BioBB IO Command Line Help

Generic usage:

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

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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

Pdb

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

Get help

Command:

pdb -h

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

This class is a wrapper for downloading a PDB 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_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH
                        Path to the output PDB 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 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..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  api_id: mmb
  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": "mmb"
  }
}

Command line

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

Api_binding_site

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

Get help

Command:

api_binding_site -h

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

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

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 JSON file with the binding sites for the requested structure. 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 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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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_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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

Alphafold

This class is a wrapper for downloading a PDB structure from the AlphaFold Protein Structure Database.

Get help

Command:

alphafold -h

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

This class is a wrapper for downloading a PDB 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_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH
                        Path to the output PDB 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 file. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

uniprot_code (string): (None) Uniprot code..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  uniprot_code: P00489

Command line

alphafold --config config_alphafold.yml --output_pdb_path output_alphafold.pdb

JSON

Common config file 

{
  "properties": {
    "uniprot_code": "P00489"
  }
}

Command line

alphafold --config config_alphafold.json --output_pdb_path output_alphafold.pdb

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): (mmb) 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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

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..
sandbox_path (string): (./) Parent path to the sandbox directory..

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

Memprotmd_sim_search

This class is a wrapper of the MemProtMD to perform advanced searches in the MemProtMD DB using its REST API.

Get help

Command:

memprotmd_sim_search -h

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

Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to perform advanced searches.

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:

collection_name (string): (refs) Name of the collection to query..
keyword (string): (None) String to search for in the database metadata. Examples are families like gpcr or porin. .
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  collection_name: refs
  keyword: porin

Command line

memprotmd_sim_search --config config_memprotmd_sim_search.yml --output_simulations output_sim_search.json

JSON

Common config file 

{
  "properties": {
    "collection_name": "refs",
    "keyword": "porin"
  }
}

Command line

memprotmd_sim_search --config config_memprotmd_sim_search.json --output_simulations output_sim_search.json