Displaying 20 results from an estimated 800 matches similar to: "Converting pdb to pqr"
2010 Feb 10
3
Using R to format a file using a server (PDB to PQR file)
I am trying to write a program that uses R and takes a pdb file, and converts
it to a pqr file. This task is simple generally, using the website,
http://pdb2pqr-1.wustl.edu/pdb2pqr/. How do you use R to input a pdb file
(that is on hand) into the upload pdb file input, and run the website and
give the return file to be a pqr file. Thanks for your help.
--
View this message in context:
2010 Apr 12
4
R GUI
I am really new with R Graphical user interfacefunctions. I am developing a
software package to calculate pKa (biochemistry) but I want to make it look
aesthetically pleasing and make it user friendly. I have heard that R has
some GUI (Graphical user interface) and you can do some really cool stuff
out there. What are the limitations and what are some resources for help. I
have found a couple of
2013 Jun 22
1
Announcing pqR - a faster version of R
I have released a new, faster, version of R, which I call pqR (for
"pretty quick" R), based on R-2.15.0. Among many other improvements,
pqR supports automatic use of multiple cores to perform numerical
computations in parallel with other numerical computations, and with
the interpretive thread. It also implements a true reference counting
scheme to reduce the amount of unnecessary
2010 May 18
1
GUI commands to call for a protein from protein data bank
What I am trying to do is use GUI function, traitr, and to call for a pdb
file and save it and then display it. I want to call for it by taking it
from the user and then displaying it on the screen. I am having problems
with that. The line pdb <- read.pdb(""ProteinCode) where proteincode should
be the name of the protein, for example 1ly2, but it always ends up being
protein. My
2013 Apr 29
2
Adding elements in data.frame subsets and also subtracting an element from the rest elements in data.frame
Dear R forum
I have a data.frame as
cashflow_df = data.frame(instrument = c("ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC","ABC", "ABC", "PQR", "PQR",
2015 Sep 19
0
New version of the R parser in pqR
I have rewritten the R parser in the new version of pqR that I
recently released (pqR-2015-09-14, at pqR-project.org). The new
version of the parser is much cleaner, is faster (sometimes quite
substantially faster), has a better interface to the read-eval-print
loop, and provides a better basis for future extensions. The deparser
has also been substantially revised in pqR, and is better
2014 Sep 07
0
New flag bit for serialized used by pqR
I will shortly be releasing a new version of pqR (you can get a test
version from pqR-project.org now - scroll to the bottom of the page).
One new feature in this version requires adding a bit to the flags
written out when data is serialized. I thought I'd let you know about
this so as to avoid any possible conflicts.
The new feature is that a few R objects are defined as constants,
which
2010 Feb 03
2
How to change output 'csv' file
Dear R helpers
After executing the R code, where the last few lines of the code are something like given below.
## Part of my R code
n = 20
........
.........
final_output = data.frame(Numbers = numbers, ABC = data1, XYZ = data2, PQR = data3)
write.csv(data.frame(Scenario = paste("Sc_", 1:n, sep = ""), final_output'), 'result.csv', row.names
2010 Feb 10
4
Readjusting the OUTPUT csv file
Dear R helpers
I have some variables say ABC, DEF, PQR, LMN and XYZ. I am choosing any three varaibles at random at a time for my analysis and name these files as input1.csv, input2.csv and input3.csv. So if I choose variables say ABC, DEF and PQR, I am passing the specifications of these variables to input1.csv, input2.csv and input3.csv respectively.
This means in another case even if I
2013 Apr 26
2
Splitting data.frame and saving to csv files
Dear R Forum,
I have a data.frame as
df = data.frame(date = c("2013-04-15", "2013-04-14", "2013-04-13", "2013-04-12", "2013-04-11"),
ABC_f = c(62.80739769,81.04525895,84.65712455,12.78237251,57.61345256),
LMN_d = c(21.16794336,54.6580401,63.8923307,87.59880367,87.07693716),
XYZ_p = c(55.8885464,94.1358684,84.0089114,98.99746696,64.71083712),
2018 Nov 27
1
Subsetting row in single column matrix drops names in resulting vector
Dmitriy Selivanov (selivanov.dmitriy at gmail.com) wrote:
> Consider following example:
>
> a = matrix(1:2, nrow = 2, dimnames = list(c("row1", "row2"), c("col1")))
> a[1, ]
> # 1
>
> It returns *unnamed* vector `1` where I would expect named vector. In fact
> it returns named vector when number of columns is > 1.
> Same issue applicable
2014 Jun 23
2
Unfixed bugs in latest R-patched
A new version of pqR is now available at pqR-project.org, which fixes
several bugs that are also present in the latest R Core patch release
(r66002). A number of bugs found previously during pqR development
are also unfixed in the latest R Core release. Here is the list of
these bugs that are unfixed in r66002 (including documentation
deficiencies), taken from the pqR bug fix and documentation
2012 May 30
3
Separate Array Variable Content
Hi,
I am new in R,
i have a matrix like this
MyMatrix <-
*ABC PQR XYZ*
10 20 30
40 50 60
70 80 90
And, i have an array containing some conditions like this,
MyArray <- c("*ABC*>50","*PQR*<50","*ABC*<30 &* XYZ*<40")
"ABC>50"
"PQR<50"
"ABC<30 & XYZ<40"
2012 Jul 10
2
Count of elements in coulmns of a matrix
Could you please tell me what is the function or method to get count of
elements in all the columns in a matrix ?
for eg :-
ABC XYZ PQR
------ ----- ------
2 3 4
4 5
5 4 3
2
Result will be like
ABC XYZ PQR
------ ----- ------
2 4 3
Could you please help me
2015 Jul 14
3
Two bugs showing up mostly on SPARC systems
In testing pqR on Solaris SPARC systems, I have found two bugs that
are also present in recent R Core versions. You can see the bugs and
fixes at the following URLs:
https://github.com/radfordneal/pqR/commit/739a4960a4d8f3a3b20cfc311518369576689f37
https://github.com/radfordneal/pqR/commit/339b7286c7b43dcc6b00e51515772f1d7dce7858
The first bug, in nls, is most likely to occur on a 64-bit
2019 Feb 03
1
Inefficiency in df$col
While doing some performance testing with the new version of pqR (see
pqR-project.org), I've encountered an extreme, and quite unnecessary,
inefficiency in the current R Core implementation of R, which I think
you might want to correct.
The inefficiency is in access to columns of a data frame, as in
expressions such as df$col[i], which I think are very common (the
alternatives of
2012 Jul 13
3
Column create and Update using function
Hi,
here i have a Max and Min values
Min <-3
Max <-6
and also a matrix like this,
ABC XYZ PQR
------ ------- -------
2 4 3
5 4 8
7 1 3
In this i need to check each particular column values are between Max and
Min value.
If the coulmn value not coming between Max and
2012 May 25
4
Hash Table - Select and Change Data iniside Matrix
Hi,
Here i have been a matrix like this,
*NAME AGE PALCE TRUE/FALSE*
ABC 20 INDIA
XYZ 30 FRANCE
PQR 40 USA
MNO 30 KENIYA
DEF 25 AUSTRALIA
Here,* TRUE/FALSE* Column containing empty values.
So my requirement what is , need to change all the *TRUE/FALSE *column value
into "*TRUE*" where *AGE =
2012 Jul 11
4
MODE , VARIANCE , NTH PERCENTAILE
Hi,
Here i have an matrix like this,
ABC PQR XYZ MNO
------ ------- ------ --------
3 6 7 15
2 12 24 15
20 5 1 2
25 50 15 35
i need to get the
"MODE" - for each column-wise
"VARIANCE" - for
2012 May 28
2
Hash Table - Select and Change Data iniside Matrix Using "Between"
Hi,
Here i have been an matrix like this,
*NAME AGE PALCE TRUE/FALSE*
ABC 20 INDIA
XYZ 30 FRANCE
PQR 40 USA
MNO 30 KENIYA
DEF 25 AUSTRALIA
GTY 34 CANADA
BNH 38 JAPAN
Here, *TRUE/FALSE *Column containing empty values.
So my requirement what is, need to change all the TRUE/FALSE