pdb_tools package

Submodules

pdb_tools.biobb_pdb_chain module

Module containing the Pdbchain class and the command line interface.

class pdb_tools.biobb_pdb_chain.Pdbchain(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbchain
Modifies the chain identifier column of a PDB file.
This tool modifies the chain identifier column of a PDB file. It can be used to change the chain identifier of a PDB file or to remove the chain identifier from a PDB file.
Parameters:

  • input_file_path (str) – PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    PDB file with selected modified chain. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • chain (string) - (‘A’) Modifies the chain identifier column of a PDB file.

    • binary_path (str) - (“pdb_chain”) Path to the pdb_chain executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_chain import biobb_pdb_chain

prop = {
    'chain': 'A'
}
biobb_pdb_chain(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb',
        properties=prop)
Info:
launch() → int[source]

Execute the Pdbchain object.

pdb_tools.biobb_pdb_chain.biobb_pdb_chain(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbchain class and execute the launch() method.

pdb_tools.biobb_pdb_chain.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_chainxseg module

Module containing the Chainxseg class and the command line interface.

class pdb_tools.biobb_pdb_chainxseg.Chainxseg(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbtidy
Swaps the segment identifier for the chain identifier.
This tool swaps the segment identifier for the chain identifier in a PDB file. It can be used to change the segment identifier of a PDB file or to remove the segment identifier from a PDB file.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    PDB file with exchanged segment and string identifier. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • binary_path (str) - (“pdb_chainxseg”) Path to the pdb_chainxseg executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_chainxseg import biobb_pdb_chainxseg

biobb_pdb_chainxseg(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb')
Info:
launch() → int[source]

Execute the Chainxseg object.

pdb_tools.biobb_pdb_chainxseg.biobb_pdb_chainxseg(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create biobb_pdb_tools.pdb_tools.pdb_chainxseg> class and execute the launch() method.

pdb_tools.biobb_pdb_chainxseg.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_delhetatm module

Module containing the Delhetatm class and the command line interface.

class pdb_tools.biobb_pdb_delhetatm.Delhetatm(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Delhetatm
Removes all HETATM records in the PDB file.
This tool removes all HETATM records in the PDB file. It can be used to remove all HETATM records from a PDB file.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    PDB file with all HETATM records removed. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • binary_path (str) - (“pdb_delhetatm”) Path to the pdb_delhetatm executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_delhetatm import biobb_pdb_delhetatm

biobb_pdb_delhetatm(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb')
Info:
launch() → int[source]

Execute the Delhetatm object.

pdb_tools.biobb_pdb_delhetatm.biobb_pdb_delhetatm(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Delhetatm class and execute the launch() method.

pdb_tools.biobb_pdb_delhetatm.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_fetch module

Module containing the Pdbfetch class and the command line interface.

class pdb_tools.biobb_pdb_fetch.Pdbfetch(output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbfetch
Downloads a structure in PDB format from the RCSB website.
This tool downloads a structure in PDB format from the RCSB website. It can be used to download a structure in PDB format from the RCSB website.
Parameters:

  • output_file_path (str) –

    PDB file of the protein selected. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • pdbid (string) - (‘1aki’) ID of the protein.

    • biounit (string) - (False) Allows downloading the (first) biological structure if selected.

    • binary_path (str) - (“pdb_fetch”) Path to the pdb_fetch executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_fetch import biobb_pdb_fetch

prop = {
    'biounit': False,
    'pdbid': '1aki'
}
biobb_pdb_fetch(output_file_path='/path/to/file.pdb',
        properties=prop)
Info:
launch() → int[source]

Execute the Pdbfetch object.

pdb_tools.biobb_pdb_fetch.biobb_pdb_fetch(output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbfetch class and execute the launch() method.

pdb_tools.biobb_pdb_fetch.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_merge module

Module containing the Pdbmerge class and the command line interface.

class pdb_tools.biobb_pdb_merge.Pdbmerge(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbmerge
Merges several PDB files into one.
This tool merges several PDB files into one. It can be used to merge several PDB files into one.
Parameters:

  • input_file_path (str) –

    ZIP file of selected protein. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_file_path (str) –

    PDB file with input PDBs merged. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • binary_path (str) - (“pdb_merge”) Path to the pdb_merge executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_merge import biobb_pdb_merge

biobb_pdb_merge(input_file_path='/path/to/input1.zip',
        output_file_path='/path/to/output.pdb')
Info:
launch() → int[source]

Execute the Pdbmerge object.

pdb_tools.biobb_pdb_merge.biobb_pdb_merge(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbmerge class and execute the launch() method.

pdb_tools.biobb_pdb_merge.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_mkensemble module

Module containing the Mkensemble class and the command line interface.

class pdb_tools.biobb_pdb_mkensemble.Mkensemble(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Mkensemble
Merges several PDB files into one multi-model (ensemble) file.
This tool merges several PDB files into one multi-model (ensemble) file. It can be used to merge several PDB files into one multi-model (ensemble) file.
Parameters:

  • input_file_path (str) –

    ZIP file of selected proteins. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_file_path (str) –

    Multi-model (ensemble) PDB file with input PDBs merged. File type: output. Sample file. Accepted formats: pdb (edam:format_3987).

  • properties (dic) –

    • binary_path (str) - (“pdb_mkensemble”) Path to the pdb_mkensemble executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_mkensemble import biobb_pdb_mkensemble

biobb_pdb_mkensemble(input_file_path='/path/to/input1.zip',
        output_file_path='/path/to/output.pdb')
Info:
launch() → int[source]

Execute the Mkensemble object.

pdb_tools.biobb_pdb_mkensemble.biobb_pdb_mkensemble(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Mkensemble class and execute the launch() method.

pdb_tools.biobb_pdb_mkensemble.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_reres module

Module containing the Pdbreres class and the command line interface.

class pdb_tools.biobb_pdb_reres.Pdbreres(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbreres
Renumbers the residues of the PDB file starting from a given number (default 1).
This tool renumbers the residues of the PDB file starting from a given number (default 1). It can be used to renumber the residues of a PDB file starting from a given number.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    Renumbered PDB file by number of redisue selected. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • number (int) - (4) Number of the protein residue.

    • binary_path (str) - (“pdb_reres”) Path to the pdb_reres executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_reres import biobb_pdb_reres

prop = {
    'number': 4
}
biobb_pdb_reres(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb',
        properties=prop)
Info:
launch() → int[source]

Execute the Pdbreres object.

pdb_tools.biobb_pdb_reres.biobb_pdb_reres(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbreres class and execute the launch() method.

pdb_tools.biobb_pdb_reres.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_seg module

Module containing the Pdbseg class and the command line interface.

class pdb_tools.biobb_pdb_seg.Pdbseg(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbseg
Modifies the segment identifier column of a PDB file.
This tool modifies the segment identifier column of a PDB file. It can be used to change the segment identifier of a PDB file or to remove the segment identifier from a PDB file.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    PDB file with segment identifier column modified. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • segment (str) - (‘B’) Default is an empty segment.

    • binary_path (str) - (“pdb_seg”) Path to the pdb_seg executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_seg import biobb_pdb_seg

prop = {
    'segment': 'A'
}
biobb_pdb_seg(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb',
        properties=prop)
Info:
launch() → int[source]

Execute the Pdbseg object.

pdb_tools.biobb_pdb_seg.biobb_pdb_seg(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbseg class and execute the launch() method.

pdb_tools.biobb_pdb_seg.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_splitmodel module

Module containing the Pdbsplitmodel class and the command line interface.

class pdb_tools.biobb_pdb_splitmodel.Pdbsplitmodel(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbsplitmodel
Splits a PDB file into several, each containing one MODEL.
This tool splits a PDB file into several, each containing one MODEL. It can be used to split a PDB file into several, each containing one MODEL.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    ZIP file containing all PDB files splited by protein model. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dic) –

    • binary_path (str) - (“pdb_splitmodel”) Path to the pdb_splitmodel executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_splitmodel import biobb_pdb_splitmodel

biobb_pdb_splitmodel(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.zip)
Info:
launch() → int[source]

Execute the Pdbsplitmodel object.

pdb_tools.biobb_pdb_splitmodel.biobb_pdb_splitmodel(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbsplitmodel class and execute the launch() method.

pdb_tools.biobb_pdb_splitmodel.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_splitseg module

Module containing the Pdbsplitseg class and the command line interface.

class pdb_tools.biobb_pdb_splitseg.Pdbsplitseg(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbsplitseg
Splits a PDB file into several, each containing one segment.
This tool splits a PDB file into several, each containing one segment. It can be used to split a PDB file into several, each containing one segment.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    ZIP file containing all PDB files splited by protein segment. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dic) –

    • binary_path (str) - (“pdb_splitseg”) Path to the pdb_splitseg executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_splitseg import biobb_pdb_splitseg

biobb_pdb_splitseg(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb')
Info:
launch() → int[source]

Execute the Pdbsplitseg object.

pdb_tools.biobb_pdb_splitseg.biobb_pdb_splitseg(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbsplitseg class and execute the launch() method.

pdb_tools.biobb_pdb_splitseg.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_tidy module

Module containing the Pdbtidy class and the command line interface.

class pdb_tools.biobb_pdb_tidy.Pdbtidy(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbtidy
Modifies the file to adhere (as much as possible) to the format specifications.
This tool modifies the file to adhere (as much as possible) to the format specifications. It can be used to fix a PDB file that does not adhere to the format specifications.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    PDB file modified according to the specifications. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • strict (bool) - (False) Does not add TER on chain breaks.

    • binary_path (str) - (“pdb_tidy”) Path to the pdb_tidy executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_tidy import biobb_pdb_tidy

prop = {
    'strict': False
}
biobb_pdb_tidy(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb',
        properties=prop)
Info:
launch() → int[source]

Execute the Pdbtidy object.

pdb_tools.biobb_pdb_tidy.biobb_pdb_tidy(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbtidy class and execute the launch() method.

pdb_tools.biobb_pdb_tidy.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_tofasta module

Module containing the Pdbtofasta class and the command line interface.

class pdb_tools.biobb_pdb_tofasta.Pdbtofasta(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tofasta Pdbtofasta
Extracts the residue sequence in a PDB file to FASTA format.
This tool extracts the residue sequence in a PDB file to FASTA format. It can be used to extract the sequence of a PDB file to FASTA format.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    FASTA file containing the aminoacids sequence. File type: output. Sample file. Accepted formats: fasta (edam:format_1929), fa (edam:format_1929).

  • properties (dic) –

    • multi (bool) - (True) Splits the different chains into different records in the FASTA file.

    • binary_path (str) - (“pdb_tofasta”) Path to the pdb_tofasta executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_tofasta import biobb_pdb_tofasta

prop = {
    'multi': True
}
biobb_pdb_tofasta(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.fasta',
        properties=prop)
Info:
launch() → int[source]

Execute the Pdbtofasta object.

pdb_tools.biobb_pdb_tofasta.biobb_pdb_tofasta(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbtofasta class and execute the launch() method.

pdb_tools.biobb_pdb_tofasta.main()[source]

Command line execution of this building block. Please check the command line documentation.

pdb_tools.biobb_pdb_uniqname module

Module containing the Delhetatm class and the command line interface.

class pdb_tools.biobb_pdb_uniqname.Pdbuniqname(input_file_path, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_pdb_tools Pdbuniqname
Renames atoms sequentially (C1, C2, O1, …) for each HETATM residue.
This tool renames atoms sequentially (C1, C2, O1, …) for each HETATM residue in a PDB file. It can be used to rename atoms sequentially for each HETATM residue in a PDB file.
Parameters:

  • input_file_path (str) –

    PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_file_path (str) –

    PDB file with all HETATM atoms renamed. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic) –

    • binary_path (str) - (“pdb_uniqname”) Path to the pdb_uniqname executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_pdb_tools.pdb_tools.biobb_pdb_uniqname import biobb_pdb_uniqname

biobb_pdb_uniqname(input_file_path='/path/to/input.pdb',
        output_file_path='/path/to/output.pdb')
Info:
launch() → int[source]

Execute the Pdbuniqname object.

pdb_tools.biobb_pdb_uniqname.biobb_pdb_uniqname(input_file_path: str, output_file_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Pdbuniqname class and execute the launch() method.

pdb_tools.biobb_pdb_uniqname.main()[source]

Command line execution of this building block. Please check the command line documentation.