parmed package

Submodules

parmed.parmed_cpinutil module

Module containing the ParmedCpinUtil class and the command line interface.

class parmed.parmed_cpinutil.ParmedCpinUtil(input_top_path, output_cpin_path, output_top_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_amber ParmedCpinUtil
Wrapper of the AmberTools (AMBER MD Package) parmed tool module.
Creates a cpin file for constant pH simulations from an AMBER topology file using parmed tool from the AmberTools MD package.
Parameters:

  • input_top_path (str) – Input AMBER topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).

  • output_cpin_path (str) –

    Output AMBER constant pH input (CPin) file. File type: output. Sample file. Accepted formats: cpin (edam:format_2330).

  • output_top_path (str) (Optional) –

    Output topology file (AMBER ParmTop). File type: output. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).

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

    • resnames (str) - (“None”) Residue names to include in CPIN file. Values: AS4, GL4, HIP, CYS, LYS, TYR.

    • igb (int) - (2) Generalized Born model which you intend to use to evaluate dynamics or protonation state swaps. Values: 1, 2, 5, 7, 8.

    • system (str) - (“Unknown”) Name of system to titrate.

    • binary_path (str) - (“cpinutil.py”) Path to the cpinutil.py executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • 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_amber.parmed.parmed_cpinutil import parmed_cpinutil
prop = {
    'igb' : 2,
    'resnames': 'AS4 GL4',
    'system': 'cln025',
    'remove_tmp': False
}
parmed_cpinutil(input_top_path='/path/to/topology.top',
              output_cpin_path='/path/to/newCpin.cpin',
              output_top_path='/path/to/newTopology.top',
              properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks input/output paths correctness

launch()[source]

Launches the execution of the ParmedCpinUtil module.

parmed.parmed_cpinutil.main()[source]
parmed.parmed_cpinutil.parmed_cpinutil(input_top_path: str, output_cpin_path: str, output_top_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Create ParmedCpinUtil method

parmed.parmed_hmassrepartition module

Module containing the ParmedHMassRepartition class and the command line interface.

class parmed.parmed_hmassrepartition.ParmedHMassRepartition(input_top_path, output_top_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_amber ParmedHMassRepartition
Wrapper of the AmberTools (AMBER MD Package) parmed tool module.
Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package.
Parameters:

  • input_top_path (str) –

    Input AMBER topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).

  • output_top_path (str) –

    Output topology file (AMBER ParmTop). File type: output. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).

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

    • binary_path (str) - (“parmed”) Path to the parmed executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • 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_amber.parmed.parmed_hmassrepartition import parmed_hmassrepartition
parmed_hmassrepartition(input_top_path='/path/to/topology.top',
                output_top_path='/path/to/newTopology.top')
Info:
check_data_params(out_log, err_log)[source]

Checks input/output paths correctness

launch()[source]

Launches the execution of the ParmedHMassRepartition module.

parmed.parmed_hmassrepartition.main()[source]
parmed.parmed_hmassrepartition.parmed_hmassrepartition(input_top_path: str, output_top_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Create ParmedHMassRepartition method