BioBB IO Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

Canonical_fasta

This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.

Get help

Command:

canonical_fasta -h
usage: canonical_fasta [-h] [-c CONFIG] -o OUTPUT_FASTA_PATH

This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.

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_FASTA_PATH, --output_fasta_path OUTPUT_FASTA_PATH
                        Path to the canonical FASTA file. Accepted formats: fasta.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_fasta_path (string): Path to the canonical FASTA file. File type: output. Sample file. Accepted formats: FASTA

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (string): (None) RSCB PDB code..
  • api_id (string): (pdbe) Identifier of the PDB REST API from which the PDB structure will be downloaded. .
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  api_id: pdbe
  pdb_code: 4i23

Command line

canonical_fasta --config config_canonical_fasta.yml --output_fasta_path canonical_fasta.fasta

JSON

Common config file

{
  "properties": {
    "pdb_code": "4i23",
    "api_id": "pdbe"
  }
}

Command line

canonical_fasta --config config_canonical_fasta.json --output_fasta_path canonical_fasta.fasta

Pdb_variants

This class creates a text file containing a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.

Get help

Command:

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

Wrapper for the UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.

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
                        Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

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

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (string): (None) RSCB PDB four letter code..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  pdb_code: 2vgb

Command line

pdb_variants --config config_pdb_variants.yml --output_mutations_list_txt output_pdb_variants.txt

JSON

Common config file

{
  "properties": {
    "pdb_code": "2vgb"
  }
}

Command line

pdb_variants --config config_pdb_variants.json --output_mutations_list_txt output_pdb_variants.txt

Api_binding_site

This class is a wrapper for the PDBe REST API Binding Sites endpoint.

Get help

Command:

api_binding_site -h
/bin/sh: 1: api_binding_site: not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_json_path (string): Path to the JSON file with the binding sites for the requested structure. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (string): (None) RSCB PDB code..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  pdb_code: 4i23

Command line

api_binding_site --config config_api_binding_site.yml --output_json_path output_binding_site.json

JSON

Common config file

{
  "properties": {
    "pdb_code": "4i23"
  }
}

Command line

api_binding_site --config config_api_binding_site.json --output_json_path output_binding_site.json

Pdb_cluster_zip

This class is a wrapper for downloading a PDB cluster from the Protein Data Bank.

Get help

Command:

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

Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/), the Protein Data Bank (https://www.rcsb.org/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a PDB cluster.

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
                        Path to the ZIP or PDB file containing the output PDB files. Accepted formats: pdb, zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_pdb_zip_path (string): Path to the ZIP file containing the output PDB files. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (string): (None) RSCB PDB code..
  • filter (string): ([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 (integer): (90) Sequence Similarity Cutoff. .
  • api_id (string): (pdbe) Identifier of the PDB REST API from which the PDB structure will be downloaded. .
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  api_id: pdbe
  cluster: 90
  filter:
  - ATOM
  - MODEL
  - ENDMDL
  pdb_code: 2vgb

Command line

pdb_cluster_zip --config config_pdb_cluster_zip.yml --output_pdb_zip_path output_pdb_cluster.zip

JSON

Common config file

{
  "properties": {
    "pdb_code": "2vgb",
    "filter": [
      "ATOM",
      "MODEL",
      "ENDMDL"
    ],
    "cluster": 90,
    "api_id": "pdbe"
  }
}

Command line

pdb_cluster_zip --config config_pdb_cluster_zip.json --output_pdb_zip_path output_pdb_cluster.zip

Mmcif

This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.

Get help

Command:

mmcif -h
usage: mmcif [-h] [-c CONFIG] -o OUTPUT_MMCIF_PATH

This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.

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_MMCIF_PATH, --output_mmcif_path OUTPUT_MMCIF_PATH
                        Path to the output MMCIF file. Accepted formats: cif, mmcif.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_mmcif_path (string): Path to the output MMCIF file. File type: output. Sample file. Accepted formats: CIF, MMCIF

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (string): (None) RSCB PDB code..
  • api_id (string): (pdbe) Identifier of the PDB REST API from which the MMCIF structure will be downloaded. .
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  api_id: pdbe
  pdb_code: 2VGB

Command line

mmcif --config config_mmcif.yml --output_mmcif_path ref_output.mmcif

JSON

Common config file

{
  "properties": {
    "pdb_code": "2VGB",
    "api_id": "pdbe"
  }
}

Command line

mmcif --config config_mmcif.json --output_mmcif_path ref_output.mmcif

Drugbank

This class is a wrapper for the Drugbank REST API.

Get help

Command:

drugbank -h
usage: drugbank [-h] [-c CONFIG] -o OUTPUT_SDF_PATH

Download a component in SDF format from the Drugbank (https://www.drugbank.ca/).

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_SDF_PATH, --output_sdf_path OUTPUT_SDF_PATH
                        Path to the output SDF component file. Accepted formats: sdf.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_sdf_path (string): Path to the output SDF component file. File type: output. Sample file. Accepted formats: SDF

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • drugbank_id (string): (None) Drugbank component id..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  drugbank_id: DB00530

Command line

drugbank --config config_drugbank.yml --output_sdf_path output_drugbank.sdf

JSON

Common config file

{
  "properties": {
    "drugbank_id": "DB00530"
  }
}

Command line

drugbank --config config_drugbank.json --output_sdf_path output_drugbank.sdf

Ligand

This class is a wrapper for downloading a PDB ligand from the Protein Data Bank.

Get help

Command:

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

Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a single PDB ligand.

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. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_pdb_path (string): 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 (string): (None) RSCB PDB ligand code..
  • api_id (string): (pdbe) Identifier of the PDB REST API from which the PDB structure will be downloaded. .
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  api_id: pdbe
  ligand_code: IBP

Command line

ligand --config config_ligand.yml --output_pdb_path output_ligand.pdb

JSON

Common config file

{
  "properties": {
    "ligand_code": "IBP",
    "api_id": "pdbe"
  }
}

Command line

ligand --config config_ligand.json --output_pdb_path output_ligand.pdb

Ideal_sdf

This class is a wrapper for downloading an ideal SDF ligand from the Protein Data Bank.

Get help

Command:

ideal_sdf -h
usage: ideal_sdf [-h] [-c CONFIG] -o OUTPUT_SDF_PATH

This class is a wrapper for downloading an ideal SDF ligand from the Protein Data Bank.

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_SDF_PATH, --output_sdf_path OUTPUT_SDF_PATH
                        Path to the output SDF file. Accepted formats: sdf.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_sdf_path (string): Path to the output SDF file. File type: output. Sample file. Accepted formats: SDF

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • ligand_code (string): (None) RSCB PDB ligand code..
  • api_id (string): (pdbe) Identifier of the PDB REST API from which the SDF structure will be downloaded. .
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  api_id: pdbe
  ligand_code: HYZ

Command line

ideal_sdf --config config_ideal_sdf.yml --output_sdf_path ref_output.sdf

JSON

Common config file

{
  "properties": {
    "ligand_code": "HYZ",
    "api_id": "pdbe"
  }
}

Command line

ideal_sdf --config config_ideal_sdf.json --output_sdf_path ref_output.sdf

Memprotmd_sim_list

This class is a wrapper of the MemProtMD to get all available membrane-protein systems from its REST API.

Get help

Command:

memprotmd_sim_list -h
usage: memprotmd_sim_list [-h] [-c CONFIG] -o OUTPUT_SIMULATIONS

Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to get all available membrane-protein systems (simulations).

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_SIMULATIONS, --output_simulations OUTPUT_SIMULATIONS
                        Path to the output JSON file. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_simulations (string): Path to the output JSON file. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  remove_tmp: false

Command line

memprotmd_sim_list --config config_memprotmd_sim_list.yml --output_simulations output_sim_list.json

JSON

Common config file

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

memprotmd_sim_list --config config_memprotmd_sim_list.json --output_simulations output_sim_list.json

Memprotmd_sim

This class is a wrapper of the MemProtMD to download a simulation using its REST API.

Get help

Command:

memprotmd_sim -h
usage: memprotmd_sim [-h] [-c CONFIG] -o OUTPUT_SIMULATION

Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to download a simulation.

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_SIMULATION, --output_simulation OUTPUT_SIMULATION
                        Path to the output simulation in a ZIP file. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_simulation (string): Path to the output simulation in a ZIP file. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (string): (None) RSCB PDB code..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  pdb_code: 1hzx

Command line

memprotmd_sim --config config_memprotmd_sim.yml --output_simulation output_sim.zip

JSON

Common config file

{
  "properties": {
    "pdb_code": "1hzx"
  }
}

Command line

memprotmd_sim --config config_memprotmd_sim.json --output_simulation output_sim.zip

Pdb

This class is a wrapper for downloading a PDB structure from the Protein Data Bank.

Get help

Command:

pdb -h
usage: pdb.py scriptfile [arg] ...

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_pdb_path (string): 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 (string): (None) RSCB PDB code..
  • filter (string): ([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..
  • api_id (string): (pdbe) Identifier of the PDB REST API from which the PDB structure will be downloaded. .
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  api_id: pdbe
  filter:
  - ATOM
  - HETATM
  pdb_code: 2VGB

Command line

pdb --config config_pdb.yml --output_pdb_path output_pdb.pdb

JSON

Common config file

{
  "properties": {
    "pdb_code": "2VGB",
    "filter": [
      "ATOM",
      "HETATM"
    ],
    "api_id": "pdbe"
  }
}

Command line

pdb --config config_pdb.json --output_pdb_path output_pdb.pdb

Structure_info

This class is a wrapper for getting all the available information of a structure from the Protein Data Bank.

Get help

Command:

structure_info -h
usage: structure_info [-h] [-c CONFIG] -o OUTPUT_JSON_PATH

This class is a wrapper for getting all the available information of a structure from the Protein Data Bank.

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_JSON_PATH, --output_json_path OUTPUT_JSON_PATH
                        Path to the output JSON file with all the structure information. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • output_json_path (string): Path to the output JSON file with all the structure information. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • pdb_code (string): (None) RSCB PDB structure code..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  pdb_code: 2VGB

Command line

structure_info --config config_structure_info.yml --output_json_path ref_str_info.json

JSON

Common config file

{
  "properties": {
    "pdb_code": "2VGB"
  }
}

Command line

structure_info --config config_structure_info.json --output_json_path ref_str_info.json