similar to: Is package "dr" appropriate for reducing the dimensionality of molecules conformational space ?

I tried to use R version of package I noticed the original MatLab Pckage is much better documented. I had a look at the R demo code "gtm_demo" and found that variable Y is used in advanced of being created: I wrote my own few lines as follows: inDir <- "C:/Documents and Settings/Monville/Alanine Dipeptide/DBP1/DHA" setwd(inDir) T <-

I have attached the signal that causes the error message in this email subject. Only columns 1 and 3 have to be considered. It is the work trajectory of a molecule migrating between two equilibrium conformations. The curve has 2 peaks, as shown in its plot. But I keep missing the 2nd one. Here is my short script: library(wmtsa) setwd("C:/Documents and Settings/Monville/Alanine

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]]

At the APL conference in Berlin on July 24 I am giving a talk about about a molecule-like notation for arrays for which some prototype code is available in R. It is a graphical notation for arrays of higher rank which makes the structure of arrays and their various concatenations intuitively apparent, and which, in my judgment, would make an excellent interface for array programming languages. I

We still have a long way to go with the data we were given by some drug discovery scientists. The problem is to select the few variables (Collective Variables), from a set of variables sampled during a Molecular Dynamics simulation, which exhibit a consistent and coherent relationship with the given minimum-work curve, all over the time it takes the molecule to migrate from the initial

Hi! I have a question concerning the rcdk package: I generated a test sdf-file with 3 molecules in it and tried to perform clustering by fingerprints and plot the results in a dendogramm. This is what I did: mols <- load.molecules ("molecules.sdf") fp.list <- lapply (mols, get.fingerprint, 'maccs') fp.dist <- fp.sim.matrix (fp.list, method='tanimoto')

Hello gurus, I have a dataframe containing two groups viz., 'control' and 'case', each of these groups contains longitudinal data for 100 subjects. I have to plot all these subjects on a single chart and then put a regression line for each of the group for all the subjects. I have written a function to do the chart grpcharts<-function (dat, group,group2,molecule,cutoff){

Dear R developers, I have a new class, which I called "Molecule", and have tried to define = a "+" operation for 2 objects of this class. This is what I have written so far, although the method is not complete = (I'm trying to look at it at intermediate stages): setMethod( f=3D"+", signature(x=3D"Molecule",y=3D"Molecule"),

Hello R Users, I am interested in using R to generate quantitative structure-activity relationships (QSARs) for small molecules given a set of molecular descriptors (the X's) and biological data (Y's) (usually tab-delimited data files). Has anyone done this using R ? Would you be willing to share your R scripts (or ideas) for doing this with me ? I am particularly interested in

Dear R-users, I am looking for a way to assign to slices of arrays where dimensionality of the array is not a-priory known. Specifically, I would like to be able to generalize the following example of dimensionality 2 to an arbitrary diminsionality: In this example we create an array x, a smaller array y and then assign y to a slice of x. > dimnmx <- list(c('a','b'),

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.

https://bugs.freedesktop.org/show_bug.cgi?id=91373 Bug ID: 91373 Summary: Nouveau fills kern.log with gigabytes of data when molecule screensaver is ran Product: xorg Version: unspecified Hardware: Other OS: All Status: NEW Severity: normal Priority: medium

Hello!!! I have a question about clustering. I'll present my problem first. I have a simulation of a protein trayectory (a file with a time series of protein 3D-coordinates), from it I can calculate the Root Mean Square desviation (RMSD) beetween any pair of structures in the trayectory, which is a rough idea of 3D similarity beetween them. If for every conformation (trayectory frame) I

Dear all, not really a R question but: If I want to check for the classification accuracy of a LDA with previous PCA for dimensionality reduction by means of the LOOCV method: Is it ok to do the PCA on the WHOLE dataset ONCE and then run the LDA with the CV option set to TRUE (runs LOOCV) -- OR-- do I need - to compute for each 'test-bag' (the n-1 observations) a PCA

Hi all, Saw on the net the wip5000 SIP wireless phone from Hitachi, a suprising rig. As anyone successfull in making it work with Asterisk? If so, how do you like it? Regards, Francois Random Thought: --------------- Molecule, n.: The ultimate, indivisible unit of matter. It is distinguished from the corpuscle, also the ultimate, indivisible unit of matter, by a closer resemblance to

Hello all, How do I actually use the output of predict.lm(..., type="terms") to predict new term values from new response values? I'm a chromatographer trying to use R (2.15.1) for one of the most common calculations in that business: - Given several chromatographic peak areas measured for control samples containing a molecule at known (increasing) concentrations, first

Dear all, I have some questions regarding the validity an implementation of statistical tests based on linear models and loess. I've searched the R-help arhives and found several informative threads that related to my questions, but there are still a few issues I'm not clear about. I'd be grateful for guidance. Background and data set: I wish to compare the growth and metabolism

Hello. I''d like to put all my data model classes into a module to avoid name clashes with other classes. However, when I do so, I get a superclass mismatch error. My class hierarchy for the class in question looks like this: class ViewCTI < ActiveRecord::Base end module ORM class Molecule < ViewCTI end end I load the model classes from the ApplicationController class

Hi Anitha, > it's surely just that dragonegg doesn't have any support for this builtin. > > ok. Just verified that Target.cpp and x86_builtins do not have iceil support. > I have this tricky situation - I use dragonegg generated LLVM IR as input to > clang for some analysis (well it is clang++ actually). Understably,clang cribs > looking at __builtin_iceil. Any idea

On 6 November 2012 14:52, Duncan Sands <baldrick at free.fr> wrote: > Hi Anitha, > > > On 06/11/12 10:19, Anitha Boyapati wrote: > >> Hi Duncan >> I am facing a build error about __builtin_iceil >> > > it's surely just that dragonegg doesn't have any support for this builtin. > ok. Just verified that Target.cpp and x86_builtins do not have