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This wiki is to be used for notes relating to the development of cath-tools.

cath-tools users are more likely to be interested in the documentation at Read the Docs.

Pages

• cath-map-clusters
• cath-resolve-hits
• cath-superpose
• Cluster Tool Notes
• Development

Short-term TODO

• Make the error for running cath-ssap in / less ugly (warn and write alignment to /tmp)
• Add dividers in cath-superpose and cath-refine-align options usage string.
• In cath-map-clusters, sort out the very slow cluster_domains::add_domain in seq_domains.insert(...).
• Commit complete-linkage cluster code.
• Add a complete-linkage clustering executable.
• Complete #2, by exposing option.
• Expose refining options (aln_glue_style)
• Add options for superposing on specified residues (Tolu)
• #49 ("Some pairs fail under cath-ssap that work with SSAP")
• #50 ("Some cath-ssaps work with --prot-src-files of PDB_DSSP but not PDB")
• Eradicate many using namespaces from the code