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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model MutateClass 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model FixSideChainClass 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
FixSideChain
object.
- input_pdb_path (str) –
-
model.fix_side_chain.
fix_side_chain
(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) → int[source]¶ Create
FixSideChain
class and execute thelaunch()
method.
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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model FixBackboneClass 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
FixBackbone
object.
- input_pdb_path (str) –
-
model.fix_backbone.
fix_backbone
(input_pdb_path: str, input_fasta_canonical_sequence_path: str, output_pdb_path: str, properties: dict = None, **kwargs) → int[source]¶ Create
FixBackbone
class and execute thelaunch()
method.
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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model FixAmidesFix 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
- input_pdb_path (str) –
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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model FixChiralityFix 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
- input_pdb_path (str) –
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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model FixAltLocsFix 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
FixAltLocs
object.
- input_pdb_path (str) –
-
model.fix_altlocs.
fix_altlocs
(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) → int[source]¶ Create
FixAltLocs
class and execute thelaunch()
method.
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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model FixSSBondsFix 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
FixSSBonds
object.
- input_pdb_path (str) –
-
model.fix_ssbonds.
fix_ssbonds
(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) → int[source]¶ Create
FixSSBonds
class and execute thelaunch()
method.
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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_model CheckingLogClass 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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
CheckingLog
object.
- input_pdb_path (str) –
-
model.checking_log.
checking_log
(input_pdb_path: str, output_log_path: str, properties: dict = None, **kwargs) → int[source]¶ Create
CheckingLog
class and execute thelaunch()
method.