added my sample 3pl1 json file with 4 muts to test the json validator
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test_tt_3pl1_example.py
Executable file
28
test_tt_3pl1_example.py
Executable file
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Fri Nov 11 11:18:52 2022
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@author: tanu
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"""
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from validator.validator import Validator
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from validator.residue_index import ResidueIndexes
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#validator = Validator("ProKinO") # Same as in the JSON
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validator = Validator("FoldX") # Same as in the JSON
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validator.load_schema()
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print("Schema loaded successfully")
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validator.load_json("tt_3pl1_example.json")
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#print("Loaded json file successfully")
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if validator.basic_checks() and validator.validate_against_schema():
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# Passed data validations
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print('Passed schema validation')
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residue_indexes = ResidueIndexes(validator.json_data)
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if residue_indexes.check_every_residue():
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# Passed the index validation
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print('Passed index validation')
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else:
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print('Failed schema validation')
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print(validator.error_log)
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87
tt_3pl1_example.json
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tt_3pl1_example.json
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{
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"data_resource": "FoldX",
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"resource_version": "5.0",
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"software_version": "5.0",
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"resource_entry_url": "http://foldxsuite.crg.eu/",
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"pdb_id": "3PL1",
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"chains": [
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{
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"residues": [
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{
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"pdb_res_label": "10",
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"aa_type": "GLN",
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"site_data": [
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{
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"site_id_ref": 1,
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"confidence_score": 1,
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"confidence_classification": "curated",
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"raw_score": 3.9475,
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"raw_score_unit": "kcal/mol",
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"aa_variant": "GLY"
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},
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{
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"site_id_ref": 2,
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"confidence_score": 1,
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"confidence_classification": "high",
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"raw_score": 2.88633,
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"raw_score_unit": "kcal/mol",
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"aa_variant": "ALA"
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}
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]
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},
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{
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"pdb_res_label": "11",
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"aa_type": "ASN",
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"site_data": [
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{
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"site_id_ref": 3,
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"confidence_score": 1,
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"confidence_classification": "curated",
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"raw_score": 1.15843,
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"raw_score_unit": "kcal/mol",
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"aa_variant": "GLY"
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}
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]
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},
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{
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"pdb_res_label": "12",
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"aa_type": "ASP",
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"site_data": [
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{
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"site_id_ref": 4,
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"confidence_score": 1,
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"confidence_classification": "high",
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"raw_score": 1.71712,
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"aa_variant": "GLY"
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}
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]
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}
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],
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"chain_label": "A"
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}
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],
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"sites": [
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{
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"site_id": 1,
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"label": "ddG"
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},
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{
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"site_id": 2,
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"label": "ddG"
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},
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{
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"site_id": 3,
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"label": "ddG"
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},
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{
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"site_id": 4,
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"label": "ddG"
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}
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],
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"evidence_code_ontology": [
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{
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"eco_term": "computational experiment",
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"eco_code": "ECO_0000006"
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}
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]
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}
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