@@ -1,8 +1,8 @@

 Package: eiR

 Type: Package

 Title: Accelerated similarity searching of small molecules

-Version: 1.27.1

-Date: 2020-3-30

+Version: 1.27.2

+Date: 2020-7-27

 Author: Kevin Horan, Yiqun Cao and Tyler Backman

 Maintainer: Thomas Girke <thomas.girke@ucr.edu>

 Suggests:   BiocStyle, knitcitations, knitr, knitrBootstrap

@@ -76,7 +76,7 @@ annoySearchAll <- function(matrixFile,dimension,numNeighbors,searchK=-1)

 eiInit <- function(inputs,dir=".",format="sdf",descriptorType="ap",append=FALSE,

 						 conn=defaultConn(dir,create=TRUE),updateByName=FALSE,

-						 cl=NULL,connSource=NULL,priorityFn = forestSizePriorities)

+						 cl=NULL,connSource=NULL,priorityFn = forestSizePriorities,skipPriorities=FALSE)

 {

 	if(!file.exists(file.path(dir,DataDir)))

@@ -137,7 +137,7 @@ eiInit <- function(inputs,dir=".",format="sdf",descriptorType="ap",append=FALSE,

 	print(paste(length(compoundIds)," loaded by eiInit"))

 	writeIddb(conn,compoundIds,file.path(dir,Main),append=append)

-	if(length(compoundIds)!=0 ){

+	if(length(compoundIds)!=0 && ! skipPriorities ){

 		descIds = getDescriptorIds(conn,compoundIds,descriptorType)

 		setPriorities(conn,priorityFn,descIds,cl=cl,connSource=connSource)

 	}

@@ -10,7 +10,7 @@

 \usage{

 	eiInit(inputs,dir=".",format="sdf",descriptorType="ap",append=FALSE,

 	conn=defaultConn(dir,create=TRUE), updateByName = FALSE, cl = NULL, connSource = NULL,

-	priorityFn = forestSizePriorities)

+	priorityFn = forestSizePriorities,skipPriorities=FALSE)

 }

 %- maybe also 'usage' for other objects documented here.

 \arguments{

@@ -24,7 +24,7 @@

       current directory.

    }

 	\item{format}{

-		The format of the data in \code{inputs}. Currenly only "sdf" and "smiles" is 

+		The format of the data in \code{inputs}. Currently only "sdf" and "smiles" is 

 		supported.

 	}

 	\item{descriptorType}{

@@ -33,7 +33,7 @@

 	}

 	\item{append}{

 		If true the given compounds will be added to an existing database

-		and the <data-dir>/Main.iddb file will be udpated with the new

+		and the <data-dir>/Main.iddb file will be updated with the new

 		compound id numbers. This should not normally be used directly, use

 		\code{\link{eiAdd}} instead to add new compounds to a database.

 	}

@@ -54,16 +54,16 @@

 	}

   \item{cl}{

      A SNOW cluster can be given here to run this function in

-     parrallel.

+     parallel.

    }

 	\item{connSource}{

-		A function returning a new database connection. Note that it is not suffient to return a

+		A function returning a new database connection. Note that it is not sufficient to return a

 		reference to an existing connection, it must be a distinct, new connection.  

 		This is needed for cluster operations

-		that make use of the database as they will each need to craete a new connection.

-		If not given, certain parts of this function will not be parrallelized.

+		that make use of the database as they will each need to create a new connection.

+		If not given, certain parts of this function will not be parallelized.

-		This function can also be used to setup the envrionment on the cluster worker nodes. For

+		This function can also be used to setup the environment on the cluster worker nodes. For

 		example, you might need to re-load libraries like RSQLite and such.

 	}

 	\item{priorityFn}{

@@ -73,9 +73,13 @@

 		'randomPriorities', and 'forestSizePriorities' (default). 

 		When several compounds map to the same descriptor, then when some functions need to go

-		from a descriptor to a compound, there is ambiguity about which compount to select. In

+		from a descriptor to a compound, there is ambiguity about which compound to select. In

 		that case, it will pick the compound with the highest priority. 

 	}

+	\item{skipPriorities}{

+		If this is true, then no priority values will be computed. See option \code{priorityFn} 

+		for an explanation of priorities.

+	}

 }

 \details{