Topology#

Form adapter and capabilities for openmm.Topology.

  • Technical Form Name: openmm.Topology

  • Form Type: class

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.openmm_Topology

Overview#

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

Supported attributes#

The openmm.Topology form container supports a total of 55 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_id, chain_type

Topological

Molecule Level

molecule_index, molecule_name, molecule_id, molecule_type

Topological

Entity Level

entity_index, entity_type

Topological

Bonds & Connectivity

bond_index, bond_type, bond_order, bond_is_aromatic, bonded_atoms, bonded_atom_pairs, inner_bonded_atoms, inner_bonded_atom_pairs, inner_bond_index, n_bonds, n_inner_bonds

Topological

Element Counts

n_atoms, n_groups, n_components, n_chains, n_molecules, n_entities, n_bonds, n_inner_bonds, n_amino_acids, n_ions, n_waters, n_small_molecules, n_peptides, n_proteins, n_dnas, n_rnas, n_lipids, n_polysaccharides, n_saccharides

Structural

Periodic Box

box, box_shape, box_angles, box_lengths, box_volume

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

extract()

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

copy()

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

add()

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

merge()

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

is_form()

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

Target Form

Form Type

API Documentation

file:pdb

file

to_file_pdb()

file:psf

file

to_file_psf()

mdtraj.Topology

class

to_mdtraj_Topology()

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.Topology

class

to_molsysmt_Topology()

networkx.Graph

class

to_networkx_Graph()

nglview.NGLWidget

class

to_nglview_NGLWidget()

openmm.Context

class

to_openmm_Context()

openmm.Modeller

class

to_openmm_Modeller()

openmm.PDBFile

class

to_openmm_PDBFile()

openmm.Simulation

class

to_openmm_Simulation()

openmm.System

class

to_openmm_System()

openmm.Topology

class

to_openmm_Topology()

parmed.Structure

class

to_parmed_Structure()

pdbfixer.PDBFixer

class

to_pdbfixer_PDBFixer()

string:amino_acids_1

string

to_string_amino_acids_1()

string:amino_acids_3

string

to_string_amino_acids_3()

string:pdb_text

string

to_string_pdb_text()

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: