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:
BiobbObject
biobb_chemistry AcpypeParamsACThis 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.
binary_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) - (‘acpype/acpype:2022.7.21’) 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:
- wrapped_software:
name: Acpype
version: 2019.10.05.12.26
license: GNU
- ontology:
name: EDAM
schema: http://edamontology.org/EDAM.owl
- 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 = None, **kwargs) int [source]
Execute the
AcpypeParamsAC
class and execute thelaunch()
method.
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, output_path_pdb, properties=None, **kwargs)[source]
Bases:
BiobbObject
biobb_chemistry AcpypeParamsCNSThis 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).
output_path_pdb (str) –
Path to the PDB 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) –
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.
binary_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) - (‘acpype/acpype:2022.7.21’) 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', output_path_top='/path/to/newPDB.pdb', properties=prop)
- Info:
- wrapped_software:
name: Acpype
version: 2019.10.05.12.26
license: GNU
- ontology:
name: EDAM
schema: http://edamontology.org/EDAM.owl
- 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, output_path_pdb: str, properties: dict | None = None, **kwargs) int [source]
Execute the
AcpypeParamsCNS
class and execute thelaunch()
method.
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:
BiobbObject
biobb_chemistry AcpypeParamsGMXThis 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.
binary_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) - (‘acpype/acpype:2022.7.21’) 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:
- wrapped_software:
name: Acpype
version: 2019.10.05.12.26
license: GNU
- ontology:
name: EDAM
schema: http://edamontology.org/EDAM.owl
- 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 = None, **kwargs) int [source]
Execute the
AcpypeParamsGMX
class and execute thelaunch()
method.
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:
BiobbObject
biobb_chemistry AcpypeParamsGMXOPLSThis 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.
binary_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) - (‘acpype/acpype:2022.7.21’) 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:
- wrapped_software:
name: Acpype
version: 2019.10.05.12.26
license: GNU
- ontology:
name: EDAM
schema: http://edamontology.org/EDAM.owl
- 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 = None, **kwargs) int [source]
Execute the
AcpypeParamsGMXOPLS
class and execute thelaunch()
method.