file:structures_yaml#

Human-authored declarative YAML structures file.

  • Technical Form Name: file:structures_yaml

  • Form Type: file

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.file_structures_yaml

Overview#

file:structures_yaml is a supported representation form in MolSysMT. Human-authored declarative YAML structures file.

Supported attributes#

The file:structures_yaml form container supports a total of 20 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Atom Level

atom_index

Topological

Element Counts

n_atoms

Structural

Coordinates & Conformations

structure_index, structure_id, 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

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

The form adapter module molsysmt.form.file_structures_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:structures_yaml.

is_form()

Returns True if the provided object is an instance of file:structures_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_structures_yaml:

Target Form

Form Type

API Documentation

file:structures_yaml

file

to_file_structures_yaml()

molsysmt.Structures

class

to_molsysmt_Structures()

molsysmt.StructuresDict

class

to_molsysmt_StructuresDict()

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: