bioconda / packages / biobb_structure_checking 3.0.2

BioBB_structure_checking performs MDWeb structure checking set as a command line utility.

Installers

conda install

  • noarch  v3.0.2
To install this package with conda run:
conda install -c bioconda biobb_structure_checking

Description

Codacy Badge removing components of the system, completing missing atoms, and some quality checking as residue quirality, amide orientation, or vdw clashes.

usage: checkStruc.py [-h] [-i INPUT_STRUCTURE_PATH] [-o OUTPUT_STRUCTURE_PATH]
                     [--version] [--data_dir DATA_DIR]
                     [--res_lib RES_LIB_PATH] [--data_lib DATA_LIBRARY_PATH]
                     [--json JSON_OUTPUT_PATH] [--quiet] [--check_only]
                     [--non_interactive] [--force_save]
                     [--pdb_server PDB_SERVER]
                     command ...
positional arguments:
  command               Command to execute (help: checkStruc 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}
  -o OUTPUT_STRUCTURE_PATH, --output OUTPUT_STRUCTURE_PATH
                        Output structure. Format PDB
  --version             show program's version number and exit
  --data_dir DATA_DIR   Override settings default data dir
  --res_lib RES_LIB_PATH
                        Override settings default residue library (AMBER prep
                        format)
  --data_lib DATA_LIBRARY_PATH
                        Override settings default data library
  --json JSON_OUTPUT_PATH
                        Cummulated checking results on a json file
  --quiet               Reduces output, removing labels and progress info
  --check_only          Perform checks, structure is not modified
  --non_interactive     Do not prompt for missing parameters
  --force_save          Force saving an output file even if no modification
  --pdb_server PDB_SERVER
                        Server for retrieving structures (default: RCSB|mmb)
  --load                Loads structure from PDB server into the local cache
  --stats               Loads structure and get basic statistics and headers

Available commands:

Available commands:

commands:  This help
command_list:      Run all tests from conf file
checkall:   Perform all checks without fixes
load: Stores structure on local cache and provide basic statistics

1. System Configuration
=======================
models [--select_model model_num]     
    Detect/Select Models
chains [--select_chains chain_ids]    
    Detect/Select Chains
inscodes
    Detects residues with insertion codes (no fix)
altloc [--select_altloc 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
remwat [--remove Yes|No]
    Remove Water molecules
remh [remh --remove Yes|No]
    Remove Hydrogen atoms from structure
mutateside [--mut mutation_list]
    Mutate side chain with minimal atom replacement. Allows multiple mutations
addH [--mode auto | pH | interactive | interactive_his]
    Add Hydrogen Atoms

2. Fix Structure Errors

amide  [--fix All|None|Residue List]    
    Detect/Fix Amide atoms Assignment
chiral [--fix All|None|Residue List]
    Detect/Fix Improper quirality
fixside [--fix All |None|Residue List]    
    Complete side chains
backbone [--fix All|None|Residue List]   
    Analyze main chain missing atoms and fragments. O, OXT atoms can be fixed

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.x
  • biopython
  • numpy
  • biobbmodel (structuremanager)
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