GromacsGroFile#

Form adapter and capabilities for openmm.GromacsGroFile.

  • Technical Form Name: openmm.GromacsGroFile

  • Form Type: class

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.openmm_GromacsGroFile

Overview#

openmm.GromacsGroFile is a supported representation form in MolSysMT. Form adapter and capabilities for openmm.GromacsGroFile.

Supported attributes#

The openmm.GromacsGroFile form container supports a total of 11 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Atom Level

atom_index, atom_name

Topological

Group Level

group_index, group_name, group_id, group_type

Topological

Element Counts

n_atoms, n_groups

Structural

Coordinates & Conformations

coordinates, n_structures

Structural

Periodic Box

box

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

extract()

Extracts a subset of atoms, groups, or structures into a new openmm.GromacsGroFile instance.

copy()

Creates an independent deep copy of the openmm.GromacsGroFile object in memory.

add()

Adds elements from another system into an existing openmm.GromacsGroFile instance.

merge()

Merges multiple systems into a single combined openmm.GromacsGroFile 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 openmm.GromacsGroFile.

is_form()

Returns True if the provided object is an instance of openmm.GromacsGroFile.

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.openmm_GromacsGroFile:

Target Form

Form Type

API Documentation

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.Structures

class

to_molsysmt_Structures()

molsysmt.Topology

class

to_molsysmt_Topology()

openmm.GromacsGroFile

class

to_openmm_GromacsGroFile()

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: