acpype package

Submodules

acpype.acpype_params_ac module

Module containing the AcpypeParamsAC class and the command line interface.

class acpype.acpype_params_ac.AcpypeParamsAC(input_path, output_path_frcmod, output_path_inpcrd, output_path_lib, output_path_prmtop, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_chemistry AcpypeParamsAC
This class is a wrapper of Acpype tool for small molecule parameterization for AMBER MD package.
Generation of topologies for Antechamber. Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. Visit the official page.
Parameters:
  • input_path (str) – Path to the input file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), mdl (edam:format_3815), mol2 (edam:format_3816).
  • output_path_frcmod (str) –

    Path to the FRCMOD output file. File type: output. Sample file. Accepted formats: frcmod (edam:format_3888).

  • output_path_inpcrd (str) –

    Path to the INPCRD output file. File type: output. Sample file. Accepted formats: inpcrd (edam:format_3878).

  • output_path_lib (str) –

    Path to the LIB output file. File type: output. Sample file. Accepted formats: lib (edam:format_3889).

  • output_path_prmtop (str) –

    Path to the PRMTOP output file. File type: output. Sample file. Accepted formats: prmtop (edam:format_3881).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • basename (str) - (“BBB”) A basename for the project (folder and output files).
    • charge (int) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype.
    • acpype_path (str) - (“acpype”) Path to the acpype 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) - (‘mmbirb/acpype:latest’) 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.acpype.acpype_params_ac import acpype_params_ac
prop = {
    'basename': 'BBB',
    'charge': 0
}
acpype_params_ac(input_path='/path/to/myStructure.mol2',
                output_path_frcmod='/path/to/newFRCMOD.frcmod',
                output_path_inpcrd='/path/to/newINPCRD.inpcrd',
                output_path_lib='/path/to/newLIB.lib',
                output_path_prmtop='/path/to/newPRMTOP.prmtop',
                properties=prop)
Info:
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 AcpypeParamsAC acpype.acpype_params_ac.AcpypeParamsAC object.

acpype.acpype_params_ac.acpype_params_ac(input_path: str, output_path_frcmod: str, output_path_inpcrd: str, output_path_lib: str, output_path_prmtop: str, properties: dict = None, **kwargs) → int[source]

Execute the AcpypeParamsAC class and execute the launch() method.

acpype.acpype_params_ac.main()[source]

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

acpype.acpype_params_cns module

Module containing the AcpypeParamsCNS class and the command line interface.

class acpype.acpype_params_cns.AcpypeParamsCNS(input_path, output_path_par, output_path_inp, output_path_top, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_chemistry AcpypeParamsCNS
This class is a wrapper of Acpype tool for small molecule parameterization for CNS/XPLOR MD package.
Generation of topologies for CNS/XPLOR. Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. Visit the official page.
Parameters:
  • input_path (str) –

    Path to the input file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), mdl (edam:format_3815), mol2 (edam:format_3816).

  • output_path_par (str) –

    Path to the PAR output file. File type: output. Sample file. Accepted formats: par (edam:format_3881).

  • output_path_inp (str) –

    Path to the INP output file. File type: output. Sample file. Accepted formats: inp (edam:format_3878).

  • output_path_top (str) –

    Path to the TOP output file. File type: output. Sample file. Accepted formats: top (edam:format_3881).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • basename (str) - (“BBB”) A basename for the project (folder and output files).
    • charge (int) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype.
    • acpype_path (str) - (“acpype”) Path to the acpype 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) - (‘mmbirb/acpype:latest’) 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.acpype.acpype_params_cns import acpype_params_cns
prop = {
    'basename': 'BBB',
    'charge': 0
}
acpype_params_cns(input_path='/path/to/myStructure.mol2',
                output_path_par='/path/to/newPAR.par',
                output_path_inp='/path/to/newINP.inp',
                output_path_top='/path/to/newTOP.top',
                properties=prop)
Info:
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 AcpypeParamsCNS acpype.acpype_params_cns.AcpypeParamsCNS object.

acpype.acpype_params_cns.acpype_params_cns(input_path: str, output_path_par: str, output_path_inp: str, output_path_top: str, properties: dict = None, **kwargs) → int[source]

Execute the AcpypeParamsCNS class and execute the launch() method.

acpype.acpype_params_cns.main()[source]

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

acpype.acpype_params_gmx module

Module containing the AcpypeParamsGMX class and the command line interface.

class acpype.acpype_params_gmx.AcpypeParamsGMX(input_path, output_path_gro, output_path_itp, output_path_top, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_chemistry AcpypeParamsGMX
This class is a wrapper of Acpype tool for generation of topologies for GROMACS.
Generation of topologies for GROMACS. Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. Visit the official page.
Parameters:
  • input_path (str) –

    Path to the input file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), mdl (edam:format_3815), mol2 (edam:format_3816).

  • output_path_gro (str) –

    Path to the GRO output file. File type: output. Sample file. Accepted formats: gro (edam:format_2033).

  • output_path_itp (str) –

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

  • output_path_top (str) –

    Path to the TOP output file. File type: output. Sample file. Accepted formats: top (edam:format_3880).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • basename (str) - (“BBB”) A basename for the project (folder and output files).
    • charge (int) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype.
    • acpype_path (str) - (“acpype”) Path to the acpype 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) - (‘mmbirb/acpype:latest’) 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.acpype.acpype_params_gmx import acpype_params_gmx
prop = {
    'basename': 'BBB',
    'charge': 0
}
acpype_params_gmx(input_path='/path/to/myStructure.mol2',
                output_path_gro='/path/to/newGRO.gro',
                output_path_itp='/path/to/newITP.itp',
                output_path_top='/path/to/newTOP.top',
                properties=prop)
Info:
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 AcpypeParamsGMX acpype.acpype_params_gmx.AcpypeParamsGMX object.

acpype.acpype_params_gmx.acpype_params_gmx(input_path: str, output_path_gro: str, output_path_itp: str, output_path_top: str, properties: dict = None, **kwargs) → int[source]

Execute the AcpypeParamsGMX class and execute the launch() method.

acpype.acpype_params_gmx.main()[source]

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

acpype.acpype_params_gmx_opls module

Module containing the AcpypeParamsGMXOPLS class and the command line interface.

class acpype.acpype_params_gmx_opls.AcpypeParamsGMXOPLS(input_path, output_path_itp, output_path_top, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_chemistry AcpypeParamsGMXOPLS
This class is a wrapper of Acpype tool for generation of topologies for OPLS/AA.
Generation of topologies for OPLS/AA. Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. Visit the official page.
Parameters:
  • input_path (str) –

    Path to the input file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), mdl (edam:format_3815), mol2 (edam:format_3816).

  • output_path_itp (str) –

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

  • output_path_top (str) –

    Path to the TOP output file. File type: output. Sample file. Accepted formats: top (edam:format_3880).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • basename (str) - (“BBB”) A basename for the project (folder and output files).
    • charge (int) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype.
    • acpype_path (str) - (“acpype”) Path to the acpype 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) - (‘mmbirb/acpype:latest’) 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.acpype.acpype_params_gmx_opls import acpype_params_gmx_opls
prop = {
    'basename': 'BBB',
    'charge': 0
}
acpype_params_gmx_opls(input_path='/path/to/myStructure.mol2',
                        output_path_itp='/path/to/newITP.itp',
                        output_path_top='/path/to/newTOP.top',
                        properties=prop)
Info:
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 AcpypeParamsGMXOPLS acpype.acpype_params_gmx_opls.AcpypeParamsGMXOPLS object.

acpype.acpype_params_gmx_opls.acpype_params_gmx_opls(input_path: str, output_path_itp: str, output_path_top: str, properties: dict = None, **kwargs) → int[source]

Execute the AcpypeParamsGMXOPLS class and execute the launch() method.

acpype.acpype_params_gmx_opls.main()[source]

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