Complete contents tree

• Introduction
• System setup
  • Dependencies
  • Optional Add-ons
  • Installation
• User guide
  • Before you start
  • Getting started
    • 1. Create an alignment file
    • 2. Calculating structural properties and plotting them
    • 3. Using the PyMOL interface
    • 4. Creating Jalview Feature files
  • Example outputs
    • Example PyMol API output
    • CDK2 Analysis
      • CDK2 Ramachandran
      • CDK2 Clustering
  • Source Code Docs
    • Scripts
      • polyphony_Ete2_tree.py
      • polyphony_PCA_plot.py
      • polyphony_calculate_all_properties.py
      • polyphony_cluster_backbones_by_PCA_loadings.py
      • polyphony_create_fasta_file.py
      • polyphony_druggable_pockets.py
      • polyphony_get_non_redundant_structures.py
      • polyphony_get_representative_structures.py
      • polyphony_get_unique_structures.py
      • polyphony_plot_Ramachandran.py
      • polyphony_plot_backbone_variation.py
      • polyphony_plot_property.py
      • polyphony_plot_property_slice.py
      • polyphony_plot_rmsd.py
      • polyphony_plot_rmsf.py
      • polyphony_plot_variability.py
      • polyphony_print_structure_report.py
      • polyphony_within_cluster_variability.py
      • polyphony_write_jalview_feature_file.py
      • polyphony_write_jalview_feature_from_PCA.py
      • polyphony_write_newick.py
    • Source Code Docs
      • Backbone
      • Bfactors
      • Comparison_Matrices
      • Contacts
      • Piccolo
      • Fpocket
      • Jalview
      • Phipsi
      • Pymol
      • Sidechains
      • Stats
      • Structural_Alignment
      • Utils
      • Trees
      • Prepare_Fasta_File
      • Plotting
      • Property_Arrays
      • Residues
      • polyphony.cfg
• To do list
• Licence (GPL)