molsysmt.basic.where_is_attribute#

molsysmt.basic.where_is_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)[source]#

Locating the item where a specific attribute is found.

A molecular system can be composed of multiple items in different forms. This function returns the item and its form where the given attribute is available. If include_none is False, items that have the attribute but with value None will be ignored.

Parameters:

  • molecular_system (molecular system) – Molecular system to be analyzed. It can be in any of the supported forms.

  • attribute (str) – Name of the attribute to search for within the molecular system.

  • include_none (bool, default=False) – Whether to ignore items that have the attribute defined but its value is None. With default value False, such items will be ignored.

  • 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:

  • item – The item in which the attribute was found.

  • str – The form of the item where the attribute was found.

Notes

  • Supported molecular-system forms are described in Forms.

  • If multiple items contain the same attribute, the last matching one is returned.

  • If no item contains the attribute both outputs will be None.

See also

molsysmt.basic.has_attribute()

Checking whether a molecular system contains a given attribute.

molsysmt.basic.get_attributes()

Retrieving the list of attributes present in a molecular system.

Examples

>>> import molsysmt as msm
>>> from molsysmt import systems
>>> structure = systems['pentalanine']['pentalanine.inpcrd']
>>> topology = systems['pentalanine']['pentalanine.prmtop']
>>> molecular_system = [topology, structure]
>>> item, form = msm.basic.where_is_attribute(molecular_system, 'box')
>>> form
'file:inpcrd'
>>> item, form = msm.basic.where_is_attribute(molecular_system, 'atom_id')
>>> form
'file:prmtop'

Tutorial with more examples

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

Added in version 1.0.0.

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