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Read aligned or un-aligned sequences from a FASTA format file.
● Data Source:
CranContrib
● Keywords: IO
● Alias: read.fasta
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lbpc
(Package: BioPhysConnectoR) :
List the Functions of the BioPhysConnectoR Package
A shortcut for ls("package:BioPhysConnectoR") to get an overview of the implemented functions.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: lbpc
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sims
(Package: BioPhysConnectoR) :
Apply a List of Different Amino Acid Sequences
For a set of sequences given in an alignment and a corresponding PDB file the covariance matrix for each sequence is computed based on the given molecular structure. The latter can be directed into a file. The Frobenius norms are computed upon request.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: sims
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fnorm
(Package: BioPhysConnectoR) :
Frobenius Norm of Two Matrices
Computation of the Frobenius norm of two matrices as the sum of the squared differences between these matrices.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: fnorm
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Matrix data are written to a specified output file.
● Data Source:
CranContrib
● Keywords: IO
● Alias: mat.write
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The model of the Self-Consistent Pair Contact Probability (SCPCP) (Micheletti et al., 2001; Hamacher et al., 2006) computes equilibrium properties of structures with known native states. For a given contact map, extracted from a PDB file or artificially created, the fraction of native contacts, the free and internal energies are computed as well as the degree to which an amino acid is in its native state conformation. The maximum number of iteration and the preferred accuracy for the approximation can be specified.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: scpcp
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get.contact.list
(Package: BioPhysConnectoR) :
Returns a List of Contacts for a given Contact Map
From a given contact map a list of contacts is computed.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: get.contact.list
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A matrix is normalized by dividing each entry [i,j] by the square root of the product of the diagonal entries [i,i] and [j,j]. The input matrix should be a square matrix with positive diagonal entries.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: mat.norm
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This function reads a PDB file and extracts data from it.
● Data Source:
CranContrib
● Keywords: IO
● Alias: extractPDB
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The Hessian matrix is computed using the interaction matrix, the contact map, and the coordinate differences.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: build.hess
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providing 
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