file:pir#

PIR/NBRF sequence file format

  • Technical Form Name: file:pir

  • Form Type: file

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.file_pir

Overview#

file:pir is a supported representation form in MolSysMT. PIR/NBRF sequence file format

Supported attributes#

The file:pir form container supports a total of 15 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Group Level

group_index, group_name, group_type

Topological

Chain Level

chain_index, chain_name, chain_id, chain_type

Topological

Entity Level

entity_index, entity_name, entity_id, entity_type

Topological

Element Counts

n_groups, n_chains, n_entities, n_amino_acids

Implemented operations#

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

Function / Module

Description

extract()

Extracts a subset of atoms, groups, or structures into a new file:pir instance.

copy()

Creates an independent deep copy of the file:pir object in memory.

add()

Adds elements from another system into an existing file:pir instance.

merge()

Merges multiple systems into a single combined file:pir object.

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:pir.

is_form()

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

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_pir:

Target Form

Form Type

API Documentation

biopython.Seq

class

to_biopython_Seq()

biopython.SeqRecord

class

to_biopython_SeqRecord()

file:fasta

file

to_file_fasta()

file:pir

file

to_file_pir()

string:amino_acids_1

string

to_string_amino_acids_1()

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: