recipe biobb_structure_checking

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

Homepage

https://github.com/bioexcel/biobb_analysis

License

APACHE / Apache Software License

Recipe

/biobb_structure_checking/meta.yaml

[![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) # 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: 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

  1. 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

  1. 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 * biobb_model (structure_manager)

package biobb_structure_checking

(downloads) docker_biobb_structure_checking

Versions

3.0.2-0, 3.0.1-0, 3.0.0-0, 1.0.7-0, 1.0.6-0, 1.0.5-0, 0.0.1-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install biobb_structure_checking

and update with:

conda update biobb_structure_checking

or use the docker container:

docker pull quay.io/biocontainers/biobb_structure_checking:<tag>

(see biobb_structure_checking/tags for valid values for <tag>)