SDFstr-class: Class "SDFstr"

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Class "SDFstr"

Description

List-like container for storing one or many molecules from an SD (or MOL) file. Each component of an SDFstr object stores the SD data line by line from a single molecule in a character vector. The SDFstr class is an intermediate container to import SD files into the more important SDFset object or to export the data back from an SDFset container to a valid SD file.

Objects from the Class

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

Slots

a:

Object of class "list" with character components

Methods

[

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

[[

signature(x = "SDFstr"): returns single component as character vector

[[<-

signature(x = "SDFstr"): replacement method for single SDFstr component

[<-

signature(x = "SDFstr"): replacement method for several SDFstr components

coerce

signature(from = "character", to = "SDFstr"): as(character, "SDFstr")

coerce

signature(from = "list", to = "SDFstr"): as(list, "SDFstr")

coerce

signature(from = "SDF", to = "SDFstr"): as(sdf, "SDFstr")

coerce

signature(from = "SDFset", to = "SDFstr"): as(sdfset, "SDFstr")

coerce

signature(from = "SDFstr", to = "list"): as(sdfstr, "list")

coerce

signature(from = "SDFstr", to = "SDFset"): as(sdfstr, "SDFset")

length

signature(x = "SDFstr"): returns length of SDFstr

sdfstr2list

signature(x = "SDFstr"): accessor method to return SDFstr as list

sdfstr2list<-

signature(x = "SDFstr"): replacement method for several SDFstr components

show

signature(object = "SDFstr"): prints summary of SDFstr

Author(s)

Thomas Girke

References

SDF format definition: http://www.symyx.com/downloads/public/ctfile/ctfile.jsp

See Also

Related classes: SDFset, AP, APset

Import function: read.SDFstr("some_SDF_file")

Examples

showClass("SDFstr")

## Instances of SDFstr class
data(sdfsample); sdfset <- sdfsample
sdfstr <- as(sdfset, "SDFstr")
sdfstr[1:4] # print summary of container content 
sdfstr[[1]] # returns character vector

## Import: sdfstr <- read.SDFstr("some_SDF_file")
## Export: write.SDF(sdfstr, "some_file.sdf")

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