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

BioPhysConnectoR (version 1.6-1)

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

10

Version

1.6-1

License

GPL-2

Maintainer

Franziska Hoffgaard

Last Published

March 2nd, 2010

Functions in BioPhysConnectoR (1.6-1)

simc

Computed Elastic Network Models for Switched-Off-List of Contacts
get.bfacs

Determine B factors
mat.sort

Sort a Matrix According to a Specified Column
mat.write

Writes Matrix Data to a File
fnorm

Frobenius Norm of Two Matrices
sim

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

List the Functions of the BioPhysConnectoR Package
aa2num

Conversion of Amino Acids into Integer Values
get.freqs

Compute the Frequencies in an Alignment
extractPDB

Extract Data from a PDB-File
BioPhysConnectoR-package

BioPhysConnectoR
build.contacts

Determine the Contact Map and Distance Matrices
scpcp

Self-Consistent Pair Contact Probability Approximation
get.mie

Mutual Information
invhess

Compute the Covariance Matrix / Inverse Hessian Matrix
build.hess

Construct the Hessian Matrix
get.contact.list

Returns a List of Contacts for a given Contact Map
get.entropy

Compute the Sequence Entropy for an Alignment
mat.norm

Normalization of a Matrix
mat.read

Read Matrix Data from a File
sims

Apply a List of Different Amino Acid Sequences
read.fasta

Read FASTA formated Sequences
build.interact

Compute the Interaction Matrix
show.code

Output of the Amino Acid Coding Scheme
get.svd

Singular Value Decomposition