MolSysView

MolSysViewer visualization native object.

• Technical Form Name: molsysviewer.MolSysView

• Form Type: class

Added in version 1.0.0.

API documentation

• Form adapter module: molsysmt.form.molsysviewer_MolSysView

Overview

molsysviewer.MolSysView is a supported representation form in MolSysMT. MolSysViewer visualization native object.

Supported attributes

The molsysviewer.MolSysView form container supports a total of 73 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Atom Level	atom_index, atom_name, atom_id, atom_type
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	bond_index, bond_type, bond_order, 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_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, alternate_location, occupancy, bioassembly, n_bioassemblies
Structural	Other Attributes	atom_index, n_atoms

Implemented operations

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

Function / Module	Description
extract()	Extracts a subset of atoms, groups, or structures into a new molsysviewer.MolSysView instance.
copy()	Creates an independent deep copy of the molsysviewer.MolSysView object in memory.
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.
get_mechanical_attributes	Module containing getters for mechanical attributes.
has_attribute()	Checks whether a specific attribute name is supported by molsysviewer.MolSysView.
is_form()	Returns True if the provided object is an instance of molsysviewer.MolSysView.

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.molsysviewer_MolSysView:

Target Form	Form Type	API Documentation
molsysmt.MolSys	class	to_molsysmt_MolSys()
molsysviewer.MolSysView	class	to_molsysviewer_MolSysView()

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().