bios2cor-package |
Correlation/covariation Analysis in Biological Sequences and Simulations |
angle2rotamer |
Converts dihedral angles to rotamers |
angles.plot |
plots the time evolution of the dihedral angles in top pairs |
Bios2cor |
Correlation/covariation Analysis in Biological Sequences and Simulations |
bios2cor |
Correlation/covariation Analysis in Biological Sequences and Simulations |
centered_pca |
Performs principal component analysis of a correlation/covariation matrix |
delta_filter |
Creation of an entropy/dynamic score delta filter for each element |
dynamic_circular |
Circular correlation |
dynamic_entropy |
Variability score |
dynamic_mi |
Mutual Information (MI) function applied to rotamers in molecular dynamics simulations |
dynamic_mip |
Mutual Information Product (MIP) function applied to rotamers in molecular dynamics simulations |
dynamic_omes |
OMES (Observed minus Expected Squared) function applied to rotamers in molecular dynamics simulations |
dynamic_structure |
Creates the data structure for the analysis of side chain dihedral angles |
elsc |
Explicit Likelihood of Subset Covariation (ELSC) function |
entropy |
Entropy score |
import.fasta |
Reads a file in FASTA format |
import.msf |
Reads a multiple sequence alignment file in MSF format |
mcbasc |
McBASC (McLachlan Based Substitution Correlation) function |
mi |
Mutual Information (MI) function |
mip |
Mutual Information product (MIP) function |
network.plot |
Creates network structure of top elements |
omes |
OMES (Observed minus Expected Squared) function |
pca_2d |
PCA projection on two dimensions |
pca_screeplot |
Creates PCA screeplot |
random.msa |
Random Alignment |
scores.boxplot |
Creates boxplots of correlation/covariation scores |
scores_entropy.plot |
Scores versus entropy graph |
top_pairs_analysis |
Calculates the number of contacts for each element of the top pairs |
write.entropy |
Writes and displays entropy values |
write.pca |
Creates a file of coordinates in PCA space |
write.pca.pdb |
PDB and PML file creation for 3D representation of PCA analysis |
write.scores |
Creates a correlation/covariation ouput file |
xyz2torsion |
Convert Cartesian Coordinates to Torsion Angles |