SMIset-class: Class '"SMIset"'

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

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)

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.