BioPhysConnectoR: BioPhysConnectoR

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

Author
Franziska 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 publication
2013-01-09 17:22:13
Maintainer
Frank Keul <keul@bio.tu-darmstadt.de>
License
GPL-2
Version
1.6-10

View on CRAN

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

Files in this package

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