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BioPhysConnectoR (version 1.6-3)

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.

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Version

Install

install.packages('BioPhysConnectoR')

Monthly Downloads

10

Version

1.6-3

License

GPL-2

Maintainer

Franziska Hoffgaard

Last Published

May 6th, 2010

Functions in BioPhysConnectoR (1.6-3)

lbpc

List the Functions of the BioPhysConnectoR Package
mat.sort

Sort a Matrix According to a Specified Column
build.interact

Compute the Interaction Matrix
BioPhysConnectoR-package

BioPhysConnectoR
mat.read

Read Matrix Data from a File
scpcp

Self-Consistent Pair Contact Probability Approximation
get.bfacs

Determine B factors
build.hess

Construct the Hessian Matrix
mat.norm

Normalization of a Matrix
sims

Apply a List of Different Amino Acid Sequences
invhess

Compute the Covariance Matrix / Inverse Hessian Matrix
get.entropy

Compute the Sequence Entropy for an Alignment
get.mie

Mutual Information
aa2num

Conversion of Amino Acids into Integer Values
fnorm

Frobenius Norm of Two Matrices
show.code

Output of the Amino Acid Coding Scheme
read.fasta

Read FASTA formated Sequences
extractPDB

Extract Data from a PDB-File
mat.write

Writes Matrix Data to a File
get.svd

Singular Value Decomposition
get.contact.list

Returns a List of Contacts for a given Contact Map
build.contacts

Determine the Contact Map and Distance Matrices
get.freqs

Compute the Frequencies in an Alignment
simc

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

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