## ----echo=FALSE, results='hide',message=FALSE,warning=FALSE,error=FALSE----
library(eiR) 
library(knitcitations)
unlink("data",recursive=TRUE)
unlink(paste("run",60,40,sep="-"),recursive=TRUE) 
set.seed(80) 
#options(citation_format="pandoc")
#cite_options(citation_format="pandoc",style="html", hyperlink="to.doc")
RefManageR:::BibOptions(style="markdown",no.print.fields=c("doi"))


## ------------------------------------------------------------------------
library(eiR) 
data(sdfsample) 
eiInit(sdfsample[1:99]) 


## ------------------------------------------------------------------------
r<- 60 
d<- 40 
runId <- eiMakeDb(r,d) 


## ----term=FALSE,fig=TRUE-------------------------------------------------
#find compounds similar to each query
result=eiQuery(runId,sdfsample[45],K=10,asSimilarity=TRUE)
print(result)

#Compare to traditional similarity search: 
data(apset)
print(cmp.search(apset,apset[45],type=3,cutoff=4,quiet=TRUE))

cid(sdfsample)=sdfid(sdfsample)
plot(sdfsample[result$target[1:4]],regenCoords=TRUE,print=FALSE)


## ----term=FALSE----------------------------------------------------------
 eiAdd(runId,sdfsample[100]) 


## ----term=FALSE----------------------------------------------------------
 eiPerformanceTest(runId,K=22) 


## ------------------------------------------------------------------------
	clustering <- eiCluster(runId,K=5,minNbrs=2,cutoff=0.5)
	byCluster(clustering)


## ------------------------------------------------------------------------
setDefaultDistance("ap", function(d1,d2) 1-cmp.similarity(d1,d2) ) 
setDefaultDistance("fp", function(d1,d2) 1-fpSim(d1,d2) ) 


## ------------------------------------------------------------------------
addTransform("ap","sdf",
	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))
	}
)

addTransform("ap",  
	toString = function(apset,conn=NULL,dir="."){
		unlist(lapply(ap(apset), function(x) paste(x,collapse=", ")))
	},
	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")  
	}
)



## ----echo=FALSE,term=FALSE-----------------------------------------------
unlink("data",recursive=TRUE)
unlink(paste("run",r,d,sep="-"),recursive=TRUE) 


## ----biblio, echo=FALSE, results='asis'----------------------------------
   bibliography()