Learn R Programming
⚠️There's a newer version (1.6-10) of this package.Take me there.

BioPhysConnectoR (version 1.6-5)

BioPhysConnectoR

Description

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

Copy Link

Version

Install

install.packages('BioPhysConnectoR')

Monthly Downloads

106

Version

1.6-5

License

GPL-2

Maintainer

Franziska Hoffgaard

Last Published

July 26th, 2010

Functions in BioPhysConnectoR (1.6-5)

scpcp

Self-Consistent Pair Contact Probability Approximation
BioPhysConnectoR-package

BioPhysConnectoR
mat.sort

Sort a Matrix According to a Specified Column
invhess

Compute the Covariance Matrix / Inverse Hessian Matrix
build.hess

Construct the Hessian Matrix
sims

Apply a List of Different Amino Acid Sequences
extractPDB

Extract Data from a PDB-File
build.contacts

Determine the Contact Map and Distance Matrices
get.entropy

Compute the Sequence Entropy for an Alignment
mat.norm

Normalization of a Matrix
read.fasta

Read FASTA formated Sequences
get.mie

Mutual Information
get.bfacs

Determine B factors
lbpc

List the Functions of the BioPhysConnectoR Package
mat.write

Writes Matrix Data to a File
get.svd

Singular Value Decomposition
mat.read

Read Matrix Data from a File
show.code

Output of the Amino Acid Coding Scheme
get.contact.list

Returns a List of Contacts for a given Contact Map
sim

Compute the Covariance Matrices and B Factors for a List of PDBs
simc

Computed Elastic Network Models for Switched-Off-List of Contacts
aa2num

Conversion of Amino Acids into Integer Values
build.interact

Compute the Interaction Matrix
get.freqs

Compute the Frequencies in an Alignment
fnorm

Frobenius Norm of Two Matrices