similar to: rcdk package, fingerprint without name?

hello , Iam working on the rcdk package ,when i start with it using the load.molecules fuction this is the error message returned Error in if (!file.exists(f) && !grep("http://", f)) stop(paste(f, ": Does not exist", : missing value where TRUE/FALSE needed could someone help me with this,thanks in advance regards Hari [[alternative HTML version deleted]]

Hi, I am a method developer in drug discovery. I have developed a similarity searching method for small (drug-like) molecules. I want to compare the performance of my method to the performance of other methods. Similarity searching methods are commonly assessed by their ability to (re)discover a set of molecules that is avtive versus a given target, given one randomly selected query molecule.

Hi, I have a package for which I'm writing a vignette. The vignette looks fine as indicated by R CMD check. However after installing the package (in my personal R library location) doing vignette('rcdk') says Warning message: vignette 'rcdk' *not* found But I can see the PDF file located under rcdk/doc in the R library directory. The header of the Rnw file is %

Hi! Just started working at a lab and have only minimal experience with R. I was wondering if there was a way to write a code that would intake a data set of chemical compounds (ex: H2O, CH3) and be able to give an output column of the molecular weight? I tried some really basic coding to try to work with a being a matrix of data with the assigned variables. if (A<-'H')

Hi, I am trying to see if I can use R to perform more rigorous regression analysis. I wonder if the fingerprint package is able to handle pipeline pilot fingerprints (ECFC6 etc) now. Thank you, Eric [[alternative HTML version deleted]]

I need help on calling the svydesign function in the survey package (although this error appears not to be specific to svydesign). I am passing parameters incorrectly but am not sure how to correct the problem. ## Call the main function PS.sim (one of mine). The dots are parameters I omitted to simplify the question. ## y.col, str.col, clus.id, and PS.col are names of columns in the object pop.

I would like to know if clogit function can be used as below clogit(group~., data=dataframe) When I try to use in above format it takes a long time, I would appreciate some pointers to get multiple combinations tested. set.seed(100) d=data.frame(x=rnorm(20)+5, x1=rnorm(20)+5, x2=rnorm(20)+5, x3=rnorm(20)+5, x4=rnorm(20)+5, x5=rnorm(20)+5, x6=rnorm(20)+5, x7=rnorm(20)+5, x8=rnorm(20)+5,

I am new to R and I suspect my problem is easily solved, but I haven't been able to figure it out without using loops. I am trying to implement Blair & Karniski's (1993) permutation test. I've included a sample data frame below. This data frame represents the conditional means (C1, C2) for 3 subjects in 2 consecutive samples of a continuous data set (e.g. ERP waveform).

Greetings, I would like to use a data.frame with strings to feed the expression() in the title of a plot. The way I did this is: molecules <-data.frame(name=c("o3","no","no2"),expression=c("quote(O[3])","quote(NO)","quote(NO[2])")) for (mol in c(5,7,9)) { plot(x, y, type="b",

> DATA [,1] [1,] -2.0314185 [2,] -0.3594015 [3,] -1.3225832 [4,] 1.5050892 [5,] -0.4535558 [6,] 3.6335036 [7,] 5.1965750 [8,] 4.2923129 [9,] 6.0913187 [10,] 4.9131070 > RESA [,1] [,2] [,3] [,4] [,5] [1,] -2.0314185 1.5050892 -1.3225832 -1.3225832 -2.0314185 [2,] -0.3594015 -0.3594015 4.2923129 -0.3594015

Dear R community, I have a project with electricity load forecasting, and I got hourly data for system load. If you haven't worked with electricity before, seasonality comes in many flavors: a daily pattern, with a peak at around 7pm; a weekly pattern, in which we use more electricity on weekdays in comparison to weekends; a winter-summer pattern, with air conditioning and heaters playing an

Dear WizaRds, I am trying to compute the (adjusted) Rand Index in order to comprehend the variable selection heuristic (VS-KM) according to Brusco/ Cradit 2001 (Psychometrika 66 No.2 p.249-270, 2001). Unfortunately, I am unable to correctly use cl_ensemble and cl_agreement (package: clue). Here is what I am trying to do: library(clue) ## Let p1..p4 be four partitions of the kind

Dear people, A somewhat clueless question follows: I just discovered that the lme function in contrib package nlme for R, while similar to the lme function in Splus, does not use the cluster function option. This difference does not appear to be documented in the V&R `R Complements' file. I have data which is divided into 6 groups The lme model is of the form (simplified from the actual

R-helpers: I am using R 2.5 on Windows XP, packages all up to date. I have run into an issue with the MIcombine function of the mitools package that I hoped some of you might be able to help with. I will work through a reproducible example to demonstrate the issue. First, make a dataset from the pbc dataset in the survival package --------------- # Make a dataset library(survival) d <-

Dear R-listers, I do clustering on tens of individuals by thousands of traits. I have known the assignment of each individual. I want to classify the individuals by randomly resampling different subsets of the traits, for example, randomly resampling 100 traits for 100 times, then 200 traits for 100 times, then 300 traits for 100 times, ,,,,,,. By each subset of traits, I do clustering of the

I anticipate lacking of prior experience with dimensionality reduction problems. Some scientists concerned with drug discovery performed several steered Molecular Dynamics simulations of the alanine-dipeptide molecule dragged by a radial force from an equilibrium conformation to another different equilibrium conformation. They sampled at regular intervals 7 dihedral angles, 5 bending angles, and

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Hi: I have calculated the Silhouette score and Dunn score after hierarchical clustering for 3 clusters: #Distance measure d <- dist(USArrests, method = "euclidean") #Hierarchical clustering hc <- hclust(dist(USArrests), "ave") #calculating silhouette value for 3 clusters sil<- silhouette(cutree(hc, k=3), d) #calculating Dunn index for 3 clusters clus <- cutree(hc,

Hi Peter, You didn't give a very specific example, but it seems to me that what you wish to do is not really complicated. I suppose you have created a table of sequences vs. say hyprophobicity, charge, etc..., something like... seq hydroph arom b0001 0.104762 0.000000 b0002 0.035122 0.065854 b0003 0.024193 0.070968 b0004 -0.096729 0.084112 b0005 -0.973469 0.091837 b0006

Hi, can anyone help me fit betabinomial model to the following dataset where each iD is a cluster in itself , if i use package aod 's betabinom model it gives an estimate of zero to phi(the correlation coeficient ) and if i fix it to the anova type estimate obtained from icc( in package aod) then it says system is exactly singular. And when i try to fit my loglikelihood by