http://bio3d.pbwiki.com/ Utilities for the analysis of protein structure and sequence data. en http://bio3d.pbwiki.com/feedlogo.gif http://pbwiki.com/ PBwiki 1.3.8 support@pbwiki.com http://bio3d.pbwiki.com/WinNotes email.hidden@example.com (barry Grant) barry Grant edited WinNotes I work mostly in a unix/linux/macosx enviroment and find the process of package construction and instatltion rather simple. However, performing the same tasks on a PC can be something of a pain.
On your UNIX box
working instaled installed version of your source only package on a UNIX box then try these easy steps.
build the package for Unix in the usuall way
install on Unix
run zip -r bio3d_1.0-5.zip bio3d
cp zip file to web space or windows box for testing
If this did not help or you don't have access to a unix box then try the steps below.
Fingers crossed
To build a package that can be run in Windows, copy your package directory to your Windows machine and try the following command:
]]> Fri, 25 Jul 2008 13:22:02 +0000 mod http://bio3d.pbwiki.com/WinNotes email.hidden@example.com (anon) anon edited WinNotes On your UNIX box
If you have a working instaled version of your source only package on a UNIX box then try these easy steps.
- buildbuild the package for Unix in the usuall way
- install
install on Unix
- then
then go to your package library dir:
/net/home/bgrant/software/R/lib/R/library
- run /net/home/bgrant/software/R/lib/R/library
run zip r -r bio3d_1.0-5.zip bio3d
cp zip file to web space :-) or windows box for testing
Fingers crossed
To build a package that can be run in Windows, copy your package directory to your Windows machine and try the following command:
]]> Fri, 25 Jul 2008 13:19:05 +0000 mod http://bio3d.pbwiki.com/WinNotes email.hidden@example.com (anon) anon edited WinNotes This page describes the rather infurating process of building R packages under Windows; or Building for Windows on Windows
I work mostly in a unix/linux/macosx enviroment and find the process of package construction and instatltion rather simple. However, performing the same tasks on a PC can be something of a pain.
On your UNIX box
If you have a working instaled version of your source only package on a UNIX box then try these easy steps.
- build the package for Unix in the usuall way
- install on Unix
- then go to your package library dir:
/net/home/bgrant/software/R/lib/R/library
- run zip r bio3d_1.0-5.zip bio3d
cp zip file to web space :-)
Fingers crossed
To build a package that can be run in Windows, copy your package directory to your Windows machine and try the following command:
]]> Fri, 25 Jul 2008 13:18:10 +0000 mod http://bio3d.pbwiki.com/FrontPage email.hidden@example.com (Barry) Barry edited FrontPage This site contains the following sections:
Tutorials
of bio3 usage bio3d usage
Manual
complete R style package manual
Vignette
task-oriented introduction to the bio3d
Utility Programs
a description of additional programs that may prove useful
]]> Wed, 07 Nov 2007 19:39:56 +0000 mod http://bio3d.pbwiki.com/manual email.hidden@example.com (Barry) Barry added manual !Even more documentation


!!Making a package manual
To create a PDF or DVI fromat manual file from the Rd files of our package use **R CMD Rd2dvi**, and possibly **dvipdf**. The eaisest route is to simply go to the directory below our package source and enter a cmd like:

| R CMD Rd2dvi --pdf --title=\"The bio3d Package\" bio3d |

where \"bio3d\" is the name of my package directory. If you use the --no-clean option a .RDsomething dir containg intermideat files will remain resident in your cwd. These are the guys to edit if you are so motivated.


!!Making a Package Vignette
A package vignette is an Sweave file that illustrates the use of the package. Because it is Sweave, it is non-bogus. The code actually works. We know it works because it worked to produce the LaTeX output!

Write a sweave latex file then run sweave on it
| Sweave(\"bio3d_vignette.Rnw\") |

then run latex
| pdflatex bio3d_vignette.txt |


!!Current bio3d vignette (not finished)
Here is the Rwn file and output PDF]]> Wed, 07 Nov 2007 19:31:38 +0000 add http://bio3d.pbwiki.com/f/bio3d_vignette.pdf email.hidden@example.com (Barry) Barry uploaded bio3d_vignette.pdf]]> Wed, 07 Nov 2007 19:30:20 +0000 upl http://bio3d.pbwiki.com/ToDo email.hidden@example.com (Barry) Barry edited ToDo Documentation to add or improve
Web site issues and improvements
package manual and vignettes to include
Priorities
write paper DONE
]]> Wed, 07 Nov 2007 19:17:19 +0000 mod http://bio3d.pbwiki.com/newSF email.hidden@example.com (barry) barry edited newSF]]> Mon, 13 Aug 2007 16:33:12 +0000 mod http://bio3d.pbwiki.com/Tutorials email.hidden@example.com (barry) barry edited Tutorials]]> Mon, 23 Jul 2007 18:52:02 +0000 mod http://bio3d.pbwiki.com/Tutorials email.hidden@example.com (barry) barry edited Tutorials]]> Mon, 23 Jul 2007 18:51:19 +0000 mod http://bio3d.pbwiki.com/Tutorials email.hidden@example.com (barry) barry edited Tutorials library(bio3d)
Read a PDB file
pdb # or fit <- read.pdb(system.file("examples/1bg2.pdb", package="bio3d"))
pdb.summary(pdb)
Extract SEQRES PDB sequence
s <- aa321(pdb$seqres)
write.fasta(id="seqres", seq=s , file="eg.fa")
Extract ATOM PDB sequence
s <- aa321(pdb$atom[pdb$calpha,"resid"])
# Lets append this to the existing FASTA file
write.fasta(id="atom", seq=s , file="eg.fa", append = TRUE)
!!! Align ATOM a]]> Mon, 23 Jul 2007 18:50:46 +0000 mod http://bio3d.pbwiki.com/Tutorials email.hidden@example.com (barry) barry edited Tutorials Introductory presentation and tutorial given to members of the McCammon Lab at the University of California, San Diego. This tutorial uses several new functions (see the New Functions page) that have not yet made it into the distributed package. If you would like to try them out, ahead of the next release, please contact bgrant@mccammon.ucsd.edu.
A number of general R tutorials and user guides are linked to from the main Rwiki. See the "Getting started" section.
Details of additional tutorials will appear here soon.
The remainder of this page details some common tasks that can be addressed with bio3d:
[Under Construction]
PDB coordinate superposition
Lets start by using bio3d to simply superpose some PDB structures
library(bio3d)
##- Setup: get all PDB file names from a certain dir 'path'
<- "/net/home/bgrant/tmp_aln" "/net/home/bgrant/mypdb_dir"
files <- list.files(path=path,
pattern="[pdb]$&]]> Mon, 23 Jul 2007 18:45:57 +0000 mod http://bio3d.pbwiki.com/Tutorials email.hidden@example.com (barry) barry edited Tutorials Introductory presentation and tutorial given to members of the McCammon Lab at the University of California, San Diego. This tutorial uses several new functions (see the New Functions page) that have not yet made it into the distributed package. If you would like to try them out, ahead of the next release, please contact bgrant@mccammon.ucsd.edu.
A number of general R tutorials and user guides are linked to from the main Rwiki. See the "Getting started" section.
Lets start by using bio3d to simply superpose some PDB structures
library(bio3d)
##- Setup: get all PDB file names from a certain dir 'path'
path <- "/net/home/bgrant/tmp_aln"
files <- list.files(path=path,
pattern="[pdb]$",
full.names=TRUE)
##- Sequence alignment
seq <- NULL
for(i in 1:length(files)) {
pdb <- read.pdb( files[i] )
seq <- seqbind(seq, aa321(pdb$atom[pdbs$calpha, "resid"]))
}
##* Make sure muscle is in your PATH]]> Mon, 23 Jul 2007 18:41:43 +0000 mod http://bio3d.pbwiki.com/SF email.hidden@example.com (barry) barry edited SF Functions to fix
read.pdb
Return addational REMARK data from PDB file (e.g. Resolution etc.)
"read.pdb" <- function (file, maxlines=50000, multi=FALSE,
rm.insert=FALSE, rm.alt=TRUE, verbose=TRUE) {
if(missing(file)) {
stop("read.pdb: please specify a PDB 'file' for reading")
}
if(!is.numeric(maxlines)) {
stop("read.pdb: 'maxlines' must be numeric")
}
if(!is.logical(multi)) {
stop("read.pdb: 'multi' must be logical TRUE/FALSE")
}
# PDB FORMAT v2.0: colpos, datatype, name, description
atom.format <- matrix(c(-6, NA, NA, # (ATOM)
5, 'numeric', "eleno", # atom_no
-1, NA, NA, # (blank)
4, 'character', "elety", # atom_ty
1, 'character', "alt", # alt_loc
4, 'character', "resid", # res_na
1, 'character', "chain", # chain_id
4, 'numeric', "resno",]]> Mon, 02 Jul 2007 12:33:20 +0000 mod http://bio3d.pbwiki.com/FrontPage email.hidden@example.com (barry) barry edited FrontPage InstallingBio3d - installation instructions.
Documentation
to R R (still rather basic, but some day...)
Why R? - some comments in response to a common question.
R command summary - quick reference to common R commands/functions
]]> Tue, 19 Jun 2007 18:14:34 +0000 mod http://bio3d.pbwiki.com/Rnotes email.hidden@example.com (barry) barry edited Rnotes]]> Tue, 19 Jun 2007 18:12:43 +0000 mod http://bio3d.pbwiki.com/Rnotes email.hidden@example.com (barry) barry edited Rnotes Emacs Speaks Statistics (or ESS) is an add-on package for emacs to allow easy editting R scripts. ESS provides a standard interface between a range of statistical programs and statistical processes. It is intended to provide assistance for interactive statistical programming and data analysis, and is based on and extends the capabilities of S-mode. The code is freely available but is not in the public domain. It is distributed under the GNU GPL from
To get your ".sf" function files rendered by ess edit the file ~/ess-5.2.5/lisp/ess-site.el
//cut(if//cut
(if (assoc "\.rR\'" ".[rR]'" auto-mode-alist) nil (setq
(setq auto-mode-alist (append '(("\.sp\'"
(append
'((".sp'" . S-mode) ("\.qsS\'"
(".[qsS]'" . S-mode) ("\.ssc\'"<]]> Tue, 19 Jun 2007 18:12:17 +0000 mod http://bio3d.pbwiki.com/OldVersions email.hidden@example.com (barry) barry edited OldVersions Older Versions
from this page. Changes the links below. Changes between versions are documented along with a description of additionalprograms that may prove useful.
bio3d_1.0-0.tar.gz
bio3d_1.0-1.tar.gz
]]> Tue, 19 Jun 2007 17:50:51 +0000 mod http://bio3d.pbwiki.com/OldVersions email.hidden@example.com (barry) barry edited OldVersions bio3d_1.0-2.tar.gz
bio3d_1.0-3.tar.gz
bio3d_1.0-3.zip
bio3d_1.0-4.tar.gz
bio3d_1.0-4.zip
]]> Tue, 19 Jun 2007 17:49:32 +0000 mod http://bio3d.pbwiki.com/OldVersions email.hidden@example.com (barry) barry edited OldVersions Older Versions
Older versions of the bio3d package can be obtained from this page. Changes between versions are documented along with a description of additionalprograms that may prove useful.
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-0.tar.gz
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-1.tar.gz
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-2.tar.gz
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-3.tar.gz
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-3.zip
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-4.tar.gz
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-4.zip
http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-5.tar.gzbio3d_1.0-0.tar.gz
bio3d_1.0-1.tar.gz
bio3d_1.0-2.tar.gz
bio3d_1.0-3.tar.gz
bio3d_1.0-3.zip
bio3d_1.0-4.tar.gz
bio3d_1.0-4.zip
bio3d_1.0-5.tar.gz]]> Tue, 19 Jun 2007 17:48:45 +0000 mod