molsysmt.basic.info#

molsysmt.basic.info(molecular_system, element='system', selection='all', structure_indices='all', syntax='MolSysMT', output_type='styler', skip_digestion=False)[source]#

Display a summary table of a molecular system or selected elements.

This function produces a formatted summary table (as a Pandas Styler, DataFrame, or Dictionary) with key attributes of a molecular system, either for the whole system or for a given element level and selection. The columns returned depend on the chosen element and on the attributes available in the underlying form(s).

Parameters:

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

  • element ({'atom', 'group', 'component', 'molecule', 'chain', 'entity', 'system'}, default 'system') – Hierarchical level for which the summary is generated.

  • selection (int, tuple, list, numpy.ndarray or str, default 'all') – Selection of elements at the specified level. It can be a 0-based index collection or a selection string parsed according to Selection syntaxes.

  • structure_indices (int, list, tuple, numpy.ndarray or str, default 'all') – Indices of the structures to be considered if the system summary is requested.

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

  • output_type ({'styler', 'dataframe', 'dictionary'}, default 'styler') – The type of the output object. ‘styler’ returns a Pandas Styler (best for notebooks), ‘dataframe’ returns a raw Pandas DataFrame, and ‘dictionary’ returns a Python dict.

  • 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 Pandas Styler wrapping a DataFrame with the summary. The exact columns depend on element and on the attributes exposed by the input form(s). Its HTML table carries the dataframe class, the same one DataFrame.to_html() emits.

Return type:

pandas.io.formats.style.Styler

Raises:

  • NotSupportedFormError – If the molecular system has an unsupported form.

  • ArgumentError – If any input argument is invalid or inconsistent, including an out-of-range structure index.

Notes

  • Supported molecular-system forms are summarized in Items and Forms.

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

  • The function hides the row index for readability using Pandas’ Styler API; you can access the underlying DataFrame via the .data attribute (depending on your Pandas version) or by rebuilding it from the original values if needed.

  • The rendered table is tagged with the dataframe class so that notebook viewers and documentation themes style it as they style any other Pandas table. Without it the table matches no theme rule and renders unstyled once compiled to HTML.

See also

molsysmt.basic.select()

Select elements from a molecular system.

molsysmt.basic.get()

Retrieve values of attributes from a molecular system.

molsysmt.basic.get_form()

Retrieve the form of a molecular system.

Examples

>>> import molsysmt as msm
>>> from molsysmt import systems
>>> molsys = msm.convert(systems['T4 lysozyme L99A']['181l.h5msm'])
>>> print(msm.info(molsys, element='entity').to_string())
index  name                       type     n atoms  n groups  n components  n chains  n molecules
0      T4 LYSOZYME                protein  1289     162       1             1         1
1      CHLORIDE ION               ion      2        2         2             2         2
2      2-HYDROXYETHYL DISULFIDE   small molecule    8        1         1         1         1
3      BENZENE                    small molecule    6        1         1         1         1
4      water                      water    136      136       136           1         136
>>> # If you are working in a Jupyter notebook, you can simply run:
>>> # msm.info(molsys, element='entity')
>>> # And the table will be displayed in a nicely formatted style by Pandas.

Tutorial with more examples

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

Added in version 1.0.0.

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