BioBB IO Command Line Help

Generic usage:

biobb_command [-h] [-c CONFIG] --in_file <in_file>  --out_file <out_file>

ligand

This class is a wrapper for the MMB PDB mirror (http://mmb.irbbarcelona.org/api/)

Get help

ligand -h
usage: ligand.py [-h] [-c CONFIG] -o OUTPUT_PDB_PATH

Wrapper for the PDB ('http://www.rcsb.org/pdb/home/home.do') mirror of the MMB group REST API ('http://mmb.irbbarcelona.org/api/') for additional help in the commandline usage please check ('https://biobb-io.readthedocs.io/en/latest/command_line.html')

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -o OUTPUT_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH
                        Path to the output PDB ligand file.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_pdb_path (str): Path to the output PDB ligand file. File type: output. Sample file. Accepted formats: pdb.

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • ligand_code (str) - (“12D”) RSCB PDB ligand code. ie: “12D”
  • remove_tmp (bool) - (True) [WF property] Remove temporal files.
  • restart (bool) - (False) [WF property] Do not execute if output files exist.

Default config

ligand -o 12D.pdb

YAML

File config

properties:
  ligand_code: 12D
ligand -c conf.yml -o 12D.pdb

JSON

String config

pdb -c '{"ligand_code":"12D"}' -o 12D.pdb

File config

{
  "properties": {
    "ligand_code":"12D"
  }
}
ligand -c conf.json -o 12D.pdb

pdb

Download PDB files from RCSB PDB API

Get help

pdb -h
usage: pdb.py [-h] [-c CONFIG] -o OUTPUT_PDB_PATH

Wrapper for the PDB ('http://www.rcsb.org/pdb/home/home.do') mirror of the MMB group REST API ('http://mmb.irbbarcelona.org/api/') for additional help in the commandline usage please check ('https://biobb-io.readthedocs.io/en/latest/command_line.html')

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -o OUTPUT_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH
                        Output file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_pdb_path (str): Path to the output PDB file. File type: output. Sample file. Accepted formats: pdb.

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (str) - (‘1ubq’) RSCB PDB code. ie: “2VGB”
  • filter (str) - ([“ATOM”, “MODEL”, “ENDMDL”]) Array of groups to be kept. If value is None or False no filter will be applied. All the possible values are defined in the official PDB specification (http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)
  • url (str) - (“https://files.rcsb.org/download/”) URL of the PDB REST API. Another option for this parameter is the MMB PDB mirror API (“http://mmb.irbbarcelona.org/api/pdb/”)
  • remove_tmp (bool) - (True) [WF property] Remove temporal files.
  • restart (bool) - (False) [WF property] Do not execute if output files exist.

Default config

pdb -o 1aki.pdb

YAML

File config

properties:
  pdb_code: 1aki
  filter: ["ATOM"]
pdb -c conf.yml -o 1aki.pdb

JSON

String config

pdb -c '{"pdb_code":"1aki", "filter":["ATOM"]}' -o 1aki.pdb

File config

{
  "properties": {
    "pdb_code":"1aki", 
    "filter":["ATOM"]
  }
}
pdb -c conf.json -o 1aki.pdb

pdb_variants

Retrieve variants from UNIPROT mapped to the selected PDB

Get help

pdb_variants -h
usage: pdb_variants.py [-h] [-c CONFIG] -o OUTPUT_MUTATIONS_LIST_TXT

Wrapper for the PDB Variants (http://www.rcsb.org/pdb/home/home.do) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for additional help in the commandline usage please check ('https://biobb-io.readthedocs.io/en/latest/command_line.html')

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -o OUTPUT_MUTATIONS_LIST_TXT, --output_mutations_list_txt OUTPUT_MUTATIONS_LIST_TXT
                        Output variants list text file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_mutations_list_txt (str): Path to the TXT file containing an ASCII comma separated values of the mutations. File type: output. Accepted formats: txt.

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (str): (“2vgb”) RSCB PDB four letter code. ie: “2ki5”.
  • url (str) - (“https://files.rcsb.org/download/”) URL of the PDB REST API. Another option for this parameter is the MMB PDB mirror API (“http://mmb.irbbarcelona.org/api/pdb/”).
  • remove_tmp (bool) - (True) [WF property] Remove temporal files.
  • restart (bool) - (False) [WF property] Do not execute if output files exist.

Default config

pdb_variants -o mutations.txt

YAML

File config

properties:
  pdb_code: 2src
pdb_variants -c conf.yml -o mutations.txt

JSON

String config

pdb_variants -c '{"pdb_code":"2src"}' -o mutations.txt

File config

{
  "properties": {
    "pdb_code":"2src"
  }
}
pdb_variants -c conf.json -o mutations.txt

pdb_cluster_zip

Download the selected similarity cluster of the selected PDB

Get help

pdb_cluster_zip -h
usage: pdb_cluster_zip.py [-h] [-c CONFIG] -o OUTPUT_PDB_ZIP_PATH

Wrapper for the PDB Cluster (http://www.rcsb.org/pdb/home/home.do) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for additional help in the commandline usage please check ('https://biobb-io.readthedocs.io/en/latest/command_line.html')

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -o OUTPUT_PDB_ZIP_PATH, --output_pdb_zip_path OUTPUT_PDB_ZIP_PATH
                        Output ZIP file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_pdb_zip_path (str): Path to the ZIP or PDB file containing the output PDB files. File type: output. Sample file. Accepted formats: pdb, zip.

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (str) - (‘2vgb’) RSCB PDB code. ie: “2VGB”
  • filter (str) - ([“ATOM”, “MODEL”, “ENDMDL”]) Array of groups to be kept. If value is None or False no filter will be applied. All the possible values are defined in the official PDB specification (http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)
  • cluster (str) - (90) Cluster number for the :meth:biobb_io.api.MmbPdb.get_pdb_cluster_zip method.
  • url (str) - (“https://files.rcsb.org/download/”) URL of the PDB REST API. Another option for this parameter is the MMB PDB mirror API (“http://mmb.irbbarcelona.org/api/pdb/”).
  • remove_tmp (bool) - (True) [WF property] Remove temporal files.
  • restart (bool) - (False) [WF property] Do not execute if output files exist.

Default config

pdb_cluster_zip -o 2vgb_cluster90.zip

YAML

File config

properties:
  pdb_code: 2src
  cluster: 95
pdb_cluster_zip -c conf.yml -o 2src_cluster95.zip

JSON

String config

pdb_cluster_zip -c '{"pdb_code":"2src", "cluster":95}' -o 2src_cluster95.zip

File config

{
  "properties": {
    "pdb_code":"2src", 
    "cluster":95
  }
}
pdb_cluster_zip -c conf.json -o 2src_cluster95.zip