BioBB PDB Command Line Help

Generic usage:

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

Biobb_pdb_fetch

Downloads a structure in PDB format from the RCSB website.

Get help

Command:

biobb_pdb_fetch -h

usage: biobb_pdb_fetch [-h] --config CONFIG --output_file_path OUTPUT_FILE_PATH

Downloads a structure in PDB format from the RCSB website.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

output_file_path (string): PDB file of the protein selected. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

pdbid (string): (1aki) ID of the protein..
biounit (string): (False) Allows downloading the (first) biological structure if selected..
binary_path (string): (pdb_fetch) Path to the pdb_fetch executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  biounit: false
  pdbid: 1nmr

Command line

biobb_pdb_fetch --config config_biobb_pdb_fetch.yml --output_file_path ref_pdb_fetch.pdb

JSON

Common config file 

{
  "properties": {
    "pdbid": "1nmr",
    "biounit": false
  }
}

Command line

biobb_pdb_fetch --config config_biobb_pdb_fetch.json --output_file_path ref_pdb_fetch.pdb

Biobb_pdb_delhetatm

Removes all HETATM records in the PDB file.

Get help

Command:

biobb_pdb_delhetatm -h

usage: biobb_pdb_delhetatm [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Removes all HETATM records in the PDB file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): PDB file with all HETATM records removed. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pdb_delhetatm) Path to the pdb_delhetatm executable binary..
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

biobb_pdb_delhetatm --config config_biobb_pdb_delhetatm.yml --input_file_path input_pdb_delhetatm.pdb --output_file_path ref_pdb_delhetatm.pdb

JSON

Common config file 

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

Command line

biobb_pdb_delhetatm --config config_biobb_pdb_delhetatm.json --input_file_path input_pdb_delhetatm.pdb --output_file_path ref_pdb_delhetatm.pdb

Biobb_pdb_tidy

Modifies the file to adhere (as much as possible) to the format specifications.

Get help

Command:

biobb_pdb_tidy -h

usage: biobb_pdb_tidy [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Modifies the file to adhere (as much as possible) to the format specifications.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): PDB file modified according to the specifications. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

strict (boolean): (False) Does not add TER on chain breaks..
binary_path (string): (pdb_tidy) Path to the pdb_tidy executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  strict: false

Command line

biobb_pdb_tidy --config config_biobb_pdb_tidy.yml --input_file_path input_pdb_tidy.pdb --output_file_path ref_pdb_tidy.pdb

JSON

Common config file 

{
  "properties": {
    "strict": false
  }
}

Command line

biobb_pdb_tidy --config config_biobb_pdb_tidy.json --input_file_path input_pdb_tidy.pdb --output_file_path ref_pdb_tidy.pdb

Biobb_pdb_chain

Modifies the chain identifier column of a PDB file.

Get help

Command:

biobb_pdb_chain -h

usage: biobb_pdb_chain [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Modifies the chain identifier column of a PDB file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): PDB file with selected modified chain. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

chain (string): (A) Modifies the chain identifier column of a PDB file..
binary_path (string): (pdb_chain) Path to the pdb_chain executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  chain: A

Command line

biobb_pdb_chain --config config_biobb_pdb_chain.yml --input_file_path input_pdb_chain.pdb --output_file_path ref_pdb_chain.pdb

JSON

Common config file 

{
  "properties": {
    "chain": "A"
  }
}

Command line

biobb_pdb_chain --config config_biobb_pdb_chain.json --input_file_path input_pdb_chain.pdb --output_file_path ref_pdb_chain.pdb

Biobb_pdb_seg

Modifies the segment identifier column of a PDB file.

Get help

Command:

biobb_pdb_seg -h

usage: biobb_pdb_seg [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Modifies the segment identifier column of a PDB file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): PDB file with segment identifier column modified. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

segment (string): (B) Default is an empty segment..
binary_path (string): (pdb_seg) Path to the pdb_seg executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  segment: B

Command line

biobb_pdb_seg --config config_biobb_pdb_seg.yml --input_file_path input_pdb_seg.pdb --output_file_path ref_pdb_seg.pdb

JSON

Common config file 

{
  "properties": {
    "segment": "B"
  }
}

Command line

biobb_pdb_seg --config config_biobb_pdb_seg.json --input_file_path input_pdb_seg.pdb --output_file_path ref_pdb_seg.pdb

Biobb_pdb_mkensemble

Merges several PDB files into one multi-model (ensemble) file.

Get help

Command:

biobb_pdb_mkensemble -h

usage: biobb_pdb_mkensemble [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Merges several PDB files into one multi-model (ensemble) file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): ZIP file of selected proteins. File type: input. Sample file. Accepted formats: ZIP
output_file_path (string): Multi-model (ensemble) PDB file with input PDBs merged. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pdb_mkensemble) Path to the pdb_mkensemble executable binary..
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

biobb_pdb_mkensemble --config config_biobb_pdb_mkensemble.yml --input_file_path input_pdb_mkensemble1.pdb --output_file_path ref_pdb_mkensemble.pdb

JSON

Common config file 

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

Command line

biobb_pdb_mkensemble --config config_biobb_pdb_mkensemble.json --input_file_path input_pdb_mkensemble1.pdb --output_file_path ref_pdb_mkensemble.pdb

Biobb_pdb_merge

Merges several PDB files into one.

Get help

Command:

biobb_pdb_merge -h

usage: biobb_pdb_merge [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Merges several PDB files into one.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): ZIP file of selected protein. File type: input. Sample file. Accepted formats: ZIP
output_file_path (string): PDB file with input PDBs merged. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pdb_merge) Path to the pdb_merge executable binary..
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

biobb_pdb_merge --config config_biobb_pdb_merge.yml --input_file_path input_pdb_merge1.pdb --output_file_path ref_pdb_merge.pdb

JSON

Common config file 

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

Command line

biobb_pdb_merge --config config_biobb_pdb_merge.json --input_file_path input_pdb_merge1.pdb --output_file_path ref_pdb_merge.pdb

Biobb_pdb_reres

Renumbers the residues of the PDB file starting from a given number (default 1).

Get help

Command:

biobb_pdb_reres -h

usage: biobb_pdb_reres [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Renumbers the residues of the PDB file starting from a given number (default 1).

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): Renumbered PDB file by number of redisue selected. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

number (integer): (4) Number of the protein residue..
binary_path (string): (pdb_reres) Path to the pdb_reres executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  number: 4

Command line

biobb_pdb_reres --config config_biobb_pdb_reres.yml --input_file_path input_pdb_reres.pdb --output_file_path ref_pdb_reres.pdb

JSON

Common config file 

{
  "properties": {
    "number": 4
  }
}

Command line

biobb_pdb_reres --config config_biobb_pdb_reres.json --input_file_path input_pdb_reres.pdb --output_file_path ref_pdb_reres.pdb

Biobb_pdb_splitseg

Splits a PDB file into several, each containing one segment.

Get help

Command:

biobb_pdb_splitseg -h

usage: biobb_pdb_splitseg [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Splits a PDB file into several, each containing one segment.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): ZIP file containing all PDB files splited by protein segment. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pdb_splitseg) Path to the pdb_splitseg executable binary..
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

biobb_pdb_splitseg --config config_biobb_pdb_splitseg.yml --input_file_path input_pdb_splitseg.pdb --output_file_path ref_pdb_splitseg.zip

JSON

Common config file 

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

Command line

biobb_pdb_splitseg --config config_biobb_pdb_splitseg.json --input_file_path input_pdb_splitseg.pdb --output_file_path ref_pdb_splitseg.zip

Biobb_pdb_splitmodel

Splits a PDB file into several, each containing one MODEL.

Get help

Command:

biobb_pdb_splitmodel -h

usage: biobb_pdb_splitmodel [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Splits a PDB file into several, each containing one MODEL.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: zip.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): ZIP file containing all PDB files splited by protein model. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pdb_splitmodel) Path to the pdb_splitmodel executable binary..
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

biobb_pdb_splitmodel --config config_biobb_pdb_splitmodel.yml --input_file_path input_pdb_splitmodel.pdb --output_file_path ref_pdb_splitmodel.zip

JSON

Common config file 

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

Command line

biobb_pdb_splitmodel --config config_biobb_pdb_splitmodel.json --input_file_path input_pdb_splitmodel.pdb --output_file_path ref_pdb_splitmodel.zip

Biobb_pdb_uniqname

Renames atoms sequentially (C1, C2, O1, …) for each HETATM residue.

Get help

Command:

biobb_pdb_uniqname -h

usage: biobb_pdb_uniqname [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Removes all HETATM records in the PDB file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): PDB file with all HETATM atoms renamed. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pdb_uniqname) Path to the pdb_uniqname executable binary..
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

biobb_pdb_uniqname --config config_biobb_pdb_uniqname.yml --input_file_path input_pdb_delhetatm.pdb --output_file_path ref_pdb_delhetatm.pdb

JSON

Common config file 

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

Command line

biobb_pdb_uniqname --config config_biobb_pdb_uniqname.json --input_file_path input_pdb_delhetatm.pdb --output_file_path ref_pdb_delhetatm.pdb

Biobb_pdb_chainxseg

Swaps the segment identifier for the chain identifier.

Get help

Command:

biobb_pdb_chainxseg -h

usage: biobb_pdb_chainxseg [-h] --config CONFIG --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Swaps the segment identifier for the chain identifier.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        Description for the first input file path. Accepted formats: pdb.
  --output_file_path OUTPUT_FILE_PATH
                        Description for the output file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): PDB file. File type: input. Sample file. Accepted formats: PDB
output_file_path (string): PDB file with exchanged segment and string identifier. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pdb_chainxseg) Path to the pdb_chainxseg executable binary..
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

biobb_pdb_chainxseg --config config_biobb_pdb_chainxseg.yml --input_file_path input_pdb_chainxseg.pdb --output_file_path ref_pdb_chainxseg.pdb

JSON

Common config file 

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

Command line

biobb_pdb_chainxseg --config config_biobb_pdb_chainxseg.json --input_file_path input_pdb_chainxseg.pdb --output_file_path ref_pdb_chainxseg.pdb