molsysmt.basic.remove#

molsysmt.basic.remove(molecular_system, selection=None, structure_indices=None, to_form=None, syntax='MolSysMT', in_place=True, 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 in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default=None) – Selection string or boolean/integer array specifying elements.

  • structure_indices (int, list, tuple, or numpy.ndarray, default=None) – Structure indices (0-based) to include or process.

  • to_form (str, list of str, or None, default=None) – Target molecular-system form; None preserves or infers the input form.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • in_place (bool, default=True) – Whether to modify the input molecular system in place.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

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. Explicit structure indices are range checked.

Notes

  • Supported molecular-system forms are summarized in Items and 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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