TODO

1. System Selection
    1.1. Detect/Select Models (models) DONE
        1.1.1 Consider multiple DONE
        1.1.2 Save split collection DONE
        1.1.3 Superimpose models DONE
        1.1.4 Build complex from biounit models DONE
    1.2. Detect/Select Chains (chains) DONE
        1.2.1 Detect mixed NA/protein chains
        1.2.2 Rebuild/fix chains DONE
        1.2.3 Select chains according to molecule type DONE
        1.2.4 Renumber chains & Residues DONE
    1.3. Detect/Select Alt Locations (altloc) DONE
    1.4. Detect Heavy Metals /Remove (metals) DONE
    1.5. Detect Ligands /Remove (ligands) DONE
        1.5.1 Process All Hetatms in a integrated way
        1.5.2 Detect modified amino acids (identidy and guess original residue)
    1.6. Detect DNA/RNA /Remove (na) DONE in chains
        1.6.1 Include NA Topology WITHDRAWN Too much adaptation needed, use BNSTopology instead
    1.7. Remove Water (remwat) DONE
        1.7.1 Remove Water molecules following interactions DONE
    1.8. Remove Hydrogen atoms (remh) DONE
    1.9. Get Sequences DONE
        1.9.1 Get sequence from PDB without canonical DONE
        1.9.2 Output FASTA file DONE

2. Fix Structure Errors/Modification
    2.1. Detect/Fix Amides Assignment (amide) DONE
        2.1.1 Amides Automatic fix DONE
    2.2. Detect/Fix Improper quirality (chiral) DONE (!! check ILE with unusual atom labels)
        2.2.1 Detect Improper quirality on CAs (chiral_ca) DONE
    2.3. Detect insertion codes/Renum (inscode) DONE
        2.3.1 Rebuild chains with proper numbering DONE
    2.4. Complete side chains (fixside) DONE
        2.4.1 Rebuild side chains (using modeller) DONE for protein
    2.5. Mutate residues (mutate) DONE
        2.5.1 Add/remove/revert modified residues
        2.5.2 Mutate DNA residues DONE
            2.5.2.1 Mutate DNA following sequence DONE
            2.5.2.2 Extend to RNA DONE
    2.6. Add hydrogens (add_hydrogens) DONE
        2.6.1 Determine protonation from environment (Hbond network, metals)
        2.6.2 Consider -SSDD- DONE
        2.6.3 PDBQT|PQR|CMIP formats DONE
        2.5.6 Consider Cap residues DONE
        2.6.4 Add hydrogens for NA chains DONE
        2.6.5 Prepare input for AutoDock with flexible residues
        2.6.6 Add Metals to residue library
    2.7. Complete backbone (backbone) DONE
        2.7.1 Complete main chains DONE
        2.7.2 Add ACE, NME caps DONE
        2.7.3 Use standard FASTA for sequence input (check uniprot and pdb Fasta's) DONE
        2.7.4 Accept/recognize GROMACS (and other non Amber) Atom names OT?
        2.7.5 Accept multiple templates
        2.7.6 Fix modelled junctions
        2.7.8 Rebuild backbone in the context of the complete molecule (also for --rebuild options)
	2.7.9 Detect and fix extra backbone atoms (like extra OXT)
    2.8 FixALL module
        - Model and Chain selected on demand
        - AltLoc to occupancy
        - Inscodes renumber chain
        - Remove ligands on demand
        - Select and Remove water molecules
        - Add hydrogens
        - Fix Amides auto
        - Fix Side Chains
        - Rebuild Side Chains (Chirality/clashes)
        - Fix Backbone (chain / missing atoms / Caps)
        - Mark SS
3. Structure Warnings
    3.1. Detect SS Bonds (getss) DONE
        3.1.1 Mark Cys in SS Bonds as CYX DONE
        3.1.2 Detect Cys-Metal bonds
    3.2. Unusual cis/trans backbone (cisbck) DONE
    3.3. Non Consecutive residues (backbone) DONE
    3.4. Possible Sequence Gaps (bckbone) DONE
        3.4.1 Fix only-CA structures (Modeller)
    3.5. Steric clashes (clashes) DONE
        3.5.1. Severe Steric clashes DONE Revise new severe clashes
        3.5.2. CA Steric Clashes NO
        3.5.3. Polar Donor Clashes DONE
        3.5.4. Polar Acceptor Clashes DONE
        3.5.5. Apolar Clashes DONE
        3.5.6. Ionic Positive Clashes DONE
        3.5.7. Ionic Negative Clashes DONE
4. Prepare alternative main scripts for specific functions
    4.1 Check only
    4.2 Prepare autodock input
    4.3 Prepare CMIP input WITHDRAWN (DONE in 2.6.3)
    4.4 Convert from MD formats DONE using --output_format
    4.5 Advanced stats including globularity, assymetric vs assembly
5. General
    5.1. Generate PDB Metadata
    5.2. Generate CIF output files DONE
    5.3. Study the use on command line pipelines
    5.4. Accept GZIP files transparently DONE

Bugs & Needed fixes
- Remove Warning about default download
- Reorganize --time_limit as it is checked after the work is done
- Reorganize --limit to avoid Biopython loading DONE