file:gro#

Gromacs gro file format

Added in version 1.0.0.

API documentation

Overview#

file:gro is a supported representation form in MolSysMT. Gromacs gro file format

The file:gro form container supports a total of 20 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Atom Level	`atom_index`, `atom_name`, `atom_id`, `atom_type`
Topological	Group Level	`group_index`, `group_name`, `group_id`, `group_type`
Topological	Chain Level	`chain_index`, `chain_name`, `chain_id`, `chain_type`
Topological	Bonds & Connectivity	`bond_index`, `bond_id`, `bond_type`, `bond_order`
Topological	Element Counts	`n_atoms`
Structural	Coordinates & Conformations	`coordinates`, `velocities`
Structural	Periodic Box	`box`
Structural	Other Attributes	`atom_index`, `n_atoms`

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

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

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_gro:

Target Form	Form Type	API Documentation
`file:gro`	`file`	`to_file_gro()`
`mdtraj.GroTrajectoryFile`	`class`	`to_mdtraj_GroTrajectoryFile()`
`mdtraj.Topology`	`class`	`to_mdtraj_Topology()`
`mdtraj.Trajectory`	`class`	`to_mdtraj_Trajectory()`
`molsysmt.GROFileHandler`	`class`	`to_molsysmt_GROFileHandler()`
`molsysmt.MolSys`	`class`	`to_molsysmt_MolSys()`
`molsysmt.Structures`	`class`	`to_molsysmt_Structures()`
`molsysmt.Topology`	`class`	`to_molsysmt_Topology()`
`nglview.NGLWidget`	`class`	`to_nglview_NGLWidget()`
`openmm.GromacsGroFile`	`class`	`to_openmm_GromacsGroFile()`
`openmm.Modeller`	`class`	`to_openmm_Modeller()`
`openmm.Topology`	`class`	`to_openmm_Topology()`