# MD Analysis of Residue Properties Using Structural Alphabets

## Documentation for package ‘MDaRes’ version 0.0.2

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

add_active_site | Retrieve and Format Active Site Annotations from UniProt
add_binding_site | Retrieve and Format Ligand Binding Site Annotations from UniProt
add_disulfide_bond | Retrieve and Format Disulfide Bond Annotations from UniProt
add_domain | Retrieve and Format Domain Annotations from UniProt
add_glycosilation | Retrieve and Format Glycosylation Annotations from UniProt
add_lipidation | Retrieve and Format Lipidation Annotations from UniProt
add_location | Retrieve and Format Location Annotations from UniProt
add_modified_residue | Retrieve and Format Modified Residue Annotations from UniProt
add_molecule_processing | Retrieve and Format Molecule Processing Annotations from UniProt
add_motive | Retrieve and Format Motif Annotations from UniProt
add_secondary_structure | Retrieve and Format Secondary Structure Annotations from UniProt
add_uniprot_annotation | Retrieve and Merge UniProt Annotations
add_variants | Retrieve and Format Protein Variants from UniProt
colnames_substring | Extract Substring from Column Names
create_annotation_df | Retrieve UniProt Protein Sequence and Format as Dataframe
do_freq_diff_plot | Save frequency-difference plot to PNG
do_freq_plot | Generate Frequency Profile Plot and Save to PNG
do_MI_plot | Generate Mutual Information Matrix Plot and Save to PNG
do_shannon_entropy_diff_plot | Save Shannon Entropy Difference Plot to PNG
do_shannon_entropy_plot | Generate Shannon Entropy Plot and Save to PNG
entropy_visualization | Visualize Shannon Entropy on a Protein Structure
freq_diff_plot | Plot Structural Frequency Differences
freq_plot | Plot Frequency Profile
get_res_numbering | Retrieve Residue Numbering from Encoded Trajectory
import_SA | Import Structural Alphabet from PDB Files
MImat | Compute Mutual Information Matrix
MI_plot | Plot Mutual Information Matrix
MI_ranking_couple | Rank Residues Based on Mutual Information
MI_ranking_median | Rank Mutual Information by Median and Collectivity
nMImat | Compute Normalized Mutual Information Matrix
SA_encoding | Encode an MD Trajectory Using a Structural Alphabet (C++ backend)
shannon_entropy | Compute Shannon Entropy and Frequency Distribution
shannon_entropy_diff_plot | Plot Shannon Entropy Difference
shannon_entropy_plot | Plot Shannon Entropy
shannon_ranking | Rank Fragments by Shannon Entropy
total_ranking | Merge Shannon Entropy and MI Rankings