XYZ#

Form adapter and capabilities for XYZ.

  • Technical Form Name: XYZ

  • Form Type: class

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.XYZ

Overview#

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

Supported attributes#

The XYZ form container supports a total of 5 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Atom Level

atom_index

Topological

Element Counts

n_atoms

Structural

Coordinates & Conformations

structure_index, coordinates, n_structures

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

extract()

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

copy()

Creates an independent deep copy of the XYZ object in memory.

add()

Adds elements from another system into an existing XYZ instance.

merge()

Merges multiple systems into a single combined XYZ 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 XYZ.

is_form()

Returns True if the provided object is an instance of XYZ.

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.XYZ:

Target Form

Form Type

API Documentation

XYZ

class

to_XYZ()

cupy_ndarray

class

to_cupy_ndarray()

file:xyznpy

file

to_file_xyznpy()

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.MolecularMechanics

class

to_molsysmt_MolecularMechanics()

molsysmt.Structures

class

to_molsysmt_Structures()

molsysmt.Topology

class

to_molsysmt_Topology()

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: