## ----echo=FALSE, results='hide',message=FALSE,warning=FALSE,error=FALSE---- options(width=120) library(fmcsR) library(knitcitations) library(ChemmineOB) RefManageR:::BibOptions(style="markdown",no.print.fields=c("doi")) sapply(read.bibtex(file="references.bib"),record_as_cited) ## ----eval=FALSE---------------------------------------------------------- ## source("http://bioconductor.org/biocLite.R") ## biocLite("fmcsR") ## ----quicktest1, eval=TRUE, fig=TRUE,fig.scap="Structures depictions of sample data."---- library(fmcsR) data(fmcstest) plot(fmcstest[1:3], print=FALSE) ## ----quicktest2, eval=TRUE, fig=TRUE------------------------------------- test <- fmcs(fmcstest[1], fmcstest[2], au=2, bu=1) plotMCS(test,regenCoords=TRUE) ## ----eval=TRUE, keep.source=TRUE----------------------------------------- library("fmcsR") # Loads the package ## ----eval=FALSE, keep.source=TRUE---------------------------------------- ## library(help="fmcsR") # Lists functions/classes provided by fmcsR ## library(help="ChemmineR") # Lists functions/classes from ChemmineR ## vignette("fmcsR") # Opens this PDF manual ## vignette("ChemmineR") # Opens ChemmineR PDF manual ## ----eval=FALSE, keep.source=TRUE---------------------------------------- ## ?fmcs ## ?"MCS-class" ## ?"SDFset-class" ## ----eval=TRUE, keep.source=TRUE----------------------------------------- data(fmcstest) sdfset <- fmcstest sdfset ## ----eval=FALSE, keep.source=TRUE---------------------------------------- ## write.SDF(sdfset, file="sdfset.sdf") ## mysdf <- read.SDFset(file="sdfset.sdf") ## ----eval=TRUE, keep.source=TRUE----------------------------------------- mcsa <- fmcs(sdfset[[1]], sdfset[[2]]) mcsa mcsb <- fmcs(sdfset[[1]], sdfset[[3]]) mcsb ## ----eval=TRUE, keep.source=TRUE----------------------------------------- fmcs(sdfset[1], sdfset[2], fast=TRUE) ## ----eval=TRUE, keep.source=TRUE----------------------------------------- slotNames(mcsa) ## ----eval=TRUE, keep.source=TRUE----------------------------------------- stats(mcsa) # or mcsa[["stats"]] mcsa1 <- mcs1(mcsa) # or mcsa[["mcs1"]] mcsa2 <- mcs2(mcsa) # or mcsa[["mcs2"]] mcsa1[1] # returns SDFset component mcsa1[[2]][1:2] # return first two index vectors ## ----eval=TRUE, fig=TRUE, keep.source=TRUE------------------------------- mcstosdfset <- mcs2sdfset(mcsa, type="new") plot(mcstosdfset[[1]], print=FALSE) ## ----eval=TRUE, keep.source=TRUE----------------------------------------- mylist <- list(stats=stats(mcsa), mcs1=mcs1(mcsa), mcs2=mcs2(mcsa)) as(mylist, "MCS") ## ----au0bu0, eval=TRUE, fig=TRUE----------------------------------------- plotMCS(fmcs(sdfset[1], sdfset[2], au=0, bu=0)) ## ----au1bu1, eval=TRUE, fig=TRUE----------------------------------------- plotMCS(fmcs(sdfset[1], sdfset[2], au=1, bu=1)) ## ----au2bu2, eval=TRUE, fig=TRUE----------------------------------------- plotMCS(fmcs(sdfset[1], sdfset[2], au=2, bu=2)) ## ----au0bu013, eval=TRUE, fig=TRUE--------------------------------------- plotMCS(fmcs(sdfset[1], sdfset[3], au=0, bu=0)) ## ----eval=TRUE, keep.source=TRUE----------------------------------------- data(sdfsample) # Loads larger sample data set sdf <- sdfsample fmcsBatch(sdf[1], sdf[1:30], au=0, bu=0) ## ----tree, eval=TRUE, fig=TRUE------------------------------------------- sdf <- sdf[1:7] d <- sapply(cid(sdf), function(x) fmcsBatch(sdf[x], sdf, au=0, bu=0, matching.mode="aromatic")[,"Overlap_Coefficient"]) d hc <- hclust(as.dist(1-d), method="complete") plot(as.dendrogram(hc), edgePar=list(col=4, lwd=2), horiz=TRUE) ## ----au0bu024, eval=TRUE, fig=TRUE--------------------------------------- plotMCS(fmcs(sdf[3], sdf[7], au=0, bu=0, matching.mode="aromatic")) ## ----sessionInfo, print=TRUE-------------------------------------------- sessionInfo() ## ----biblio, echo=FALSE, results='asis'---------------------------------- #hack to get rid of latex code returned by certain doi sites (e.g. crosscite.org) fix = function(t) gsub("\\$\\\\(l|r)brace\\$", "", t) suppressWarnings({ sink(tempfile()) b<<-bibliography() sink(NULL) }) for(i in 1:length(b)) b[i]$title = fix(b[i]$title) b