Biobb-structure-checking

Bug Fixes
- backbone
- Fixed interactive behaviour when missing sequences
- mutateside
- Fixed bug. Mutated residue was deleted when using --rebuild

Extended functions
- input
- Added assembly download from wwpdb.
- Added --overwrite_cache to refresh cached structures.
- improved recognition of CA-only structures.
- Added automated sequence download for retrieved structure in PDB format
- --sequence accepts remote download as pdb:{pdb_id}
- Added remote downloads (structure and sequence) from plain URL's (http(s) only).
- output
- Added optional logging of building errors (as --build-warnings).
- Improved phrasing for some log errors.
- run_time
- Atom limit check made after download to avoid useless work.
- Added --time_limit to avoid too lengthy runs. Useful on massive analysis.
- add_hydrogen
- Full list of residues now requires --verbose.
Deprecated
- input
- Use of alternative pdb servers (--pdb_servers) for biounits/assemblies. Command-line parameter retained for back-compatibility.
Bug Fixes
- input
- Default download moved to https (instead of ftp) to avoid detected network restrictions.
- sequences.
- Fixed errors in sequence recognition when non-protein and non-na chain.
- Fixed FASTA headers when no gaps.
- models/chains/sequences. Fixed errors when differences in chain composition among models. All models are now analyzed as independent entities.
- Added error message when --rebuild is applied to N term residue. Fix pending.

Extended functions
- amide
- Added --fix auto option to automatically find best fix combination.
- chains
- Added --rename. fixes empty chain labels.
- Added --renumber. allow to renumber/reorganize chains and residues.
- Added --rem_inscodes. removes insertion codes on renumbering.
- Added --rebuild. rebuild chains labels and residue ids from backbone connectivity.
- inscodes
- Added --renumber. Rebuild residue numbering to remove insertion codes.
- models
- Added --build_complex. Converts biounit's selected models into actual complexes.
- sequences
- Added --output_fasta. Writes sequences found in an external FASTA file.
- json
- Extended information on json summary output.
- input format
- File format for remote download can be defined using extension as in pdb:2ki5.pdb
- output format
- Added mmCif output (only atom records).
- input management
- Added --nocache to avoid caching downloaded structures.
- Added --copy_input to recover a copy of the input structure.
- Added --coords_only to discard chain labels and residue ids from input. Used to revover faulty structure files.
Bug Fixes
- Added missing defaults for Notebook execution.
- Ionized/tautomeric residue names recognized.
- Fixed behaviour of structure headers output with missing entries.

Extended functions
- Structure details
- Added hydrogen atoms count
- Input files
- Support for PQR format
- backbone, sequences
- Input Sequences are automatically assigned to the appropriate chain. No special requirements for FASTA headers
- add_hydrogen
- Extended to support Nucleic Acids
- sequences
- Structure sequence is always reported even in the absence of canonical one
- chains
- Unlabelled chains can be fixed.
Bug Fixes
- Fixed banner format
- Fixed residue id on metals output
- Removed required usage N and C terms 4-letter residue names except of requested output

New Functions
- Support for PDBQT files
- add_hydrogen
- Multiple charge sets accepted (currently ADP, CMIP)

New Functions

Extended functions
- Adding new option --keep_canonical_resnames to revert output to canonical residue names when modified by any operation.

- models
- Select multiple models
- Superimpose current models
- Output models as multiple PDB files

Bug Fixes

- add_hydrogen
- Extended to Nucleic Acids
- added option to keep canonical residue names
Bug Fixes
- add_hydrogen
- Forced upper case for FF names