Metadata-Version: 2.1
Name: biobb-structure-checking
Version: 3.0.0
Summary: BioBB_structure_checking performs MDWeb structure checking tool set as a command line utility.
Home-page: https://github.com/bioexcel/biobb_structure_checking
Author: Biobb developers
Author-email: josep.gelpi@bsc.es
License: UNKNOWN
Project-URL: Documentation, http://BioBB_structure_checking.readthedocs.io/en/latest/
Project-URL: Bioexcel, https://bioexcel.eu/
Description: [![Codacy Badge](https://api.codacy.com/project/badge/Grade/376891e43cab4cc591fb78ea43dfd380)](https://www.codacy.com/app/jlgelpi/structureChecking?utm_source=mmb.irbbarcelona.org&amp;utm_medium=referral&amp;utm_content=gitlab/BioExcel/structureChecking&amp;utm_campaign=Badge_Grade)
        # Structure Checking from MDWeb
        
        check_structure performs MDWeb structure checking set as a command line
        utility.
        
        It includes some structure manipulation options like selecting models or chains,
        removing components of the system, completing missing atoms, and some quality
        checking as residue quirality, amide orientation, or vdw clashes.
        ```
        usage: check_structure [-h] [-i INPUT_STRUCTURE_PATH]
                               [--file_format FILE_FORMAT] [--sequence FASTA_SEQ_PATH]
                               [--pdb_server PDB_SERVER] [--cache_dir CACHE_DIR_PATH]
                               [--res_lib RES_LIBRARY_PATH]
                               [--data_lib DATA_LIBRARY_PATH]
                               [-o OUTPUT_STRUCTURE_PATH] [--json JSON_OUTPUT_PATH]
                               [--quiet] [--limit ATOM_LIMIT] [--debug] [--force_save]
                               [--check_only] [--non_interactive] [--version]
                               command ...
        
        
        positional arguments:
          command               Command to execute (help: check_structure commands)
          options               Specific command options
        
        optional arguments:
          -h, --help            show this help message and exit
          -i INPUT_STRUCTURE_PATH, --input INPUT_STRUCTURE_PATH Input structure. Formats PDB|mmCIF. Remote pdb:{pdbid}.
                                Biounits pdb:{pdbid}.{bn}. Biounits require MMB server
          -o OUTPUT_STRUCTURE_PATH, --output OUTPUT_STRUCTURE_PATH
                                Output structure. PDB Format
          --json JSON_OUTPUT_PATH
                                Summary activities on a json file
          --file_format FILE_FORMAT
                                Format for retrieving structures (default=mmCif|pdb|xml)
          --sequence FASTA_SEQ_PATH
                                Canonical sequence in FASTA format, pdb_chain[,chain] in header
          --pdb_server PDB_SERVER
                                Remote server for retrieving structures (default|MMB)
          --cache_dir CACHE_DIR_PATH
                                Path for structure's cache directory (default: ./tmpPDB)
          --res_lib RES_LIBRARY_PATH
                                Override settings default residue library (AMBER prep format)
          --data_lib DATA_LIBRARY_PATH
                                Override settings default data library
          --quiet               Reduces output, removing labels and progress info
          --limit ATOM_LIMIT    Limit on number of atoms, 0: nolimit
          --debug               Add debug information
          --force_save          Force saving an output file even if no modification
          --check_only          Perform checks only, structure is not modified
          --non_interactive     Do not prompt for missing parameters
          --version             show program's version number and exit
        ```
        
        ## Available commands:
        
        ```
        commands:     Help on available commands
        command_list: Run all tests from conf file
        checkall:     Perform all checks without fixes
        fixall:       Performs a default fix (v1.2)
        load:         Stores structure on local cache and provide basic statistics
        
        1. System Configuration
        =======================
        models [--select model_num]
            Detect/Select Models
        chains [--select chain_ids]
            Detect/Select Chains
        inscodes [--renum]
            Detects residues with insertion codes. No fix provided.
        altloc [--select occupancy| alt_id | list of res_id:alt_id]
            Detect/Select Alternative Locations
        metals [--remove All | None | Met_ids_list | Residue_list]
            Detect/Remove Metals
        ligands [--remove All | None | Res_type_list | Residue_list]
            Detect/Remove Ligands
        water [--remove Yes|No]
            Remove Water molecules
        rem_hydrogen [--remove Yes|No]
            Remove Hydrogen atoms from structure
        mutateside [--mut mutation_list] [--no_check_clashes]
            Mutate side chain with minimal atom replacement. Allows multiple mutations.
            Check generated clashes except --no_check_clashes set
        add_hydrogen [--add_mode auto | pH | list | interactive | interactive_his] [--no_fix_side] [--keep_h]
            Add Hydrogen Atoms. Auto: std changes at pH 7.0. His->Hie. pH: set pH value
            list: Explicit list as [*:]HisXXHid, Interactive[_his]: Prompts for all selectable residues
            Fixes missing side chain atoms unless --no_fix_side is set
            Existing hydrogen atoms are remove before adding new ones unless --keep_h set.
        
        2. Fix Structure Errors
        
        amide  [--fix All|None|Residue List] [--no_recheck]
            Detect/Fix Amide atoms Assignment
            Amide contacts are recheck unless --no_recheck
        chiral [--fix All|None|Residue List] [--no_check_clashes]
            Detect/Fix Improper quirality
            Checks generated clashes unless --no_check_clashes set
        fixside [--fix All |None|Residue List] [--no_check_clashes]
            Complete side chains
            Checks generated clashes unless --no_check_clashes set
        backbone [--fix_atoms All|None|Residue List]
                 [--fix_main All|None|Break list]
                 [--add_caps All|None|Break list]
                 [--no_recheck]
                 [--no_check_clashes]
            Analyze main chain missing atoms and fragments.
            --fix_atoms O, OXT atoms can be fixed
            --fix_main Missing fragments filled using comparative modelling (Modeller License needed)
            --add_caps Adds ACE and NME residues as necessary, preserving existing atoms
            Rechecks beckbone on each op unless --no_recheck is set.
            Generated clashes are checked unless --no_check_clashes
        
        3. Structure Warnings
        
        cistransbck Analyzes cis-trans dihedrals on backbone atoms
        getss      Detect SS Bonds
        clashes    Steric clashes (Severe, Apolar, Polar Donors, Polar Acceptors,
                   Ionic Positive, Ionic Negative)
        ```
        ### Dependencies
        * python 3.7
        * biopython 1.76
        * numpy
        * biobb_structure_manager 3.0.0
        * modeller 9.23 (optional)
        
Keywords: Bioinformatics Workflows BioExcel Compatibility
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Requires-Python: ==3.7.*
Description-Content-Type: text/markdown
