MDMC.exporters.configurations package

Submodules

MDMC.exporters.configurations.ase module

Export structures via ASE

class MDMC.exporters.configurations.ase.ASEExporter(file_name: str)[source]

Bases: Exporter

Use ASE to export to any format supported by ASE.

write(obj: Structure, **settings: dict) → None[source]

Write to any format supported by ASE.

Parameters:

  • obj (Structure) – The structure to export.

  • **settings – format: str The format to write to. If not given, will be inferred from the file name.

MDMC.exporters.configurations.packmol_input module

A module for a class to export a packmol input file

class MDMC.exporters.configurations.packmol_input.PackmolInputExporter(file_name: str)[source]

Bases: Exporter

A class to export PackmolSetup objects into packmol input files

INDENT = '  '
write(setup: PackmolSetup, structure_file_names: dict, output_name: str = 'output_file.pdb', **settings: dict) → None[source]

Write the data contained in a PackmolSetup object to a packmol input file

Parameters:

  • setup (PackmolSetup) – A PackmolSetup object which contains the molecules and constraints for the setup.

  • output_name (str) – The filename of the output file.

  • structure_file_names (dict) – A dictionary mapping structures in the system to corresponding file names.

Module contents

Exporters for molecular dynamics configurations.

class MDMC.exporters.configurations.ASEExporter(file_name: str)[source]

Bases: Exporter

Use ASE to export to any format supported by ASE.

write(obj: Structure, **settings: dict) → None[source]

Write to any format supported by ASE.

Parameters:

  • obj (Structure) – The structure to export.

  • **settings – format: str The format to write to. If not given, will be inferred from the file name.

class MDMC.exporters.configurations.PackmolInputExporter(file_name: str)[source]

Bases: Exporter

A class to export PackmolSetup objects into packmol input files

INDENT = '  '
write(setup: PackmolSetup, structure_file_names: dict, output_name: str = 'output_file.pdb', **settings: dict) → None[source]

Write the data contained in a PackmolSetup object to a packmol input file

Parameters:

  • setup (PackmolSetup) – A PackmolSetup object which contains the molecules and constraints for the setup.

  • output_name (str) – The filename of the output file.

  • structure_file_names (dict) – A dictionary mapping structures in the system to corresponding file names.