molsysmt.basic.remove#

molsysmt.basic.remove(molecular_system, selection=None, structure_indices=None, to_form=None, syntax='MolSysMT', skip_digestion=False)[source]#

Removing atoms or structures from a molecular system.

This function returns a new molecular system after removing the atoms and/or structures specified via selection and structure_indices. If selection is None, no atoms are removed. If structure_indices is None, no structures are removed. Optionally, the resulting system can be returned in a different form with to_form.

Parameters:

  • molecular_system (molecular system) – Molecular system provided in any of the supported forms.

  • selection (str, tuple, list or numpy.ndarray, optional) – Atoms to remove, as a 0-based index collection or a selection string parsed according to Selection syntaxes. If ‘all’, all atoms are removed. If None, no atoms are removed.

  • structure_indices (int, tuple, list, numpy.ndarray or 'all', optional) – 0-based indices of structures to remove. If ‘all’, all frames are removed. If None, no structures are removed.

  • to_form (str, optional) – Output form of the resulting molecular system. If omitted, the output form matches the input 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.

Returns:

A new molecular system with the selected atoms and/or structures removed. The form of the returned system is either specified by to_form or inferred from the input.

Return type:

molecular system

Raises:

  • NotSupportedFormError – If the molecular system is provided in an unsupported form.

  • ArgumentError – If the selection or structure_indices are invalid or incompatible with the system.

Notes

  • Supported molecular-system forms are summarized in Forms.

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

  • Removal is implemented by selecting the complementary indices and delegating to molsysmt.basic.extract(), minimizing data copies when possible.

See also

molsysmt.select()

Select atoms or structures from a molecular system.

molsysmt.basic.extract()

Extract a subset of atoms/structures into a new molecular system.

Examples

>>> import molsysmt as msm
>>> system = msm.convert('1B3T')
>>> msm.get(system, n_chains=True)
8
>>> new_system = msm.remove(system, selection='chain_id=="A" or chain_id=="B"')
>>> msm.get(new_system, n_chains=True)
6

Tutorial with more examples

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

Added in version 1.0.0.

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