Learn R Programming

BioPhysConnectoR (version 1.6-10)

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

55

Version

1.6-10

License

GPL-2

Maintainer

Frank Keul

Last Published

January 9th, 2013

Functions in BioPhysConnectoR (1.6-10)

get.svd

Singular Value Decomposition
build.contacts

Determine the Contact Map and Distance Matrices
mat.norm

Normalization of a Matrix
fnorm

Frobenius Norm of Two Matrices
sim

Compute the Covariance Matrices and B Factors for a List of PDBs
get.mie

Mutual Information
extractPDB

Extract Data from a PDB-File
mat.read

Read Matrix Data from a File
mat.sort

Sort a Matrix According to a Specified Column
show.code

Output of the Amino Acid Coding Scheme
mat.write

Writes Matrix Data to a File
aa2num

Conversion of Amino Acids into Integer Values
get.entropy

Compute the Sequence Entropy for an Alignment
BioPhysConnectoR-package

BioPhysConnectoR
get.contact.list

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

Determine B factors
read.fasta

Read FASTA formated Sequences
scpcp

Self-Consistent Pair Contact Probability Approximation
build.hess

Construct the Hessian Matrix
invhess

Compute the Covariance Matrix / Inverse Hessian Matrix
get.freqs

Compute the Frequencies in an Alignment
sims

Apply a List of Different Amino Acid Sequences
simc

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

List the Functions of the BioPhysConnectoR Package
build.interact

Compute the Interaction Matrix