SMIset-class {ChemmineR} | R Documentation

## Class `"SMIset"`

### Description

List-like container for storing SMILES strings of many compounds.

### Objects from the Class

Objects can be created by calls of the form `new("SMIset", ...)`.

### Slots

`smilist`:

  Object of class `"list"` with compound identifiers stored in name slots

### Methods

[

  `signature(x = "SMIset")`: subsetting of class with bracket operator

[[

  `signature(x = "SMIset")`: returns single component as `SMI` object

[<-

  `signature(x = "SMIset")`: replacement method for one or many entries

as.character

  `signature(x = "SMIset")`: returns content as named character vector

c

  `signature(x = "SMIset")`: concatenates two `SMIset` containers

cid

  `signature(x = "SMIset")`: returns compound identifiers

cid<-

  `signature(x = "SMIset")`: replacement method for compound identifiers

coerce

  `signature(from = "character", to = "SMIset")`: `as(character, "SMIset")`

coerce

  `signature(from = "list", to = "SMIset")`: `as(list, "SMIset")`

coerce

  `signature(from = "SMIset", to = "SMI")`: `as(smiset, "SMI")`

length

  `signature(x = "SMIset")`: returns number of entries stored in object

show

  `signature(object = "SMIset")`: prints summary of `SMIset`

view

  `signature(x = "SMIset")`: prints extended summary of `SMIset`

### Author(s)

Thomas Girke

### References

SMILES (Simplified molecular-input line-entry system) format definition: http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

### See Also

Related classes: SMI, SDF, SDFset

Import function: read.SMIset("some_SMILES_file")

Export function: write.SMI(smiset, "some_file.smi")

### Examples

    showClass("SMIset")

    ## Instances of SMIset class
    data(smisample); smiset <- smisample
    smiset; view(smiset[1:4])
    smiset[[1]]

    ## Import and store SMILES file in SMIset container
    # smiset <- read.SMIset("some_SMILES_file")

    ## Miscellaneous accessor methods
    cid(smiset[1:4])
    (smivec <- as.character(smiset[1:4]))

    ## Construct SMIset from named vector
    as(smivec, "SMIset")

    ## Assigning compound IDs and keeping them unique
    unique_ids <- makeUnique(cid(smiset))
    cid(smiset) <- unique_ids

    ## Export SMIset to SMILES file
    # write.SMI(smiset[1:4], file="sub.smi", cid=TRUE)

[Package ChemmineR version 3.46.0 Index]