file:cif.gz

Form adapter and capabilities for file:cif.gz.

• Technical Form Name: file:cif.gz

• Form Type: file

Added in version 1.0.0.

API documentation

• Form adapter module: molsysmt.form.file_cif_gz

Overview

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

Supported attributes

The file:cif.gz form container supports a total of 65 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, inner_bonded_atoms, 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, coordinates, velocities, n_structures
Structural	Periodic Box	box, box_shape, box_angles, box_lengths, box_volume
Structural	Trajectory Metadata	time
Structural	Crystallographic & Bioassembly	b_factor, alternate_location, bioassembly, n_bioassemblies
Structural	Other Attributes	atom_index, n_atoms

Implemented operations

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

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

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_cif_gz:

Target Form	Form Type	API Documentation
file:cif.gz	file	to_file_cif_gz()
file:h5msm	file	to_file_h5msm()
mmcif.PdbxContainers.DataContainer	class	to_mmcif_PdbxContainers_DataContainer()
molsysmt.MolSys	class	to_molsysmt_MolSys()
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:

• 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().