Topology

Form adapter and capabilities for MDAnalysis.Topology.

• Technical Form Name: MDAnalysis.Topology

• Form Type: class

Added in version 1.0.0.

API documentation

• Form adapter module: molsysmt.form.MDAnalysis_Topology

Overview

MDAnalysis.Topology is a supported representation form in MolSysMT. Form adapter and capabilities for MDAnalysis.Topology.

Supported attributes

The MDAnalysis.Topology form container supports a total of 52 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Atom Level	atom_index, atom_name, atom_id, atom_type, formal_charge
Topological	Group Level	group_index, group_name, group_id, group_type
Topological	Component Level	component_index, component_name, component_id, component_type
Topological	Chain Level	chain_index, chain_name, chain_id, chain_type
Topological	Molecule Level	molecule_index, molecule_name, molecule_id, molecule_type
Topological	Entity Level	entity_index, entity_name, entity_id, entity_type
Topological	Bonds & Connectivity	connectivity_completeness, bond_index, bond_type, bond_order, fractional_bond_order, bond_is_aromatic, bond_evidence, bonded_atoms, n_bonds
Topological	Element Counts	n_atoms, n_groups, n_components, n_chains, n_molecules, n_entities, n_bonds, n_amino_acids, n_nucleotides, n_ions, n_waters, n_small_molecules, n_peptides, n_proteins, n_dnas, n_rnas, n_lipids, n_polysaccharides, n_saccharides
Structural	Other Attributes	atom_index, n_atoms

Implemented operations

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

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

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.MDAnalysis_Topology:

Target Form	Form Type	API Documentation
MDAnalysis.Topology	class	to_MDAnalysis_Topology()
molsysmt.Topology	class	to_molsysmt_Topology()

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:

• Convert: Converting between any molecular system representations with molsysmt.basic.convert().

• Get attributes: Querying all supported attributes for any form with molsysmt.form.get_attributes().

• Has attribute: Testing attribute availability for a form with molsysmt.form.has_attribute().