{
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        "author": "Biobb developers",
        "author_email": "josep.gelpi@bsc.es",
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        "classifiers": [
            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 3.6"
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        "description": "[![Codacy Badge](https://api.codacy.com/project/badge/Grade/376891e43cab4cc591fb78ea43dfd380)](https://www.codacy.com/app/jlgelpi/structureChecking?utm_source=mmb.irbbarcelona.org&utm_medium=referral&utm_content=gitlab/BioExcel/structureChecking&utm_campaign=Badge_Grade)\n# Structure Checking from MDWeb\n\ncheck_structure performs MDWeb structure checking set as a command line\nutility.\n\nIt includes some structure manipulation options like selecting models or chains,\nremoving components of the system, completing missing atoms, and some quality\nchecking as residue quirality, amide orientation, or vdw clashes.\n\n```\nusage: checkStruc.py [-h] [-i INPUT_STRUCTURE_PATH] [-o OUTPUT_STRUCTURE_PATH]\n                     [--version] [--data_dir DATA_DIR]\n                     [--res_lib RES_LIB_PATH] [--data_lib DATA_LIBRARY_PATH]\n                     [--json JSON_OUTPUT_PATH] [--quiet] [--check_only]\n                     [--non_interactive] [--force_save]\n                     [--pdb_server PDB_SERVER]\n                     command ...\npositional arguments:\n  command               Command to execute (help: checkStruc commands)\n  options               Specific command options\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -i INPUT_STRUCTURE_PATH, --input INPUT_STRUCTURE_PATH\n                        Input structure. Formats PDB|mmCIF. Remote pdb:{pdbid}\n  -o OUTPUT_STRUCTURE_PATH, --output OUTPUT_STRUCTURE_PATH\n                        Output structure. Format PDB\n  --version             show program's version number and exit\n  --data_dir DATA_DIR   Override settings default data dir\n  --res_lib RES_LIB_PATH\n                        Override settings default residue library (AMBER prep\n                        format)\n  --data_lib DATA_LIBRARY_PATH\n                        Override settings default data library\n  --json JSON_OUTPUT_PATH\n                        Cummulated checking results on a json file\n  --quiet               Reduces output, removing labels and progress info\n  --check_only          Perform checks, structure is not modified\n  --non_interactive     Do not prompt for missing parameters\n  --force_save          Force saving an output file even if no modification\n  --pdb_server PDB_SERVER\n                        Server for retrieving structures (default: RCSB|mmb)\n  --load                Loads structure from PDB server into the local cache\n  --stats               Loads structure and get basic statistics and headers\n\nAvailable commands:\n\n```\n\n## Available commands:\n\n```\ncommands:  This help\ncommand_list:      Run all tests from conf file\ncheckall:   Perform all checks without fixes\nload: Stores structure on local cache and provide basic statistics\n\n1. System Configuration\n=======================\nmodels [--select_model model_num]     \n    Detect/Select Models\nchains [--select_chains chain_ids]    \n    Detect/Select Chains\ninscodes\n    Detects residues with insertion codes (no fix)\naltloc [--select_altloc occupancy| alt_id | list of res_id:alt_id]\n    Detect/Select Alternative Locations\nmetals [--remove All | None | Met_ids_list | Residue_list]   \n    Detect/Remove Metals\nligands [--remove All | None | Res_type_list | Residue_list]\n    Detect/Remove Ligands\nremwat [--remove Yes|No]\n    Remove Water molecules\nremh [remh --remove Yes|No]\n    Remove Hydrogen atoms from structure\nmutateside [--mut mutation_list]\n    Mutate side chain with minimal atom replacement. Allows multiple mutations\naddH [--mode auto | pH | interactive | interactive_his]\n    Add Hydrogen Atoms\n\n2. Fix Structure Errors\n\namide  [--fix All|None|Residue List]    \n    Detect/Fix Amide atoms Assignment\nchiral [--fix All|None|Residue List]\n    Detect/Fix Improper quirality\nfixside [--fix All |None|Residue List]    \n    Complete side chains\nbackbone [--fix All|None|Residue List]   \n    Analyze main chain missing atoms and fragments. O, OXT atoms can be fixed\n\n3. Structure Warnings\n\ncistransbck Analyzes cis-trans dihedrals on backbone atoms\ngetss      Detect SS Bonds\nclashes    Steric clashes (Severe, Apolar, Polar Donors, Polar Acceptors,\n           Ionic Positive, Ionic Negative)\n\n```\n### Dependencies\n* python 3.x\n* biopython\n* numpy\n* biobb_model (structure_manager)\n\n\n",
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