search for: molecul

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&...

...9; 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){ dat2<-dat[grep(group,dat$Group),] ylim=log2(c(min(dat2[,molecule],na.rm=T)+4,max(dat2[,molecule],na.rm=T)+1)) all.sub.id<-dat2$Subject.ID if (group=='control'){ col=c('blue') }else{col=c('red')} if(group2=='case'){ col2=c('red') }else{ co...

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 4 atom pair distances all along the trajectory from the ini...

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 del...

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 Component: Driver/nouveau Assignee: nouveau at lists.freedesktop.org...

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 programm...

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') f...

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') A<-a[50,3] else (B<-'O') B<-a[86,3] ifelse (A=='H',A<-a[50,3],ifelse(B=='O',B<-a[86,3],0] I was thinking to have the...

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 R codes for optimizing variabl...

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 the atom, also the ultimate, indivisible unit of matter ... The ion differs from the molecule, the corpuscle and the atom in that i...

...::badd:ecaf, TLS: SSL_read() failed: error:14094418:SSL routines:SSL3_READ_BYTES:tlsv1 alert unknown ca: SSL alert number 48, session=<ZcMRtlPLqgAgAQRwHwkCA/2/UI5KKVbF> Ciao, luigi - -- / +--[Luigi Rosa]-- \ I will tell you a great secret, Captain. Perhaps the greatest of all time. The molecules of your body are the same molecules that make up this station and the nebula outside, that burn inside the stars themselves. We are star stuff, we are the universe made manifest, trying to figure itself out. As we have both learned, sometimes the universe requires a change of perspective."...

I'm running into an a problem with x11 forwarding over ssh I'm trying to run an application (rasmol - molecule viewing program) which when using the the default setup for x11 forwarding causes the following error: X Error of failed request: BadAccess (attempt to access private resource denied) Major opcode of failed request: 132 (MIT-SHM) Minor opcode of failed request: 1 (X_ShmAttach) S...

...ng for some analysis (well it is clang++ actually). Understably,clang cribs looking at __builtin_iceil. Any idea how to resolve that as well? clang++ -O2 -march=bdver2 -mno-fma -save-temps -mfma4 -ffp-contract=fast -DSPEC_CPU_LP64 Compute.o ComputeList.o ComputeNonbondedUtil.o LJTable.o Molecule.o Patch.o PatchList.o ResultSet.o SimParameters.o erf.o spec_namd.o -o namd spec_namd.o: In function `main': spec_namd.ll:(.text+0x2a3): undefined reference to `__builtin_iceil' > Please open a bug report with a minimal test case > Will do. Thanks -Anitha...

...f2....f10 as independent variables.It is giving the following error. Also i want that i shoul get one predicted value for each row(y). What should i do. Please help me out i will be thankful to you. i<-read.table("data.txt",header=FALSE) i V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 1 molecule f1 f2 f3 f4 f5 f6 f7 f8 f9 f10 2 m1 3 7 0 3 0 0 0 1 1 1 3 m2 2 7 0 2 0 2 0 1 0 1 4 m3 0 0 0 3 0 0 0 3 1 0 5 m4 3 7 0 1 3 0 0 0 0 1 attach(i) out<-lm(y~x1+x2+x3+x4+x5+x6+x7+x8+x9+x10) Error in eval(expr, envir, enclos) :...

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", main=eval(substitute(expression(paste(mol," Year 2005")), list(mol=eval(...

...ut 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 derive a linear regression model relating the known concentration (predictor) to the observed peak area (response) - Then, given peak areas from new (real) samples containing unknown amounts of the molecule, use the model to predict concentrati...

...hmark here again). Any idea? g++ -march=bdver2 -save-temps -fplugin=/home/anboyapa/install/bin/dragonegg.so -O2 -march=bdver2 -save-temps -fplugin=/home/anboyapa/install/bin/dragonegg.so -mno-fma -mfma4 -ffast-math -DSPEC_CPU_LP64 Compute.o ComputeList.o ComputeNonbondedUtil.o LJTable.o Molecule.o Patch.o PatchList.o ResultSet.o SimParameters.o erf.o spec_namd.o -o namd spec_namd.o: In function `main': spec_namd.C:(.text+0x2a3): undefined reference to `__builtin_iceil' collect2: error: ld returned 1 exit status specmake: *** [namd] Error 1 On 5 November 20...

Ok, I've got a user, I just built him a C 7 machine. The new one has an ATI card; the old had an NVidia card. I got it to use the radeon driver, so it looks ok (he has a very wide screen). However... he has a program that renders a molecule (which you see as many connected lines, in various colors). However... it used to display it against a black background, and suddenly, it's a transparent background, showing what's under that window. Anyone got any ideas about that? mark

...ing and out-licensing, and the choice between semi block buster and block buster model. The report not only analyses the large structural changes and dynamic shifts in the Industry, it also takes an in-depth look at new revenue models. Another area of analysis is the shift from chemical-based small molecules to biology-based large molecules like antibodies and protein, and what new opportunities this has created in the Industry. To download the full report and view the table of contents click here. http://www.jsbintelligence.com/template.asp?docId=22&docName=Pharma-Report-Form Should you be th...

...ltin_iceil. Any idea how to resolve that as well? adding dragonegg support for iceil would solve both problems. Ciao, Duncan. > clang++ -O2 -march=bdver2 -mno-fma -save-temps -mfma4 -ffp-contract=fast > -DSPEC_CPU_LP64 Compute.o ComputeList.o ComputeNonbondedUtil.o LJTable.o > Molecule.o Patch.o PatchList.o ResultSet.o SimParameters.o erf.o > spec_namd.o -o namd > spec_namd.o: In function `main': > spec_namd.ll:(.text+0x2a3): undefined reference to `__builtin_iceil' > > Please open a bug report with a minimal test case > > Wil...