molsysmt.basic.get_attributes#

molsysmt.basic.get_attributes(molecular_system, include_none=False, output_type='dictionary', skip_digestion=False)[source]#

Retrieving available attributes from a molecular system.

This function inspects the input molecular system and reports which attributes are available according to MolSysMT’s attribute registry. The result can be returned either as a dictionary mapping attribute names to booleans or as a list containing only the present attributes.

Parameters:

  • molecular_system (molecular system) – Molecular system to analyze, in any of the supported forms.

  • include_none (bool, default False) – Whether to consider attributes with value None as present when probing availability. If True, attributes that exist but currently hold None will be marked as present.

  • output_type ({'dictionary', 'list'}, default 'dictionary') – Format of the returned result. If 'dictionary', returns all supported attributes as keys with boolean values indicating presence. If 'list', returns only the names of attributes present in the molecular system.

  • 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:

If output_type == 'dictionary': dictionary with attribute names as keys and booleans as values indicating availability. If output_type == 'list': list with the names of attributes present.

Return type:

dict or list

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.

  • Selection strings must follow one of the syntaxes described in Selection syntaxes.

See also

molsysmt.basic.has_attribute()

Check whether a specific attribute exists in a molecular system.

molsysmt.basic.get_form()

Retrieve the form of a molecular system.

molsysmt.basic.get()

Retrieve attribute values from a molecular system.

Examples

>>> import molsysmt as msm
>>> molsys = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'])
>>> attributes = msm.get_attributes(molsys)
>>> attributes['box']
True
>>> attributes['forcefield']
False
>>> output = msm.get_attributes(molsys, output_type='list')
>>> isinstance(output, list)
True
>>> 'molecule_id' in output
True
>>> 'forcefield' in output
False

Tutorial with more examples

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

Added in version 1.0.0.

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