ambertools package

Submodules

ambertools.reduce_add_hydrogens

Module containing the ReduceAddHydrogens class and the command line interface.

class ambertools.reduce_add_hydrogens.ReduceAddHydrogens(input_path, output_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_chemistry ReduceAddHydrogens
This class is a wrapper of the Ambertools reduce module for adding hydrogens to a given structure.
Reduce is a program for adding or removing hydrogens to a Protein DataBank (PDB) molecular structure file.

Parameters:

input_path (str) – Path to the input file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).
output_path (str) –
Path to the output file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- flip (bool) - (False) add H and rotate and flip NQH groups
- noflip (bool) - (False) add H and rotate groups with no NQH flips
- nuclear (bool) - (False) use nuclear X-H distances rather than default electron cloud distances
- nooh (bool) - (False) remove hydrogens on OH and SH groups
- oh (bool) - (True) add hydrogens on OH and SH groups (default)
- his (bool) - (False) create NH hydrogens on HIS rings (usually used with -HIS)
- noheth (bool) - (False) do not attempt to add NH proton on Het groups
- rotnh3 (bool) - (True) allow lysine NH3 to rotate (default)
- norotnh3 (bool) - (False) do not allow lysine NH3 to rotate
- rotexist (bool) - (False) allow existing rotatable groups (OH, SH, Met-CH3) to rotate
- rotexoh (bool) - (False) allow existing OH & SH groups to rotate
- allalt (bool) - (True) process adjustments for all conformations (default)
- onlya (bool) - (False) only adjust ‘A’ conformations
- charges (bool) - (False) output charge state for appropriate hydrogen records
- dorotmet (bool) - (False) allow methionine methyl groups to rotate (not recommended)
- noadjust (bool) - (False) do not process any rot or flip adjustments
- metal_bump (float) - (None) [0~5|0.005] H ‘bumps’ metals at radius plus this
- non_metal_bump (float) - (None) [0~5|0.005] ‘bumps’ nonmetal at radius plus this
- build (bool) - (False) add H, including His sc NH, then rotate and flip groups (except for pre-existing methionine methyl hydrogens)
- binary_path (str) - (“reduce”) Path to the reduce executable binary.
- remove_tmp (bool) - (True) [WF property] Remove temporal files.
- restart (bool) - (False) [WF property] Do not execute if output files exist.
- sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.
- container_path (str) - (None) Container path definition.
- container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.
- container_volume_path (str) - (‘/tmp’) Container volume path definition.
- container_working_dir (str) - (None) Container working directory definition.
- container_user_id (str) - (None) Container user_id definition.
- container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

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

from biobb_chemistry.ambertools.reduce_add_hydrogens import reduce_add_hydrogens
prop = {
    'flip': False,
    'charges': True,
    'build': False
}
reduce_add_hydrogens(input_path='/path/to/myStructure.pdb',
                    output_path='/path/to/newStructure.pdb',
                    properties=prop)

Info:

wrapped_software:
- name: AmberTools Reduce
- version: >=20.0
- license: GNU
ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl

check_data_params(out_log, err_log)[source]: Checks all the input/output paths and parameters

create_cmd(container_io_dict, out_log, err_log)[source]: Creates the command line instruction using the properties file settings

launch() → int[source]: Execute the ReduceAddHydrogens ambertools.reduce_add_hydrogens.ReduceAddHydrogens object.

ambertools.reduce_add_hydrogens.main()[source]: Command line execution of this building block. Please check the command line documentation.

ambertools.reduce_add_hydrogens.reduce_add_hydrogens(input_path: str, output_path: str, properties: dict | None = None, **kwargs) → int[source]: Execute the ReduceAddHydrogens class and execute the launch() method.

ambertools.reduce_remove_hydrogens

Module containing the ReduceRemoveHydrogens class and the command line interface.

class ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens(input_path, output_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_chemistry ReduceRemoveHydrogens
This class is a wrapper of the Ambertools reduce module for removing hydrogens from a given structure.
Reduce is a program for adding or removing hydrogens to a Protein DataBank (PDB) molecular structure file.

Parameters:

input_path (str) –
Path to the input file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).
output_path (str) –
Path to the output file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
- binary_path (str) - (“reduce”) Path to the reduce executable binary.
- remove_tmp (bool) - (True) [WF property] Remove temporal files.
- restart (bool) - (False) [WF property] Do not execute if output files exist.
- sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.
- container_path (str) - (None) Container path definition.
- container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.
- container_volume_path (str) - (‘/tmp’) Container volume path definition.
- container_working_dir (str) - (None) Container working directory definition.
- container_user_id (str) - (None) Container user_id definition.
- container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

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

from biobb_chemistry.ambertools.reduce_remove_hydrogens import reduce_remove_hydrogens
prop = { }
reduce_remove_hydrogens(input_path='/path/to/myStructure.pdb',
                        output_path='/path/to/newStructure.pdb',
                        properties=prop)

Info:

wrapped_software:
- name: AmberTools Reduce
- version: >=20.0
- license: GNU
ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl

check_data_params(out_log, err_log)[source]: Checks all the input/output paths and parameters

create_cmd(container_io_dict, out_log, err_log)[source]: Creates the command line instruction using the properties file settings

launch() → int[source]: Execute the ReduceRemoveHydrogens ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens object.

ambertools.reduce_remove_hydrogens.main()[source]: Command line execution of this building block. Please check the command line documentation.

ambertools.reduce_remove_hydrogens.reduce_remove_hydrogens(input_path: str, output_path: str, properties: dict | None = None, **kwargs) → int[source]: Execute the ReduceRemoveHydrogens class and execute the launch() method.