BioPhysConnectoR: BioPhysConnectoR
Version 1.6-10

Utilities and functions to investigate the relation between biomolecular structures, their interactions, and the evolutionary information revealed in sequence alignments of these molecules.

AuthorFranziska Hoffgaard <hoffgaard@bio.tu-darmstadt.de>, with contributions from Philipp Weil <weil@bio.tu-darmstadt.de> and Kay Hamacher <hamacher@bio.tu-darmstadt.de>
Date of publication2013-01-09 17:22:13
MaintainerFrank Keul <keul@bio.tu-darmstadt.de>
LicenseGPL-2
Version1.6-10
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BioPhysConnectoR")

Getting started

Package overview

Popular man pages

BioPhysConnectoR-package: BioPhysConnectoR
build.contacts: Determine the Contact Map and Distance Matrices
get.svd: Singular Value Decomposition
mat.norm: Normalization of a Matrix
mat.sort: Sort a Matrix According to a Specified Column
simc: Computed Elastic Network Models for Switched-Off-List of...
sims: Apply a List of Different Amino Acid Sequences
See all...

All man pages Function index File listing

Man pages

aa2num: Conversion of Amino Acids into Integer Values
BioPhysConnectoR-package: BioPhysConnectoR
build.contacts: Determine the Contact Map and Distance Matrices
build.hess: Construct the Hessian Matrix
build.interact: Compute the Interaction Matrix
build.invhess: Compute the Covariance Matrix / Inverse Hessian Matrix
extractPDB: Extract Data from a PDB-File
fnorm: Frobenius Norm of Two Matrices
freq2p: Compute the Frequencies in an Alignment
get.bfacs: Determine B factors
get.contact.list: Returns a List of Contacts for a given Contact Map
get.entropy: Compute the Sequence Entropy for an Alignment
get.mie: Mutual Information
get.svd: Singular Value Decomposition
lbpc: List the Functions of the BioPhysConnectoR Package
mat.norm: Normalization of a Matrix
mat.read: Read Matrix Data from a File
mat.sort: Sort a Matrix According to a Specified Column
mat.write: Writes Matrix Data to a File
read.fasta: Read FASTA formated Sequences
scpcp: Self-Consistent Pair Contact Probability Approximation
show.code: Output of the Amino Acid Coding Scheme
sim: Compute the Covariance Matrices and B Factors for a List of...
simc: Computed Elastic Network Models for Switched-Off-List of...
sims: Apply a List of Different Amino Acid Sequences

Functions

BioPhysConnectoR Man page Man page
aa2num Man page Source code
build.contacts Man page Source code
build.hess Man page Source code
build.interact Man page Source code
build.invhess Man page Source code
extractPDB Man page Source code
fnorm Man page Source code
freq1p Man page Source code
freq2p Man page Source code
get.bfacs Man page Source code
get.contact.list Man page Source code
get.cov Man page Source code
get.entropy Man page Source code
get.entropy2p Man page Source code
get.mie Man page Source code
get.svd Man page Source code
lbpc Man page Source code
mat.norm Man page Source code
mat.read Man page Source code
mat.sort Man page Source code
mat.write Man page Source code
onLoad Source code
read.fasta Man page
scpcp Man page Source code
show.code Man page Source code
sim Man page Source code
simc Man page Source code
sims Man page Source code

Files

MD5
NAMESPACE
R
R/build.invhess.r
R/show.code.r
R/get.svd.r
R/get.contact.list.r
R/read.fasta.R
R/sims.r
R/fnorm.r
R/get.entropy.r
R/mat.read.r
R/mat.sort.r
R/sim.r
R/scpcp.r
R/build.hess.r
R/extractPDB.r
R/aa2num.r
R/lbpc.r
R/build.contacts.r
R/mat.norm.r
R/get.bfacs.r
R/mat.write.r
R/zzz.r
R/h2p.r
R/get.cov.r
R/simc.r
R/get.mie.r
R/build.interact.r
R/freqs.r
man
man/build.contacts.Rd
man/aa2num.Rd
man/get.entropy.Rd
man/build.interact.Rd
man/show.code.Rd
man/get.mie.Rd
man/mat.sort.Rd
man/BioPhysConnectoR-package.Rd
man/freq2p.Rd
man/read.fasta.Rd
man/lbpc.Rd
man/sims.Rd
man/fnorm.Rd
man/mat.write.Rd
man/scpcp.Rd
man/get.contact.list.Rd
man/mat.norm.Rd
man/extractPDB.Rd
man/build.hess.Rd
man/get.bfacs.Rd
man/sim.Rd
man/simc.Rd
man/mat.read.Rd
man/build.invhess.Rd
man/get.svd.Rd
DESCRIPTION
inst
inst/1EBY.pdb
inst/mj2.txt
inst/align.fasta
inst/1KZK.pdb
inst/mj1.txt
inst/2UXZ.pdb
src
src/meths.c
src/meths2.c
BioPhysConnectoR documentation built on May 20, 2017, 4:32 a.m.