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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
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.