file:molsys_yaml#

Human-authored declarative YAML molecular system file.

  • Technical Form Name: file:molsys_yaml

  • Form Type: file

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.file_molsys_yaml

Overview#

file:molsys_yaml is a supported representation form in MolSysMT. Human-authored declarative YAML molecular system file.

Supported attributes#

The file:molsys_yaml form container supports a total of 51 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Atom Level

atom_index, atom_name, atom_id, atom_type, isotope

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

Structural

Coordinates & Conformations

structure_index, structure_id, coordinates, n_structures

Structural

Periodic Box

box, box_shape, box_angles, box_lengths, box_volume

Structural

Trajectory Metadata

time

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

get_topological_attributes

Module containing getters for topological attributes.

get_structural_attributes

Module containing getters for structural attributes.

has_attribute()

Checks whether a specific attribute name is supported by file:molsys_yaml.

is_form()

Returns True if the provided object is an instance of file:molsys_yaml.

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_molsys_yaml:

Target Form

Form Type

API Documentation

file:molsys_yaml

file

to_file_molsys_yaml()

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.MolSysDict

class

to_molsysmt_MolSysDict()

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: