SDFset-class: Class "SDFset"

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Class "SDFset"

Description

List-like container for storing one or many objects of class SDF each containing the structure definition information of molecules provided by an SD/MOL file. The SDFset is the most important class in the ChemmmineR package for accessing and manipulating information stored in SD files.

Objects from the Class

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

Slots

SDF:

Object of class "list" storing SDF components

ID:

Object of class "character" storing compound identifiers

Methods

[

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

[[

signature(x = "SDFset"): returns single component as SDF object

[[<-

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

[<-

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

atomblock

signature(x = "SDFset"): returns all atom blocks as list

atomcount

signature(x = "SDFset"): returns all atom frequencies as list

bondblock

signature(x = "SDFset"): returns all bond blocks as list

obmol

signature(x = "SDFset"): returns pointers to OBMol objects as a vector

c

signature(x = "SDFset"): concatenates two SDFset containers

cid

signature(x = "SDFset"): returns all compound identifiers from ID slot

header<-

signature(x = "SDFset"): replacement method for header block

atomblock<-

signature(x = "SDFset"): replacement method for atom block

bondblock<-

signature(x = "SDFset"): replacement method for bond block

datablock<-

signature(x = "SDFset"): replacement method for data block

coerce

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

coerce

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

coerce

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

coerce

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

coerce

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

coerce

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

datablock

signature(x = "SDFset"): returns all data blocks as list

datablocktag

signature(x = "SDFset"): returns all data blocks as named as list with subsetting support

header

signature(x = "SDFset"): returns all header blocks as list

length

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

plot

signature(x = "SDFset"): plots one or many molecule structures from SDFset object

sdfid

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

SDFset2list

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

SDFset2SDF

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

SDFset2SDF<-

signature(x = "SDFset"): replacement method for SDFset component in SDFset using accessor method

show

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

view

signature(x = "SDFset"): prints extended summary of SDFset

SDFset

SDFset(SDF, ID): interface to SDFset constructor

Author(s)

Thomas Girke

References

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

See Also

Related classes: SDF, SDFstr, AP, APset

Import function: read.SDFset("some_SDF_file")

Export function: write.SDF(sdfset, "some_file.sdf")

Examples

showClass("SDFset")

## Instances of SDFset class
data(sdfsample); sdfset <- sdfsample
sdfset; view(sdfset[1:4])
sdfset[[1]]

## Import and store SD File in SDFset container
# sdfset <- read.SDFset("some_SDF_file")

## Miscellaneous accessor methods
header(sdfset[1:4])
atomblock(sdfset[1:4])
atomcount(sdfset[1:4])
bondblock(sdfset[1:4])
datablock(sdfset[1:4])

## Assigning compound IDs and keeping them unique
cid(sdfset); sdfid(sdfset)
unique_ids <- makeUnique(sdfid(sdfset))
cid(sdfset) <- unique_ids

## Convert data block to matrix
blockmatrix <- datablock2ma(datablocklist=datablock(sdfset)) # Converts data block to matrix  
numchar <- splitNumChar(blockmatrix=blockmatrix) # Splits to numeric and character matrix
numchar[[1]][1:4,]; numchar[[2]][1:4,]

## Compute atom frequency matrix, molecular weight and formula
propma <- data.frame(MF=MF(sdfset), MW=MW(sdfset), atomcountMA(sdfset))
propma[1:4, ]

## Assign matrix data to data block
datablock(sdfset) <- propma 
view(sdfset[1:4])

## String Searching in SDFset
grepSDFset("650001", sdfset, field="datablock", mode="subset") # To return index, set mode="index")

## Export SDFset to SD file
# write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE)

## Plot molecule structure of SDF 
plot(sdfset[1:4]) # plots to R graphics device
# sdf.visualize(sdfset[1:4]) # viewing in browser

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