jarvisPatrick_cJarvis Patrick Clustering in C code
jobToken-classClass '"jobToken"'
launchCMToolLaunch a Tool on ChemMine Tools
listCMToolsList all available ChemMine Tools
listFeaturesList Features
loadSdfLoad SDF and SMILES Data
makeUniqueUniquify CMP names
maximallyDissimilarMaximally Dissimilar
nearestNeighborsNearest Neighbors
parBatchByIndexParallel Batch By Index
plotStrucPlot compound structures
propOBProperties from OpenBabel
pubchemCidToSDFImport Compounds from PubChem
pubchemFPencodingEnncoding of PubChem Fingerprints
pubchemSDFSearchPubChem Similarity (Fingerprint) Search
pubchemSmilesSearchPubChem Similarity (Fingerprint) SMILES Search
read.APRead Atom Pair/Fingerprint Strings
read.SDFindexExtract Molecules from SD File by Line Index
read.SDFsetSD file to 'SDFset'
read.SDFstrSD file to 'SDFstr'
read.SMIsetSMILES file to 'SMIset'
regenerateCoordsRe-generate 2D Coordinates
resultObtain the resulting output data from a ChemMine Tools Job
ringsRing and Aromaticity Perception
sdf2apAtom pair library
SDF2apcmp'SDF' to 'list' for AP generation
sdf2list'SDF' to 'list'
sdf2smiles'SDFset' to 'character' Convert 'SDFset' to SMILES...
sdf2str'SDF' to 'SDFstr'
SDF-classClass "SDF"
sdfidReturn SDF compound IDs
sdfsampleSD file in 'SDFset' object
SDFset2list'SDFset' to 'list'
SDFset2SDF'SDFset' to list with many 'SDF'
SDFset-classClass "SDFset"
sdfstr2list'SDFstr' to 'list'
SDFstr-classClass "SDFstr"
sdfStreamStreaming through large SD files
sdf.subsetSubset a SDF and return SDF segements for selected compounds
sdf.visualizeVisualize an SDFset online using ChemMine Tools
searchSimPubChem Similarity (Fingerprint) Search
searchStringPubChem Similarity (Fingerprint) SMILES Search
selectInBatchesSelect in Batches
setPrioritiesSet Priorities
smartsSearchOBSMARTS Search OB
SMI-classClass '"SMI"'
smiles2sdfConvert SMILES ('character') to 'SDFset'
smisampleSMILES file in 'SMIset' object
SMIset-classClass '"SMIset"'
statusGet Status of a ChemMine Tools Job
toolDetailsDetailed instructions for each ChemMine Tools web tool
trimNeighborsTrim Neighbors
validSDFValidity check of SDFset
viewViewing of complex objects
write.SDFSDF export function
write.SDFsplitSDF split function
write.SMISMI export function
girke-lab/ChemmineR documentation built on Feb. 22, 2018, 3:04 p.m.