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| aa2num | Conversion of Amino Acids into Integer Values |
| BioPhysConnectoR | 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 |
| freq1p | Compute the Frequencies in an Alignment |
| 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.cov | Compute the Covariance Matrix / Inverse Hessian Matrix |
| get.entropy | Compute the Sequence Entropy for an Alignment |
| get.entropy2p | 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 |
| 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 PDBs |
| simc | Computed Elastic Network Models for Switched-Off-List of Contacts |
| sims | Apply a List of Different Amino Acid Sequences |