file:xtc#

Form adapter and capabilities for file:xtc.

Added in version 1.0.0.

API documentation

Overview#

file:xtc is a supported representation form in MolSysMT. Form adapter and capabilities for file:xtc.

The file:xtc form container supports a total of 6 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Element Counts	`n_atoms`
Structural	Coordinates & Conformations	`structure_id`, `coordinates`, `n_structures`
Structural	Periodic Box	`box`
Structural	Trajectory Metadata	`time`
Structural	Other Attributes	`n_atoms`

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

Function / Module	Description
`extract()`	Extracts a subset of atoms, groups, or structures into a new `file:xtc` instance.
`copy()`	Creates an independent deep copy of the `file:xtc` object in memory.
`add()`	Adds elements from another system into an existing `file:xtc` instance.
`merge()`	Merges multiple systems into a single combined `file:xtc` 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:xtc`.
`is_form()`	Returns `True` if the provided object is an instance of `file:xtc`.

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_xtc:

Target Form	Form Type	API Documentation
`file:h5msm`	`file`	`to_file_h5msm()`
`file:xtc`	`file`	`to_file_xtc()`
`mdtraj.Trajectory`	`class`	`to_mdtraj_Trajectory()`
`mdtraj.XTCTrajectoryFile`	`class`	`to_mdtraj_XTCTrajectoryFile()`
`molsysmt.Structures`	`class`	`to_molsysmt_Structures()`