file:h5msm

Form adapter and capabilities for file:h5msm.

• Technical Form Name: file:h5msm

• Form Type: file

Added in version 1.0.0.

API documentation

• Form adapter module: molsysmt.form.file_h5msm

Overview

file:h5msm is a supported representation form in MolSysMT. Form adapter and capabilities for file:h5msm.

Supported attributes

The file:h5msm form container supports a total of 93 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Atom Level	atom_index, atom_name, atom_id, atom_type, isotope, formal_charge, atom_is_aromatic, n_unpaired_electrons, n_implicit_hydrogens, allows_implicit_hydrogens, atom_stereochemistry
Topological	Group Level	group_index, group_name, group_id, group_type
Topological	Component Level	component_completeness, component_evidence, 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_id, bond_type, bond_order, fractional_bond_order, bond_is_aromatic, bond_is_conjugated, bond_stereochemistry, bond_stereo_atom_indices, bond_donor_atom_index, bond_acceptor_atom_index, bond_joins_components, bond_evidence, bonded_atoms, bonded_atom_pairs, inner_bonded_atoms, inner_bonded_atom_pairs, inner_bond_index, n_bonds, n_inner_bonds
Topological	Chemical States	chemical_state_index, chemical_state_id, n_chemical_states, reference_chemical_state_index
Topological	Element Counts	n_atoms, n_groups, n_components, n_chains, n_molecules, n_entities, n_bonds, n_inner_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	Coordinates & Conformations	structure_index, structure_id, structure_chemical_state_index, coordinates, velocities, n_structures
Structural	Periodic Box	box, box_shape, box_angles, box_lengths, box_volume
Structural	Trajectory Metadata	time, potential_energy, kinetic_energy, total_energy, temperature
Structural	Crystallographic & Bioassembly	b_factor
Structural	Other Attributes	atom_index, n_atoms

Implemented operations

The form adapter module molsysmt.form.file_h5msm implements the following functions and modules:

Function / Module	Description
extract()	Extracts a subset of atoms, groups, or structures into a new file:h5msm instance.
copy()	Creates an independent deep copy of the file:h5msm object in memory.
add()	Adds elements from another system into an existing file:h5msm instance.
merge()	Merges multiple systems into a single combined file:h5msm 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:h5msm.
is_form()	Returns True if the provided object is an instance of file:h5msm.

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.file_h5msm:

Target Form	Form Type	API Documentation
file:h5msm	file	to_file_h5msm()
molsysmt.H5MSMFileHandler	class	to_molsysmt_H5MSMFileHandler()
molsysmt.MolSys	class	to_molsysmt_MolSys()
molsysmt.Structures	class	to_molsysmt_Structures()
molsysmt.Topology	class	to_molsysmt_Topology()
nglview.NGLWidget	class	to_nglview_NGLWidget()
string:amino_acids_1	string	to_string_amino_acids_1()
string:amino_acids_3	string	to_string_amino_acids_3()

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().