api

A module containing different API functions for reading and writing restart files.

Summary

Functions:

read_restart_file	API function for reading a restart file.
write_restart_file	API function for reading a restart file.

Reference

read_restart_file(

filename: str,

moldescriptor_filename: str | None = None,

reference_residues: Residues | None = None,

md_engine_format: MDEngineFormat | str = MDEngineFormat.PQ,

) → AtomicSystem

API function for reading a restart file.

Parameters:

• filename (str) – The filename of the restart file.

• moldescriptor_filename (str | None, optional) – The filename of the moldescriptor file that is read by the MoldescriptorReader to obtain the reference residues of the system, by default None

• reference_residues (Residues | None, optional) – The reference residues of the system, in general these are obtained by the MoldescriptorReader - only used if moldescriptor_filename is None, by default None

• md_engine_format (MDEngineFormat | str, optional) – The format of the restart file, by default MDEngineFormat.PQ

Returns:

The AtomicSystem object including the Topology with the molecular types.

Return type:

AtomicSystem

write_restart_file(

atomic_system: AtomicSystem,

filename: str | None = None,

md_engine_format: MDEngineFormat | str = MDEngineFormat.PQ,

mode: FileWritingMode | str = 'w',

) → None

API function for reading a restart file.

Parameters:

• atomic_system (AtomicSystem) – The AtomicSystem object to write.

• filename (str) – The filename of the restart file.

• md_engine_format (MDEngineFormat | str, optional) – The format of the restart file, by default MDEngineFormat.PQ

• mode (FileWritingMode | str, optional) – The mode of the file. Either ‘w’ for write, ‘a’ for append or ‘o’ for overwrite. The default is ‘w’.