Man pages for girke-lab/ChemmineR-release
Cheminformatics Toolkit for R
| addDescriptorType | Add Descriptor Type |
| addNewFeatures | Add New Features |
| ap | Return atom pair component of 'AP/APset' |
| AP-class | Class "AP" |
| apfp | Frequent Atom Pairs |
| apset | Atom pairs stored in 'APset' object |
| apset2descdb | 'APset' to list-style AP database |
| APset-class | Class "APset" |
| atomblock | Return atom block |
| atomcount | Molecular property functions |
| atomprop | Standard atomic weights |
| atomsubset | Subset SDF/SDFset Objects by Atom Index to Obtain... |
| batchByIndex | Batch by Index |
| bondblock | Return bond block |
| 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 |
| canonicalize | Canonicalize |
| canonicalNumbering | Canonical Numbering |
| cid | Return compound IDs |
| 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... |
| cmp.search | Search a descriptor database for compounds similar to query... |
| cmp.similarity | Compute similarity between two compounds using their... |
| conMA | Bond Matrices |
| connections | Database Connections |
| datablock | Return data block |
| datablock2ma | SDF data blocks to matrix |
| db.explain | Explain an atom-pair descriptor or an array of atom-pair... |
| db.subset | Subset a descriptor database and return a sub-database for... |
| dbTransaction | DB Transaction |
| desc2fp | Fingerprints from descriptor vectors |
| draw_sdf | draw_sdf |
| exactMassOB | Exact Mass (Monoisotopic Mass) |
| ExtSDF-class | Class "ExtSDF" |
| findCompounds | Find Compounds in Database |
| findCompoundsByName | Find compound by name |
| fingerprintOB | Fingerprints from OpenBabel |
| fold | Fold |
| foldCount | foldCount |
| fp2bit | Convert base 64 fingerprints to binary |
| FP-class | Class '"FP"' |
| FPset-class | Class '"FPset"' |
| fpSim | Fingerprint Search |
| fptype | fptype |
| fromNNMatrix | From Nearest Neighbor Matrix |
| genAPDescriptors | Generate AP Descriptors |
| generate3DCoords | Generate 3D Coords |
| genParameters | Generate Parameters |
| getAllCompoundIds | Get ALl Compound Ids |
| 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 |
| header | Return header block |
| initDb | Iinitialize SQL Database |
| jarvisPatrick | Jarvis-Patrick Clustering |
| jarvisPatrick_c | Jarvis Patrick Clustering in C code |
| jobToken-class | Class '"jobToken"' |
| launchCMTool | Launch a Tool on ChemMine Tools |
| listCMTools | List all available ChemMine Tools |
| listFeatures | List Features |
| loadSdf | Load SDF and SMILES Data |
| makeUnique | Uniquify CMP names |
| maximallyDissimilar | Maximally Dissimilar |
| nearestNeighbors | Nearest Neighbors |
| numBits | numBits |
| obmol | obmol |
| parBatchByIndex | Parallel Batch By Index |
| plotStruc | Plot compound structures |
| propOB | Properties from OpenBabel |
| pubchemFPencoding | Enncoding of PubChem Fingerprints |
| 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 |
| sdf2ap | Atom 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-class | Class "SDF" |
| sdfid | Return SDF compound IDs |
| sdfsample | SD file in 'SDFset' object |
| SDFset2list | 'SDFset' to 'list' |
| SDFset2SDF | 'SDFset' to list with many 'SDF' |
| SDFset-class | Class "SDFset" |
| sdfstr2list | 'SDFstr' to 'list' |
| SDFstr-class | Class "SDFstr" |
| sdfStream | Streaming through large SD files |
| sdf.subset | Subset a SDF and return SDF segements for selected compounds |
| sdf.visualize | Visualize an SDFset online using ChemMine Tools |
| searchSim | PubChem Similarity (Fingerprint) Search |
| searchString | PubChem Similarity (Fingerprint) SMILES Search |
| selectInBatches | Select in Batches |
| setPriorities | Set Priorities |
| smartsSearchOB | SMARTS Search OB |
| SMI-class | Class '"SMI"' |
| smiles2sdf | Convert SMILES ('character') to 'SDFset' |
| smisample | SMILES file in 'SMIset' object |
| SMIset-class | Class '"SMIset"' |
| status | Get Status of a ChemMine Tools Job |
| toolDetails | Detailed instructions for each ChemMine Tools web tool |
| trimNeighbors | Trim Neighbors |
| validSDF | Validity check of SDFset |
| view | Viewing of complex objects |
| write.SDF | SDF export function |
| write.SDFsplit | SDF split function |
| write.SMI | SMI export function |
