file:top#

GROMACS topology file format

Added in version 1.0.0.

API documentation

Overview#

file:top is a supported representation form in MolSysMT. GROMACS topology file format

The file:top form container supports a total of 0 attributes:

Category	Subcategory / Level	Supported Attributes
—	—	No direct attributes exposed

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

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

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_top:

Target Form	Form Type	API Documentation
`file:top`	`file`	`to_file_top()`
`molsysmt.MolSys`	`class`	`to_molsysmt_MolSys()`
`molsysmt.Topology`	`class`	`to_molsysmt_Topology()`
`parmed.GromacsTopologyFile`	`class`	`to_parmed_GromacsTopologyFile()`