file:xyznpy#

XYZ file format like saved with Numpy

Added in version 1.0.0.

API documentation

Overview#

file:xyznpy is a supported representation form in MolSysMT. XYZ file format like saved with Numpy

The file:xyznpy form container supports a total of 5 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Atom Level	`atom_index`
Topological	Element Counts	`n_atoms`
Structural	Coordinates & Conformations	`structure_index`, `coordinates`, `n_structures`
Structural	Other Attributes	`atom_index`, `n_atoms`

The form adapter module molsysmt.form.file_xyznpy implements the following functions and modules:

Function / Module	Description
`extract()`	Extracts a subset of atoms, groups, or structures into a new `file:xyznpy` instance.
`copy()`	Creates an independent deep copy of the `file:xyznpy` object in memory.
`add()`	Adds elements from another system into an existing `file:xyznpy` instance.
`merge()`	Merges multiple systems into a single combined `file:xyznpy` object.
`append_structures()`	Appends new coordinate frames or trajectories to the structures container.
`get_topological_attributes`	Module containing getters for topological attributes.
`get_structural_attributes`	Module containing getters for structural attributes.
`set`	Module containing setters for updating coordinates, box dimensions, or attributes in-place.
`iterators`	Module providing iterators for streaming trajectory frames and structures.
`has_attribute()`	Checks whether a specific attribute name is supported by `file:xyznpy`.
`is_form()`	Returns `True` if the provided object is an instance of `file:xyznpy`.

Note

Each form adapter in MolSysMT implements only the specific functions that are meaningful for its data model.

The following table lists all direct conversion functions implemented in molsysmt.form.file_xyznpy:

Target Form	Form Type	API Documentation
`XYZ`	`class`	`to_XYZ()`
`file:xyznpy`	`file`	`to_file_xyznpy()`