pmx package

Submodules

pmxbiobb.pmxanalyse module

pmxbiobb.pmxgentop module

Module containing the PMX gentop class and the command line interface.

class pmxbiobb.pmxgentop.Pmxgentop(input_top_zip_path: str, output_top_zip_path: str, properties: dict | None = None, **kwargs)

Bases: BiobbObject

biobb_pmx Pmxgentop

Wrapper class for the PMX gentop module.

Generate a topology file for a morphing simulation.

Parameters:

• input_top_zip_path (str) – Path the input GROMACS topology TOP and ITP files in zip format. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

• output_top_zip_path (str) –

  Path the output TOP topology in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• properties (dic) –

  • force_field (str) - (“amber99sb-star-ildn-mut”) Force field to use. If input_top_zip_path is a top file, it’s not necessary to specify the forcefield, as it will be determined automatically. If input_top_zip_path is an itp file, then it’s needed.

  • split (bool) - (False) Write separate topologies for the vdW and charge transformations.

  • scale_mass (bool) - (False) Scale the masses of morphing atoms so that dummies have a mass of 1.

  • gmx_lib (str) - (“$CONDA_PREFIX/lib/python3.7/site-packages/pmx/data/mutff/”) Path to the GMXLIB folder in your computer.

  • binary_path (str) - (“pmx”) Path to the PMX command line interface.

  • 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) Path to the binary executable of your container.

  • container_image (str) - (“gromacs/gromacs:latest”) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxgentop import pmxgentop
prop = {
    'gmx_lib': '/path/to/myGMXLIB/',
    'force_field': 'amber99sb-star-ildn-mut'
}
pmxgentop(input_top_zip_path='/path/to/myTopology.zip',
        output_top_zip_path='/path/to/newTopology.zip',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX gentop

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

launch() → int

Execute the Pmxgentop pmx.pmxgentop.Pmxgentop object.

pmxbiobb.pmxgentop.pmxgentop(input_top_zip_path: str, output_top_zip_path: str, properties: dict | None = None, **kwargs) → int

biobb_pmx Pmxgentop

Wrapper class for the PMX gentop module.

Generate a topology file for a morphing simulation.

Parameters:

• input_top_zip_path (str) –

  Path the input GROMACS topology TOP and ITP files in zip format. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

• output_top_zip_path (str) –

  Path the output TOP topology in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• properties (dic) –

  • force_field (str) - (“amber99sb-star-ildn-mut”) Force field to use. If input_top_zip_path is a top file, it’s not necessary to specify the forcefield, as it will be determined automatically. If input_top_zip_path is an itp file, then it’s needed.

  • split (bool) - (False) Write separate topologies for the vdW and charge transformations.

  • scale_mass (bool) - (False) Scale the masses of morphing atoms so that dummies have a mass of 1.

  • gmx_lib (str) - (“$CONDA_PREFIX/lib/python3.7/site-packages/pmx/data/mutff/”) Path to the GMXLIB folder in your computer.

  • binary_path (str) - (“pmx”) Path to the PMX command line interface.

  • 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) Path to the binary executable of your container.

  • container_image (str) - (“gromacs/gromacs:latest”) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxgentop import pmxgentop
prop = {
    'gmx_lib': '/path/to/myGMXLIB/',
    'force_field': 'amber99sb-star-ildn-mut'
}
pmxgentop(input_top_zip_path='/path/to/myTopology.zip',
        output_top_zip_path='/path/to/newTopology.zip',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX gentop

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

pmxbiobb.pmxmutate module

pmxbiobb.pmxatom_mapping module

Module containing the PMX atom_mapping class and the command line interface.

class pmxbiobb.pmxatom_mapping.Pmxatom_mapping(input_structure1_path: str, input_structure2_path: str, output_pairs1_path: str, output_pairs2_path: str, output_log_path: str, output_structure1_path: str | None = None, output_structure2_path: str | None = None, output_morph1_path: str | None = None, output_morph2_path: str | None = None, output_scaffold1_path: str | None = None, output_scaffold2_path: str | None = None, output_score_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: BiobbObject

biobb_pmx Pmxatom_mapping

Wrapper class for the PMX atom_mapping module.

Perform atom mapping between two ligand structures.

Parameters:

• input_structure1_path (str) –

  Path to the input ligand structure file 1. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• input_structure2_path (str) –

  Path to the input ligand structure file 2. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• output_pairs1_path (str) –

  Path to the output pairs for the ligand structure 1. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• output_pairs2_path (str) –

  Path to the output pairs for the ligand structure 2. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• output_log_path (str) – Path to the log file. File type: output. Accepted formats: log (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

• output_structure1_path (str) (Optional) – Path to the superimposed structure for the ligand structure 1. File type: output. Accepted formats: pdb (edam:format_1476).

• output_structure2_path (str) (Optional) – Path to the superimposed structure for the ligand structure 2. File type: output. Accepted formats: pdb (edam:format_1476).

• output_morph1_path (str) (Optional) – Path to the morphable atoms for the ligand structure 1. File type: output. Accepted formats: pdb (edam:format_1476).

• output_morph2_path (str) (Optional) – Path to the morphable atoms for the ligand structure 2. File type: output. Accepted formats: pdb (edam:format_1476).

• output_scaffold1_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 1. File type: output. Accepted formats: ndx (edam:format_2033).

• output_scaffold2_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 2. File type: output. Accepted formats: ndx (edam:format_2033).

• output_score_path (str) (Optional) – Path to the morphing score. File type: output. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• properties (dic) –

  • noalignment (bool) - (False) Should the alignment method be disabled.

  • nomcs (bool) - (False) Should the MCS method be disabled.

  • noH2H (bool) - (True) Should non-polar hydrogens be discarded from morphing into any other hydrogen.

  • H2Hpolar (bool) - (False) Should polar hydrogens be morphed into polar hydrogens.

  • H2Heavy (bool) - (False) Should hydrogen be morphed into a heavy atom.

  • RingsOnly (bool) - (False) Should rings only be used in the MCS search and alignemnt.

  • dMCS (bool) - (False) Should the distance criterium be also applied in the MCS based search.

  • swap (bool) - (False) Try swapping the molecule order which would be a cross-check and require double execution time.

  • nochirality (bool) - (True) Perform chirality check for MCS mapping.

  • distance (float) - (0.05) Distance (nm) between atoms to consider them morphable for alignment approach.

  • timeout (int) - (10) Maximum time (s) for an MCS search.

  • 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) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxatom_mapping import pmxatom_mapping
prop = {
    'no-alignment' : True,
    'distance': 0.05
}
pmxatom_mapping(input_structure1_path='/path/to/myStructure1.pdb',
        input_structure2_path='/path/to/myStructure2.pdb',
        output_pairs1_path='/path/to/myPairs1.dat',
        output_pairs2_path='/path/to/myPairs2.dat',
        output_log_path='/path/to/myLog.log',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX atom_mapping

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

launch() → int

Execute the Pmxmutate pmx.pmxmutate.Pmxmutate object.

pmxbiobb.pmxatom_mapping.pmxatom_mapping(input_structure1_path: str, input_structure2_path: str, output_pairs1_path: str, output_pairs2_path: str, output_log_path: str, output_structure1_path: str | None = None, output_structure2_path: str | None = None, output_morph1_path: str | None = None, output_morph2_path: str | None = None, output_scaffold1_path: str | None = None, output_scaffold2_path: str | None = None, output_score_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_pmx Pmxatom_mapping

Wrapper class for the PMX atom_mapping module.

Perform atom mapping between two ligand structures.

Parameters:

• input_structure1_path (str) –

  Path to the input ligand structure file 1. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• input_structure2_path (str) –

  Path to the input ligand structure file 2. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• output_pairs1_path (str) –

  Path to the output pairs for the ligand structure 1. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• output_pairs2_path (str) –

  Path to the output pairs for the ligand structure 2. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• output_log_path (str) – Path to the log file. File type: output. Accepted formats: log (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

• output_structure1_path (str) (Optional) – Path to the superimposed structure for the ligand structure 1. File type: output. Accepted formats: pdb (edam:format_1476).

• output_structure2_path (str) (Optional) – Path to the superimposed structure for the ligand structure 2. File type: output. Accepted formats: pdb (edam:format_1476).

• output_morph1_path (str) (Optional) – Path to the morphable atoms for the ligand structure 1. File type: output. Accepted formats: pdb (edam:format_1476).

• output_morph2_path (str) (Optional) – Path to the morphable atoms for the ligand structure 2. File type: output. Accepted formats: pdb (edam:format_1476).

• output_scaffold1_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 1. File type: output. Accepted formats: ndx (edam:format_2033).

• output_scaffold2_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 2. File type: output. Accepted formats: ndx (edam:format_2033).

• output_score_path (str) (Optional) – Path to the morphing score. File type: output. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• properties (dic) –

  • noalignment (bool) - (False) Should the alignment method be disabled.

  • nomcs (bool) - (False) Should the MCS method be disabled.

  • noH2H (bool) - (True) Should non-polar hydrogens be discarded from morphing into any other hydrogen.

  • H2Hpolar (bool) - (False) Should polar hydrogens be morphed into polar hydrogens.

  • H2Heavy (bool) - (False) Should hydrogen be morphed into a heavy atom.

  • RingsOnly (bool) - (False) Should rings only be used in the MCS search and alignemnt.

  • dMCS (bool) - (False) Should the distance criterium be also applied in the MCS based search.

  • swap (bool) - (False) Try swapping the molecule order which would be a cross-check and require double execution time.

  • nochirality (bool) - (True) Perform chirality check for MCS mapping.

  • distance (float) - (0.05) Distance (nm) between atoms to consider them morphable for alignment approach.

  • timeout (int) - (10) Maximum time (s) for an MCS search.

  • 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) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxatom_mapping import pmxatom_mapping
prop = {
    'no-alignment' : True,
    'distance': 0.05
}
pmxatom_mapping(input_structure1_path='/path/to/myStructure1.pdb',
        input_structure2_path='/path/to/myStructure2.pdb',
        output_pairs1_path='/path/to/myPairs1.dat',
        output_pairs2_path='/path/to/myPairs2.dat',
        output_log_path='/path/to/myLog.log',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX atom_mapping

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

pmxbiobb.pmxcreate_top module

Module containing the PMX create_top class and the command line interface.

class pmxbiobb.pmxcreate_top.Pmxcreate_top(input_topology1_path: str, input_topology2_path: str, output_topology_path: str, properties: dict | None = None, **kwargs)

Bases: BiobbObject

biobb_pmx Pmxcreate_top

Wrapper class for the PMX create_top module.

Create a complete ligand topology file from two input topology files.

Parameters:

• input_topology1_path (str) –

  Path to the input topology file 1. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• input_topology2_path (str) –

  Path to the input topology file 2. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• output_topology_path (str) –

  Path to the complete ligand topology file. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• properties (dic) –

  • force_field (str) - (“amber99sb-star-ildn-mut.ff”) Force-field to be included in the generated topology.

  • water (str) - (“tip3p”) Water model to be included in the generated topology.

  • system_name (str) - (“Pmx topology”) System name to be included in the generated topology.

  • mols (list) - ([[‘Protein’,1],[‘Ligand’,1]]) Molecules to be included in the generated topology.

  • 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) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxcreate_top import pmxcreate_top
prop = {
    'remove_tmp' : True
}
pmxcreate_top(input_topology1_path='/path/to/myTopology1.itp',
        input_topology2_path='/path/to/myTopology2.itp',
        output_topology_path='/path/to/myMergedTopology.zip',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX create_top

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

launch() → int

Execute the Pmxcreate_top pmx.pmxcreate_top.Pmxcreate_top object.

pmxbiobb.pmxcreate_top.pmxcreate_top(input_topology1_path: str, input_topology2_path: str, output_topology_path: str, properties: dict | None = None, **kwargs) → int

biobb_pmx Pmxcreate_top

Wrapper class for the PMX create_top module.

Create a complete ligand topology file from two input topology files.

Parameters:

• input_topology1_path (str) –

  Path to the input topology file 1. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• input_topology2_path (str) –

  Path to the input topology file 2. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• output_topology_path (str) –

  Path to the complete ligand topology file. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

• properties (dic) –

  • force_field (str) - (“amber99sb-star-ildn-mut.ff”) Force-field to be included in the generated topology.

  • water (str) - (“tip3p”) Water model to be included in the generated topology.

  • system_name (str) - (“Pmx topology”) System name to be included in the generated topology.

  • mols (list) - ([[‘Protein’,1],[‘Ligand’,1]]) Molecules to be included in the generated topology.

  • 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) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxcreate_top import pmxcreate_top
prop = {
    'remove_tmp' : True
}
pmxcreate_top(input_topology1_path='/path/to/myTopology1.itp',
        input_topology2_path='/path/to/myTopology2.itp',
        output_topology_path='/path/to/myMergedTopology.zip',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX create_top

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

pmxbiobb.pmxligand_hybrid module

Module containing the PMX ligand_hybrid class and the command line interface.

class pmxbiobb.pmxligand_hybrid.Pmxligand_hybrid(input_structure1_path: str, input_structure2_path: str, input_topology1_path: str, input_topology2_path: str, output_log_path: str, output_structure1_path: str, output_structure2_path: str, output_topology_path: str, output_atomtypes_path: str, input_scaffold1_path: str | None = None, input_scaffold2_path: str | None = None, input_pairs_path: str | None = None, properties: dict | None = None, **kwargs)

Bases: BiobbObject

biobb_pmx Pmxligand_hybrid

Wrapper class for the PMX ligand_hybrid module.

Create a hybrid topology and structure based on two ligand structures.

Parameters:

• input_structure1_path (str) –

  Path to the input ligand structure file 1. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• input_structure2_path (str) –

  Path to the input ligand structure file 2. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• input_topology1_path (str) –

  Path to the input ligand topology file 1. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• input_topology2_path (str) –

  Path to the input ligand topology file 2. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• input_pairs_path (str) (Optional) –

  Path to the input atom pair mapping. File type: input. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• input_scaffold1_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 1. File type: input. Accepted formats: ndx (edam:format_2033).

• input_scaffold2_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 2. File type: input. Accepted formats: ndx (edam:format_2033).

• output_log_path (str) – Path to the log file. File type: output. Accepted formats: log (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

• output_structure1_path (str) –

  Path to the output hybrid structure based on the ligand 1. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

• output_structure2_path (str) –

  Path to the output hybrid structure based on the ligand 2. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

• output_topology_path (str) –

  Path to the output hybrid topology. File type: output. Sample file. Accepted formats: itp (edam:format_3883).

• output_atomtypes_path (str) –

  Path to the atom types for the output hybrid topology. File type: output. Sample file. Accepted formats: itp (edam:format_3883).

• properties (dic) –

  • fit (bool) - (False) Fit ligand structure 1 onto ligand structure 2 (Only used if input_pairs_path is provided).

  • split (bool) - (False) Split the topology into separate transitions.

  • scDUMm (float) - (1.0) Scale dummy masses using the counterpart atoms.

  • scDUMa (float) - (1.0) Scale bonded dummy angle parameters.

  • scDUMd (float) - (1.0) Scale bonded dummy dihedral parameters.

  • deAng (bool) - (False) Decouple angles composed of 1 dummy and 2 non-dummies.

  • distance (float) - (0.05) Distance (nm) between atoms to consider them morphable for alignment approach (Only used if input_pairs_path is not provided).

  • 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) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxligand_hybrid import pmxligand_hybrid
prop = {
    'fit' : True,
    'distance': 0.05
}
pmxligand_hybrid(input_structure1_path='/path/to/myStructure1.pdb',
        input_structure2_path='/path/to/myStructure2.pdb',
        input_topology1_path='/path/to/myTopology1.pdb',
        input_topology2_path='/path/to/myTopology2.pdb',
        input_pairs_path='/path/to/myPairs.dat',
        output_log_path='/path/to/myLog.log',
        output_structure1_path='/path/to/myStructureOutput1.pdb',
        output_structure2_path='/path/to/myStructureOutput2.pdb',
        output_topology_path='/path/to/myTopologyOutput.pdb',
        output_atomtypes_path='/path/to/myAtomTypesOutput.pdb',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX ligand_hybrid

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

launch() → int

Execute the Pmxmutate pmx.pmxmutate.Pmxmutate object.

pmxbiobb.pmxligand_hybrid.pmxligand_hybrid(input_structure1_path: str, input_structure2_path: str, input_topology1_path: str, input_topology2_path: str, output_log_path: str, output_structure1_path: str, output_structure2_path: str, output_topology_path: str, output_atomtypes_path: str, input_scaffold1_path: str | None = None, input_scaffold2_path: str | None = None, input_pairs_path: str | None = None, properties: dict | None = None, **kwargs) → int

biobb_pmx Pmxligand_hybrid

Wrapper class for the PMX ligand_hybrid module.

Create a hybrid topology and structure based on two ligand structures.

Parameters:

• input_structure1_path (str) –

  Path to the input ligand structure file 1. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• input_structure2_path (str) –

  Path to the input ligand structure file 2. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

• input_topology1_path (str) –

  Path to the input ligand topology file 1. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• input_topology2_path (str) –

  Path to the input ligand topology file 2. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

• input_pairs_path (str) (Optional) –

  Path to the input atom pair mapping. File type: input. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

• input_scaffold1_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 1. File type: input. Accepted formats: ndx (edam:format_2033).

• input_scaffold2_path (str) (Optional) – Path to the index of atoms to consider for the ligand structure 2. File type: input. Accepted formats: ndx (edam:format_2033).

• output_log_path (str) – Path to the log file. File type: output. Accepted formats: log (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).

• output_structure1_path (str) –

  Path to the output hybrid structure based on the ligand 1. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

• output_structure2_path (str) –

  Path to the output hybrid structure based on the ligand 2. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

• output_topology_path (str) –

  Path to the output hybrid topology. File type: output. Sample file. Accepted formats: itp (edam:format_3883).

• output_atomtypes_path (str) –

  Path to the atom types for the output hybrid topology. File type: output. Sample file. Accepted formats: itp (edam:format_3883).

• properties (dic) –

  • fit (bool) - (False) Fit ligand structure 1 onto ligand structure 2 (Only used if input_pairs_path is provided).

  • split (bool) - (False) Split the topology into separate transitions.

  • scDUMm (float) - (1.0) Scale dummy masses using the counterpart atoms.

  • scDUMa (float) - (1.0) Scale bonded dummy angle parameters.

  • scDUMd (float) - (1.0) Scale bonded dummy dihedral parameters.

  • deAng (bool) - (False) Decouple angles composed of 1 dummy and 2 non-dummies.

  • distance (float) - (0.05) Distance (nm) between atoms to consider them morphable for alignment approach (Only used if input_pairs_path is not provided).

  • 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) Path to the binary executable of your container.

  • container_image (str) - (None) Container Image identifier.

  • container_volume_path (str) - (“/inout”) Path to an internal directory in the container.

  • container_working_dir (str) - (None) Path to the internal CWD in the container.

  • container_user_id (str) - (None) User number id to be mapped inside the container.

  • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

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

from biobb_pmx.pmxbiobb.pmxligand_hybrid import pmxligand_hybrid
prop = {
    'fit' : True,
    'distance': 0.05
}
pmxligand_hybrid(input_structure1_path='/path/to/myStructure1.pdb',
        input_structure2_path='/path/to/myStructure2.pdb',
        input_topology1_path='/path/to/myTopology1.pdb',
        input_topology2_path='/path/to/myTopology2.pdb',
        input_pairs_path='/path/to/myPairs.dat',
        output_log_path='/path/to/myLog.log',
        output_structure1_path='/path/to/myStructureOutput1.pdb',
        output_structure2_path='/path/to/myStructureOutput2.pdb',
        output_topology_path='/path/to/myTopologyOutput.pdb',
        output_atomtypes_path='/path/to/myAtomTypesOutput.pdb',
        properties=prop)

Info:

• wrapped_software:

  • name: PMX ligand_hybrid

  • version: >=1.0.1

  • license: GNU

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

pmxbiobb.pmxmerge_ff module