Nothing
#############################################
# This code is subject to the license as stated in DESCRIPTION.
# Using this software implies acceptance of the license terms:
# - GPL 2
#
# (C) by F. Hoffgaard, P. Weil, and K. Hamacher in 2009.
#
# keul(AT)bio.tu-darmstadt.de
#
#
# http://www.kay-hamacher.de
#############################################
sim<-function(pdbs,mj1=NULL,mj2=NULL,mj.avg=FALSE,alpha=82,cuts=169,path=getwd(),cluster=NULL){
if(is.null(mj1)){
mj1<-mat.read(system.file("mj1.txt",package="BioPhysConnectoR"))
}
if(is.null(mj2)){
mj2<-mat.read(system.file("mj2.txt",package="BioPhysConnectoR"))
}
if(mj.avg){
mj1<-matrix(data=mean(mj1),nrow=20,ncol=20)
mj2<-matrix(data=mean(mj2),nrow=20,ncol=20)
}
cores<-1
if(!is.null(cluster)){
clusterEvalQ(cluster,library(BioPhysConnectoR))
cores<-length(cluster)
}
sim.func<-function(arg){
library.dynam("BioPhysConnectoR",package="BioPhysConnectoR");
p<-extractPDB(arg)
fn<-unlist(strsplit(gsub("\\\\","/",arg),split="/"))
fn<-fn[length(fn)]
file.name<-unlist(strsplit(fn,split=".pdb"))[1]
seq<-p$caseq
n<-p$lca
nr3<-3*n
b<-p$b
d<-p$chains
s<-aa2num(seq,0,verbose=FALSE) #0 da es an C-Programm weitergereicht wird
interaction.mat<-build.interact(s,mj1,mj2,d,alpha)
out<-build.contacts(n,cuts,p$coords)
contact.mat<-out$cm
deltas<-out$deltas
cov.mat<-get.cov(contact.mat,interaction.mat,deltas);
beta<-get.bfacs(cov.mat)
write.table(cov.mat,col.names=FALSE,row.names=FALSE,quote=FALSE,file=paste(path,"/cov_matrix_",file.name,".out",sep=""))
write(beta,file=paste(path,"/b_factors_",file.name,".out",sep=""),sep="\n")
}
fun<-function(pdbs){
return(lapply(pdbs,sim.func))
}
pdbs<-as.list(pdbs)
lpdb<-length(pdbs)
if(cores > lpdb){
cores<-lpdb
}
ll<-floor(lpdb/cores)
overlap<-lpdb%%cores
npdb<-list()
it<-0
for(i in 1:cores){
it<-it+1
if(overlap>=i){
itn<-it+ll
}else{
itn<-it+ll-1
}
npdb[[i]]<-pdbs[it:itn]
it<-itn
}
pdbs<-npdb
if(!is.null(cluster)){
parLapply(cluster,pdbs,fun)
}else{
lapply(pdbs,fun)
}
return(1)
}
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