Biobb-structure-checking

Bug Fixes
- Remove pinned numpy dependency

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Bug Fixes
- Fixed tests
- Fixed behaviour with --non_interactive and missing command options


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Extended functions

- Jupyter Notebook support extended
- Help(command) function
- Settings accepted also as Python dictionaries-

- add_hydrogen
- Added support for multiple atom type sets (currently ADP, CMIP)
- Added support for pqr, pdbqt, cmip output formats following file extension
- Added support for pqr input format
- Terminal residue names available on 3 or 4 letter (N-, C-) codes

- command_list
- Added support for inline command lists

- mutationside
- Added support for RNA mutations
Bug Fixes
- Fix charge assignment for modified residues and terminals
- Fixed wrong assigment of RNA residues as protein
- Fixed tests
- Fixed behaviour with --non_interactive and missing command options

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New functions
- sequences
- prints both canonical and structural sequences (protein or NA).

Extended functions
- mutateside
- added support for mutation of DNA/RNA residues
- --na_seq allows to set a desired final sequence in a single operation (for DNA duplexes)
- chains
- allows to select chains according to molecular type (protein | dna | rna | na).
- Improved guess of chain type.
- getss
- can now mark CYS residues as part of SSBonds. Further commands like add_hydrogen reacts accordingly
- load
- can now be used to convert downloaded cif to pdb format using --force_save
- Modeller based commands
- adapted to support Modeller >= 10.1
- several commands
- adapted to work with NA chains

- Extended support for verbosity
- Default verbosity has been reduced to errors and warnigs
- --nv --quiet removes all progress reports
- -v adds extra progress report (original default)

Bugs fixed
- clashes, add_hydrogen did not work for modified or cap residues
- mutateside crashed when trying to delete already modified atoms
- added error message when chains will remove all chains in the structure
- added error message when mutateside has no available mutations

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Extended functionality
- Added support for biopython 1.78

Bugs fixed
- backbone
- added error messages for incorrect or missing FASTA sequences
- backbone reconstruction crashed when not all chains sequences were available even if missing chains where not needed

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New functions
- --rename_terms
- Rename N and C terms as NXXX, CXXX

Extended functions:
- mutateside & fixside --rebuild
- Use Modeller for building the side chains, include conformational search
- backbone --extra_gap
- Allows to use more residues from the built model to fill backbone breaks (experimental)
- add_hydrogen --add_charges
- Adds point charges to atoms and produces a PDBQT output suitable for autodock

Bug fixes
- --debug
- Psutils import failed even when --debug was not requested
- backbone
- Residue internal pointers corrupted when backbone was modified