AmberRestartFile#

Form adapter and capabilities for mdtraj.AmberRestartFile.

  • Technical Form Name: mdtraj.AmberRestartFile

  • Form Type: class

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.mdtraj_AmberRestartFile

Overview#

mdtraj.AmberRestartFile is a supported representation form in MolSysMT. Form adapter and capabilities for mdtraj.AmberRestartFile.

Supported attributes#

The mdtraj.AmberRestartFile form container supports a total of 11 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

Periodic Box

box, box_shape, box_angles, box_lengths, box_volume

Structural

Trajectory Metadata

time

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

extract()

Extracts a subset of atoms, groups, or structures into a new mdtraj.AmberRestartFile instance.

copy()

Creates an independent deep copy of the mdtraj.AmberRestartFile object in memory.

add()

Adds elements from another system into an existing mdtraj.AmberRestartFile instance.

merge()

Merges multiple systems into a single combined mdtraj.AmberRestartFile 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 mdtraj.AmberRestartFile.

is_form()

Returns True if the provided object is an instance of mdtraj.AmberRestartFile.

Note

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

Supported conversions#

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

Target Form

Form Type

API Documentation

mdtraj.AmberRestartFile

class

to_mdtraj_AmberRestartFile()

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.Structures

class

to_molsysmt_Structures()

See also

Foundations & Object Architecture:

  • The Molecular System: The fundamental definition of a molecular system, forms, and attributes in MolSysMT.

  • MolSys: In-depth architectural guide on the native molsysmt.MolSys container.

  • Topology: Architectural specification of the native Topology object.

  • Structures: Architectural specification of the native Structures object.

Form Tools & Conversions: