configuration package

Submodules

model.mutate module

Module containing the Mutate class and the command line interface.

class model.mutate.Mutate(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model Mutate
Class to mutate one amino acid by another in a 3d structure.
Mutate side chain with minimal atom replacement. if the use_modeller property is added the Modeller suite will be used to optimize the side chains.
Parameters:

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

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • mutation_list (str) - (None) Mutation list in the format “Chain:WT_AA_ThreeLeterCode Resnum MUT_AA_ThreeLeterCode” (no spaces between the elements) separated by commas. If no chain is provided as chain code all the chains in the pdb file will be mutated. ie: “A:ALA15CYS”

    • use_modeller (bool) - (False) Use Modeller suite to optimize the side chains.

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.mutate import mutate
prop = { 'mutation_list': 'A:Val2Ala',
         'use_modeller': True }
mutate(input_pdb_path='/path/to/myStructure.pdb',
       output_pdb_path='/path/to/newStructure.pdb',
       properties=prop)
Info:
launch() → int[source]

Execute the Mutate object.

model.mutate.main()[source]
model.mutate.mutate(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Mutate class and execute the launch() method.

model.fix_side_chain module

Module containing the FixSideChain class and the command line interface.

class model.fix_side_chain.FixSideChain(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model FixSideChain
Class to model the missing atoms in amino acid side chains of a PDB.
Model the missing atoms in amino acid side chains of a PDB using biobb_structure_checking if the use_modeller property is added the Modeller suite will also be used to rebuild the missing atoms.
Parameters:

  • input_pdb_path (str) –

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

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • use_modeller (bool) - (False) Use Modeller suite to rebuild the missing side chain atoms.

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.fix_side_chain import fix_side_chain
prop = { 'use_modeller': True }
fix_side_chain(input_pdb_path='/path/to/myStructure.pdb',
              output_pdb_path='/path/to/newStructure.pdb',
              properties=prop)
Info:
launch() → int[source]

Execute the FixSideChain object.

model.fix_side_chain.fix_side_chain(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create FixSideChain class and execute the launch() method.

model.fix_side_chain.main()[source]

model.fix_backbone module

Module containing the FixBackbone class and the command line interface.

class model.fix_backbone.FixBackbone(input_pdb_path: str, input_fasta_canonical_sequence_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model FixBackbone
Class to model the missing atoms in the backbone of a PDB structure.
Model the missing atoms in the backbone of a PDB structure using biobb_structure_checking and the Modeller suite.
Parameters:

  • input_pdb_path (str) –

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

  • input_fasta_canonical_sequence_path (str) –

    Input FASTA file path. File type: input. Sample file. Accepted formats: fasta (edam:format_1476).

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • add_caps (bool) - (False) Add caps to terminal residues.

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.fix_backbone import fix_backbone
prop = { 'restart': False }
fix_backbone(input_pdb_path='/path/to/myStructure.pdb',
             input_fasta_canonical_sequence_path='/path/to/myCanonicalSequence.fasta',
              output_pdb_path='/path/to/newStructure.pdb',
              properties=prop)
Info:
launch() → int[source]

Execute the FixBackbone object.

model.fix_backbone.fix_backbone(input_pdb_path: str, input_fasta_canonical_sequence_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create FixBackbone class and execute the launch() method.

model.fix_backbone.main()[source]

model.fix_amides module

Module containing the FixAmides class and the command line interface.

class model.fix_amides.FixAmides(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model FixAmides
Fix amide groups from residues.
Flip the clashing amide groups to avoid clashes.
Parameters:

  • input_pdb_path (str) –

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

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.fix_amides import fix_amides
prop = { 'restart': False }
fix_amides(input_pdb_path='/path/to/myStructure.pdb',
           output_pdb_path='/path/to/newStructure.pdb',
           properties=prop)
Info:
launch() → int[source]

Execute the FixAmides object.

model.fix_amides.fix_amides(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create FixAmides class and execute the launch() method.

model.fix_amides.main()[source]

model.fix_chirality module

Module containing the FixChirality class and the command line interface.

class model.fix_chirality.FixChirality(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model FixChirality
Fix chirality errors of residues.
Fix stereochemical errors in residue side-chains changing It’s chirality.
Parameters:

  • input_pdb_path (str) –

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

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.fix_chirality import fix_chirality
prop = { 'restart': False }
fix_chirality(input_pdb_path='/path/to/myStructure.pdb',
              output_pdb_path='/path/to/newStructure.pdb',
              properties=prop)
Info:
launch() → int[source]

Execute the FixChirality object.

model.fix_chirality.fix_chirality(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create FixChirality class and execute the launch() method.

model.fix_chirality.main()[source]

model.fix_altlocs module

Module containing the FixAltLocs class and the command line interface.

class model.fix_altlocs.FixAltLocs(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model FixAltLocs
Fix alternate locations from residues.
Parameters:

  • input_pdb_path (str) –

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

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • altlocs (list) - (None) List of alternate locations to fix. Format: [“A339:A”, “A171:B”, “A768:A”]; where for each residue the format is as follows: “<chain><residue id>:<chosen alternate location>”. If empty, no action will be executed.

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.fix_altlocs import fix_altlocs
prop = { 'altlocs': ['A339:A', 'A171:B', 'A768:A'] }
fix_altlocs(input_pdb_path='/path/to/myStructure.pdb',
           output_pdb_path='/path/to/newStructure.pdb',
           properties=prop)
Info:
launch() → int[source]

Execute the FixAltLocs object.

model.fix_altlocs.fix_altlocs(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create FixAltLocs class and execute the launch() method.

model.fix_altlocs.main()[source]

model.fix_ssbonds module

Module containing the FixSSBonds class and the command line interface.

class model.fix_ssbonds.FixSSBonds(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model FixSSBonds
Fix SS bonds from residues.
Parameters:

  • input_pdb_path (str) –

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

  • output_pdb_path (str) –

    Output PDB file path. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.fix_ssbonds import fix_ssbonds
prop = { 'restart': False }
fix_ssbonds(input_pdb_path='/path/to/myStructure.pdb',
           output_pdb_path='/path/to/newStructure.pdb',
           properties=prop)
Info:
launch() → int[source]

Execute the FixSSBonds object.

model.fix_ssbonds.fix_ssbonds(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create FixSSBonds class and execute the launch() method.

model.fix_ssbonds.main()[source]

model.checking_log module

Module containing the CheckingLog class and the command line interface.

class model.checking_log.CheckingLog(input_pdb_path: str, output_log_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_model CheckingLog
Class to check the errors of a PDB structure.
Check the errors of a PDB structure and create a report log file.
Parameters:

  • input_pdb_path (str) –

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

  • output_log_path (str) –

    Output report log file path. File type: output. Sample file. Accepted formats: log (edam:format_2330).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • modeller_key (str) - (None) Modeller license key.

    • binary_path (str) - (“check_structure”) Path to the check_structure 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_model.model.checking_log import checking_log
prop = { 'restart': False }
checking_log(input_pdb_path='/path/to/myStructure.pdb',
             output_log_path='/path/to/myReport.log',
             properties=prop)
Info:
launch() → int[source]

Execute the CheckingLog object.

model.checking_log.checking_log(input_pdb_path: str, output_log_path: str, properties: dict | None = None, **kwargs) → int[source]

Create CheckingLog class and execute the launch() method.

model.checking_log.main()[source]