apfid 0.2.0

APFID - Arbitrary Protein Fragment IDentifier parser

APFID

APFID stands for Arbitrary Protein Fragment IDentifier and serves as unique identificator of molecular structure fragment in databases such as PDB, AlphaFold or user own database if necessary. It can be found useful to identify and store data in the researches dealing with structural motifs or domains on a big scale. It is used specifically by PSSKB.ORG database as structure identifier and alo in some structural researches performed by Laboratory of structural proteomics in the IBMC, Moscow.

This library contains basic parser utility to work with APFIDs using Python 3.10+.

APFID structure:

commonly, it looks like this: 1YSI_A111_A191 but there are some options described below

Apfid contains of three underscore-separated parts:

• experiment_id: Identificator in Database: PDB ID, Alphafold ID or user-given one
• Start position: chain ID and residue no
• End position: chain ID and residue no

Note: chain ID must represent code used in PDB structure file, not in deposition details. At rcsb.org the correct ID is described as Auth ID.

To identify the whole chain, one can use short form with {experiment_id}_{chain_id} and ommit what follows. So 1EDI_A is absolutely correct APFID.

In some cases, second underscore can be replaced with "-", so 1YSI_A111_A191 is equal to 1YSI_A111-A191

APFIDv2

Is more forgiving yet not used before in our structures way to identify structure. Basic rules are:

{experiment_id}[:{model}]_{chain_id}[{start}_[{chain2_id}_]{end}]

where:

• experiment_id: Identificator in Database: PDB ID, Alphafold ID or user-given one
• model: ID of the model in the same file (can be ommited to fallback to zero, or first model). Added to navigate through NMR and MD
• chain_id: ID of the chain to begin
• chain2_id: ID of the chain to end. if differs, all the chains alphabetically within chain_id and chain2_id are included. not fully implemented yet as no cases are really imaginable
• start, end: numbers of residues in chains

examples:

1YSI_A111_A191
1YSI:10_A111_191
1YSI:10_A111-191
1YSI:10_A
1YSI_A

Databases ID:

ID is register-insensitive, e.g. APFID 1EDI_A is equal to 1edi_A (but none are equal to 1edi_a as register can be crucial to chain ID)

For AlphaFold can be used structre ID in form of AF-Q8RX87-F1-V2.

User databases experiment_ids (for example, structures uploaded by users in PSSKB services) should have prefix 'USR' and total length not equal to 4. Letters, numders and hyphens are allowed.

INSTALLATION

pip install apfid

USAGE

Парсинг из строки:

from apfid import parse_apfid
apf = parse_apfid('1YSI_A111_A191')
print(apf)
# 1YSI_A111_A191
print(apf.upper())
# 1YSI_A111_A191
print(apf.lower())
# 1ysi_A111_A191
print(apf.experiment_id)
# 1YSI
print(apf.chain_id, apf.start, apf.end)
# A 111 191

Создание из параметров:

from apfid import Apfid
apf = Apfid('1YSQ', 'A', 111, 191, 10, version=2)
apf.upper()
# '1YSQ:10_A111_191'