SDF-class: Class "SDF"

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Class "SDF"

Description

Container for storing every element of a single molecule defined in an SD/MOL file without information loss in a list-like container. The import occurs via the SDFstr container class. The header block is stored as named character vector, the atom/bond blocks as matrices and the data block as named character vector.

Objects from the Class

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

Slots

header:

Object of class "character"

atomblock:

Object of class "matrix"

bondblock:

Object of class "matrix"

datablock:

Object of class "character"

obmolRef:

Object of class "ExternalReferenceOrNULL"

version:

Object of class "character"

Methods

[

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

[[

signature(x = "SDF"): returns one of the four object components

[[<-

signature(x = "SDF"): replacement method for the four sub-components

[<-

signature(x = "SDF"): replacement method for the four sub-components

atomblock

signature(x = "SDF"): returns atom block as matrix

atomcount

signature(x = "SDF"): returns atom frequency

bondblock

signature(x = "SDF"): returns bond block as matrix

obmol

signature(x = "SDF"): returns an OBMol pointer

coerce

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

coerce

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

coerce

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

coerce

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

coerce

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

coerce

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

coerce

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

datablock

signature(x = "SDF"): returns data block as named character vector

datablocktag

signature(x = "SDF"): returns data block as named character vector with subsetting support

header

signature(x = "SDF"): returns header block as named character vector

plot

signature(x = "SDF"): plots molecule structure for SDF object

sdf2list

signature(x = "SDF"): returns SDF object as list

sdf2str

signature(sdf = "SDF"): returns SDF object as character vector

sdfid

signature(x = "SDF"): returns molecule ID field from header block

show

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

Author(s)

Thomas Girke

References

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

See Also

Related classes: SDFset, SDFstr, AP, APset

Examples

showClass("SDF")

## Instances of SDF class
data(sdfsample); sdfset <- sdfsample
(sdf <- sdfset[[1]]) # returns first molecule in sdfset as SDF object

## Accessing SDF components
header(sdf); atomblock(sdf); bondblock(sdf); datablock(sdf)
sdfid(sdf)

## Plot molecule structure of SDF 
plot(sdf) # plots to R graphics device
# sdf.visualize(sdf) # viewing in browser

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