molsysmt.basic.copy#

molsysmt.basic.copy(molecular_system, output_filename=None, skip_digestion=False)[source]#

Creating an independent copy of a molecular system.

This function returns a deep copy of the input molecular system, fully detached from the original. If the input is in a file-based form and output_filename is provided, the copy is written to a new file using the corresponding form handler.

Parameters:

  • molecular_system (molecular system) – Molecular system to duplicate, in any of the supported forms. A list/tuple of molecular systems is also accepted, in which case a list is returned.

  • output_filename (str, optional) – Path for the output file when copying a file-based form. If omitted, the copy is returned using a temporary filename.

  • skip_digestion (bool, default False) –

    Whether to skip MolSysMT’s internal argument digestion mechanism.

    MolSysMT includes a built-in digestion system that validates and normalizes function arguments. This process checks types, shapes, and values, and automatically adjusts them when possible to meet expected formats.

    Setting skip_digestion=True disables this process, which may improve performance in workflows where inputs are already validated. Use with caution: only set this to True if you are certain all input arguments are correct and consistent.

Returns:

A new molecular system (or list of systems if the input is a sequence), independent of the original and in the same form as the input. When output_filename is given for a file-based form, the returned object follows the form-specific handler’s semantics (typically the path or a file-form handle).

Return type:

molecular system or list of molecular systems

Raises:

  • NotSupportedFormError – If the input molecular system has an unsupported form.

  • ArgumentError – If input arguments are invalid or inconsistent.

Notes

  • Supported molecular-system forms are summarized in Forms.

See also

molsysmt.basic.convert()

Convert a molecular system into another form.

Examples

>>> import molsysmt as msm
>>> molsys_A = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'])
>>> molsys_B = msm.copy(molsys_A)
>>> msm.compare(molsys_A, molsys_B, rule='equal')
True
>>> id(molsys_A) == id(molsys_B)
False

Tutorial with more examples

See the following tutorial for a practical demonstration of how to use this function, along with additional examples: Copy.

Added in version 1.0.0.

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