molsysmt.basic.view#

molsysmt.basic.view(molecular_system=None, selection='all', structure_indices='all', viewer='MolSysViewer', syntax='MolSysMT', skip_digestion=False)[source]#

Visualizing a molecular system.

This function displays a molecular system using an external interactive 3D visualization library inside a Jupyter notebook. The visualization backend can be selected by the viewer argument.

Parameters:

  • molecular_system (molecular system, default=None) – Molecular system in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • structure_indices (int, list, tuple, or numpy.ndarray, default='all') – Structure indices (0-based) to include or process.

  • viewer (str, default='MolSysViewer') – Viewer backend used to create the interactive representation.

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

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

Returns:

Visualization widget returned by the selected viewer. For ‘MolSysViewer’, this is a molsysviewer.MolSysView instance. For ‘NGLView’, this is an nglview.NGLWidget instance.

Return type:

object

Raises:

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

  • ArgumentError – If one or more input arguments are invalid, including a malformed selection or an out-of-range element or structure index.

  • ModuleNotFoundError – If the requested viewer backend is not available in the current environment.

Notes

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

  • Selection syntaxes and valid query expressions are described in Selection syntaxes.

  • Selections and structure indices are validated before the viewer backend is created.

See also

molsysmt.basic.select()

Selecting atoms or elements from a molecular system.

Examples

The following example illustrates how to visualize only the protein component of a molecular system:

>>> import molsysmt as msm
>>> molecular_system = msm.systems['T4 lysozyme L99A']['181l.h5msm']
>>> msm.basic.view(molecular_system, selection='molecule_type=="protein"')
<molsysviewer.viewer.MolSysView object at 0x...>

Select an alternative backend (requires nglview):

>>> msm.basic.view(molecular_system, selection='molecule_type=="protein"', viewer='NGLView')
NGLWidget()

Tutorial with more examples

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

Added in version 1.0.0.

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