molsysmt.basic.contains#

molsysmt.basic.contains(molecular_system, selection='all', syntax='MolSysMT', skip_digestion=False, **kwargs)[source]#

Checking whether a molecular system contains specific elements or satisfies conditions.

This function returns a boolean indicating whether the molecular system, or a selected subset of it, satisfies a set of conditions expressed via keyword arguments. Each keyword corresponds to an attribute to check, and its value specifies the condition to apply.

Parameters:

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

  • selection (str, tuple, list or numpy.ndarray, default 'all') – Subset of atoms the conditions are applied to. Either a 0-based index collection or a selection string parsed according to Selection syntaxes. The default ‘all’ applies the conditions to the entire system.

  • syntax (str, default 'MolSysMT') – Selection syntax used when selection is a string. See Selection syntaxes.

  • 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.

  • **kwargs –

    Attribute conditions expressed as attribute=value pairs, where the value can be: - True: the attribute must be present and non-zero/non-empty on the selected subset. - False: the attribute must be absent or zero/empty on the selected subset. - int: the attribute (interpreted as a count/size) must be greater than or equal to

    the given integer (threshold).

Returns:

True if all specified conditions are satisfied by the selected subset of the system; otherwise, False.

Return type:

bool

Raises:

  • NotSupportedFormError – If the molecular system is not in a supported 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.select()

Select elements from a molecular system.

molsysmt.basic.is_composed_of()

Check if a molecular system is composed of specific types of elements.

Examples

>>> import molsysmt as msm
>>> molsys = msm.systems['T4 lysozyme L99A']['181l.h5msm']
>>> msm.contains(molsys, waters=True, ions=True)
True
>>> msm.contains(molsys, selection='atom_name=="CL"')
True
>>> msm.contains(molsys, selection='molecule_type!="water"', waters=True)
False

User guide

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

Added in version 1.0.0.

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