addTransform: Add Transform
In girke-lab/eiR-release: Accelerated similarity searching of small molecules

Description Usage Arguments Value Author(s) See Also Examples

View source: R/measures.R

New descriptor types can be added using the addTransform function. These transforms are basically just ways to read descriptors from compound definitions, and to convert descriptors between string and object form. This conversion is required because descriptors are stored as strings in the SQL database, but are used by the rest of the program as objects.

There are two main components that need to be added. The addTransform function takes the name of the transform and two functions, toString, and toObject. These have slightly different meanings depending on the component you are adding. The first component to add is a transform from a chemical compound format, such as SDF, to a descriptor format, such as atom pair (AP), in either string or object form. The toString function should take any kind of chemical compound source, such an SDF file, an SDF object or an SDFset, and output a string representation of the descriptors. Since this function can be written in terms of other functions that will be defined, you can usually accept the default value of this function. The toObject function should take the same kind of input, but output the descriptors as an object. The actual return value is a list containing the names of the compounds (in the names field), and the actual descriptor objects ( in the descriptors field).

The second component to add is a transform that converts between string and object representations of descriptors. In this case the toString function takes descriptors in object form and returns a string representation for each. The toObject function performs the inverse operation. It takes descriptors in string form and returns them as objects. The objects returned by this function will be exactly what is handed to the distance function, so you need to make sure that the two match each other.

1	addTransform(descriptorType, compoundFormat = NULL, toString = NULL, toObject)

`descriptorType`	The name of the type of the descritor being added.
`compoundFormat`	The format of the compound data the descriptor will be extracted from.
`toString`	A function with three arguments, the data, an SQL connection object, and a directory name. The last two are optional and can be set to a default value of NULL if not used in the body of the function. If this parameter is NULL and compoundFormat is not NULL, then a default function will be used for this value.
`toObject`	A function with three arguments, the data, an SQL connection object, and a directory name. The last two are optional and can be set to a default value of NULL if not used in the body of the function. If compoundFormat is not NULL, then the return value of this function should be a list with the fields "names" and "descriptors", containing the compound names and descriptor objects, respectivly. If compoundFormat is NULL, then the return value should be a collection of descriptor objects, in whatever format the distance function for this descrptor type requires.

No value returned.

Kevin Horan

setDefaultDistance

	# adding support for atompair (ap) descriptors extracted from
	# sdf formmatted data.

    #first component
    addTransform("ap-example","sdf-example",
        # Any sdf source -> APset
        toObject = function(input,conn=NULL,dir="."){
            sdfset=if(is.character(input) && file.exists(input)){
                read.SDFset(input)
            }else if(inherits(input,"SDFset")){
                input
            }else{
                stop(paste("unknown type for 'input', or filename does not exist. type found:",class(input)))
            }
            list(names=sdfid(sdfset),descriptors=sdf2ap(sdfset))
        }
    )

    #second component
    addTransform("ap-example",  
        # APset -> string,
        toString = function(apset,conn=NULL,dir="."){
            unlist(lapply(ap(apset), function(x) paste(x,collapse=", ")))
        },
        # string or list -> AP set list
        toObject= function(v,conn=NULL,dir="."){ 
            if(inherits(v,"list") || length(v)==0)
                return(v)

            as( if(!inherits(v,"APset")){
                    names(v)=as.character(1:length(v));  
                    read.AP(v,type="ap",isFile=FALSE)
                } else v,
                "list")  
        }
    )