pmx package

Submodules

pmxbiobb.pmxanalyse module

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

class pmxbiobb.pmxanalyse.Pmxanalyse(input_a_xvg_zip_path: str, input_b_xvg_zip_path: str, output_result_path: str, output_work_plot_path: str, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_pmx Pmxanalyse
Wrapper class for the PMX analyse module.
Analyze the work values from the dgdl.xvg files of the A and B states to calculate the free energy difference between two states.
Parameters:

  • input_a_xvg_zip_path (str) – Path the zip file containing the dgdl.xvg files of the A state. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • input_b_xvg_zip_path (str) –

    Path the zip file containing the dgdl.xvg files of the B state. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_result_path (str) –

    Path to the TXT results file. File type: output. Sample file. Accepted formats: txt (edam:format_2330).

  • output_work_plot_path (str) –

    Path to the PNG plot results file. File type: output. Sample file. Accepted formats: png (edam:format_3603).

  • properties (dic) –

    • method (str) - (“CGI BAR JARZ”) Choose one or more estimators to use. Values: CGI (Crooks Gaussian Intersection), BAR (Bennet Acceptance Ratio), JARZ (Jarzynski’s estimator).

    • temperature (float) - (298.15) [0~1000|0.05] Temperature in Kelvin.

    • nboots (int) - (0) [0~1000|1] Number of bootstrap samples to use for the bootstrap estimate of the standard errors.

    • nblocks (int) - (1) [0~1000|1] Number of blocks to divide the data into for an estimate of the standard error.

    • integ_only (bool) - (False) Whether to do integration only.

    • reverseB (bool) - (False) Whether to reverse the work values for the backward (B->A) transformation.

    • skip (int) - (1) [0~1000|1] Skip files.

    • slice (str) - (None) Subset of trajectories to analyze. Provide list slice, e.g. “10 50” will result in selecting dhdl_files[10:50].

    • rand (int) - (None) [0~1000|1] Take a random subset of trajectories. Default is None (do not take random subset).

    • index (str) - (None) Zero-based index of files to analyze (e.g. “0 10 20 50 60”). It keeps the dhdl.xvg files according to their position in the list, sorted according to the filenames.

    • prec (int) - (2) [0~100|1] The decimal precision of the screen/file output.

    • units (str) - (“kJ”) The units of the output. Values: kJ (Kilojoules), kcal (Kilocalories), kT (the product of the Boltzmann constant k and the temperature).

    • no_ks (bool) - (False) Whether to do a Kolmogorov-Smirnov test to check whether the Gaussian assumption for CGI holds.

    • nbins (int) - (20) [0~1000|1] Number of histograms bins for the plot.

    • dpi (int) - (300) [72~2048|1] Resolution of the plot.

    • 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) - (“/data”) 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.pmxanalyse import pmxanalyse
prop = {
    'method': 'CGI BAR JARZ',
    'temperature': 298.15,
    'dpi': 600
}
pmxanalyse(input_a_xvg_zip_path='/path/to/myAStateFiles.zip',
           input_b_xvg_zip_path='/path/to/myBStateFiles.zip',
           output_result_path='/path/to/newResults.txt',
           output_work_plot_path='/path/to/newResults.png',
           properties=prop)
Info:
launch() → int[source]

Execute the Pmxanalyse pmx.pmxanalyse.Pmxanalyse object.

pmxbiobb.pmxanalyse.main()[source]

Command line execution of this building block. Please check the command line documentation.

pmxbiobb.pmxanalyse.pmxanalyse(input_a_xvg_zip_path: str, input_b_xvg_zip_path: str, output_result_path: str, output_work_plot_path: str, properties: Dict | None = None, **kwargs) → int[source]

Execute the Pmxanalyse class and execute the :meth:`launch() <pmx.pmxanalyse.Pmxanalyse.launch> method.

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)[source]

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:
launch() → int[source]

Execute the Pmxgentop pmx.pmxgentop.Pmxgentop object.

pmxbiobb.pmxgentop.main()[source]

Command line execution of this building block. Please check the command line documentation.

pmxbiobb.pmxgentop.pmxgentop(input_top_zip_path: str, output_top_zip_path: str, properties: Dict | None = None, **kwargs) → int[source]

Execute the Pmxgentop class and execute the :meth:`launch() <pmx.pmxgentop.Pmxgentop.launch> method.

pmxbiobb.pmxmutate module

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

class pmxbiobb.pmxmutate.Pmxmutate(input_structure_path: str, output_structure_path: str, input_b_structure_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_pmx Pmxmutate
Wrapper class for the PMX mutate module.
Mutate residues in a protein structure.
Parameters:

  • input_structure_path (str) –

    Path to the input structure file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).

  • output_structure_path (str) –

    Path to the output structure file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).

  • input_b_structure_path (str) (Optional) – Path to the mutated input structure file. File type: input. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).

  • properties (dic) –

    • mutation_list (str) - (“2Ala”) Mutation list in the format “Chain:Resnum MUT_AA_Code” or “Chain:Resnum MUT_NA_Code” (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:15CYS”. Possible MUT_AA_Code: ‘ALA’, ‘ARG’, ‘ASN’, ‘ASP’, ‘ASPH’, ‘ASPP’, ‘ASH’, ‘CYS’, ‘CYS2’, ‘CYN’, ‘CYX’, ‘CYM’, ‘CYSH’, ‘GLU’, ‘GLUH’, ‘GLUP’, ‘GLH’, ‘GLN’, ‘GLY’, ‘HIS’, ‘HIE’, ‘HISE’, ‘HSE’, ‘HIP’, ‘HSP’, ‘HISH’, ‘HID’, ‘HSD’, ‘ILE’, ‘LEU’, ‘LYS’, ‘LYSH’, ‘LYP’, ‘LYN’, ‘LSN’, ‘MET’, ‘PHE’, ‘PRO’, ‘SER’, ‘SP1’, ‘SP2’, ‘THR’, ‘TRP’, ‘TYR’, ‘VAL’. Possible MUT_NA_Codes: ‘A’, ‘T’, ‘C’, ‘G’, ‘U’.

    • force_field (str) - (“amber99sb-star-ildn-mut”) Forcefield to use.

    • resinfo (bool) - (False) Show the list of 3-letter -> 1-letter residues.

    • 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) - (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.pmxmutate import pmxmutate
prop = {
    'mutation_list': '2Ala, 3Val',
    'gmx_lib': '/path/to/myGMXLIB/',
    'force_field': 'amber99sb-star-ildn-mut'
}
pmxmutate(input_structure_path='/path/to/myStructure.pdb',
        output_structure_path='/path/to/newStructure.pdb',
        input_b_structure_path='/path/to/myStructureB.pdb'
        properties=prop)
Info:
launch() → int[source]

Execute the Pmxmutate pmx.pmxmutate.Pmxmutate object.

pmxbiobb.pmxmutate.main()[source]

Command line execution of this building block. Please check the command line documentation.

pmxbiobb.pmxmutate.pmxmutate(input_structure_path: str, output_structure_path: str, input_b_structure_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Execute the Pmxmutate class and execute the :meth:`launch() <pmx.pmxmutate.Pmxmutate.launch> method.

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)[source]

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. Sample file. 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. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_structure2_path (str) (Optional) –

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

  • output_morph1_path (str) (Optional) –

    Path to the morphable atoms for the ligand structure 1. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_morph2_path (str) (Optional) –

    Path to the morphable atoms for the ligand structure 2. File type: output. Sample file. 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. Sample file. 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. Sample file. Accepted formats: ndx (edam:format_2033).

  • output_score_path (str) (Optional) –

    Path to the morphing score. File type: output. Sample file. 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:
launch() → int[source]

Execute the Pmxmutate pmx.pmxmutate.Pmxmutate object.

pmxbiobb.pmxatom_mapping.main()[source]

Command line execution of this building block. Please check the command line documentation.

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[source]

Execute the Pmxatom_mapping class and execute the :meth:`launch() <pmx.pmxatom_mapping.Pmxatom_mapping.launch> method.

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)[source]

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:
launch() → int[source]

Execute the Pmxcreate_top pmx.pmxcreate_top.Pmxcreate_top object.

pmxbiobb.pmxcreate_top.main()[source]

Command line execution of this building block. Please check the command line documentation.

pmxbiobb.pmxcreate_top.pmxcreate_top(input_topology1_path: str, input_topology2_path: str, output_topology_path: str, properties: Dict | None = None, **kwargs) → int[source]

Execute the Pmxcreate_top class and execute the :meth:`launch() <pmx.pmxmcreate_top.Pmxmcreate_top.launch> method.

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)[source]

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. Sample file. 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. Sample file. Accepted formats: ndx (edam:format_2033).

  • output_log_path (str) –

    Path to the log file. File type: output. Sample file. 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:
launch() → int[source]

Execute the Pmxmutate pmx.pmxmutate.Pmxmutate object.

pmxbiobb.pmxligand_hybrid.main()[source]

Command line execution of this building block. Please check the command line documentation.

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[source]

Execute the Pmxligand_hybrid class and execute the :meth:`launch() <pmx.pmxligand_hybrid.Pmxligand_hybrid.launch> method.

pmxbiobb.pmxmerge_ff module

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

class pmxbiobb.pmxmerge_ff.Pmxmerge_ff(input_topology_path: str, output_topology_path: str, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_pmx Pmxmerge_ff
Wrapper class for the PMX merge_ff module.
Merge ligand topology files.
Parameters:

  • input_topology_path (str) –

    Path to the input ligand topologies as a zip file containing a list of itp files. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_topology_path (str) –

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

  • properties (dic) –

    • 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.pmxmerge_ff import pmxmerge_ff
prop = {
    'remove_tmp' : True
}
pmxmerge_ff(input_topology_path='/path/to/myTopologies.zip',
        output_topology_path='/path/to/myMergedTopology.itp',
        properties=prop)
Info:
launch() → int[source]

Execute the Pmxmerge_ff pmx.pmxmerge_ff.Pmxmerge_ff object.

pmxbiobb.pmxmerge_ff.main()[source]

Command line execution of this building block. Please check the command line documentation.

pmxbiobb.pmxmerge_ff.pmxmerge_ff(input_topology_path: str, output_topology_path: str, properties: Dict | None = None, **kwargs) → int[source]

Execute the Pmxmerge_ff class and execute the :meth:`launch() <pmx.pmxmerge_ff.Pmxmerge_ff.launch> method.